Open access

RNA Polymerase II Phosphorylation and Gene Expression Regulation

Written By

Olga Calvo and Alicia García

Submitted: December 1st, 2011 Published: September 6th, 2012

DOI: 10.5772/48490

Chapter metrics overview

2,665 Chapter Downloads

View Full Metrics

1. Introduction

RNA polymerases (RNAPs) are among the most important cellular enzymes. They are present in all living organisms from Bacteria and Archaea to Eukarya and are responsible for DNA-dependent transcription. Although in Bacteria and Archaea there is only one RNAP, Eukarya possess up to three RNAPs in animals (I, II and III) and five in plants (IV and V) [1-2]. All of the RNAPs are evolutionarily related and have common structural and functional properties. The minimally conserved structural organization is represented by the bacterial enzyme, which contains only 4 subunits (α, α’, β, β’), whereas Archaea and Eukarya RNAPs are composed of 12 subunits (Rpb1-Rpb12) [3]. In prokaryotes, one RNAP transcribes all of the genes into all of the RNAs, however, in eukaryotes, this is achieved by three RNAPs. RNAPI transcribes genes that encode for 18S and 28S ribosomal RNAs; RNAPIII transcribes short genes, such as tRNAs and 5S ribosomal RNA, and RNAPII transcribes all protein-coding genes and genes for small noncoding RNAs (e.g., small nuclear RNAs (snRNAs) that are involved in splicing). The largest catalytic subunits of all three eukaryotic polymerases share homology among themselves and with the largest subunit of bacterial polymerase [4]. Solely the largest subunit of RNAPII (Rpb1) contains an unusual evolutionarily conserved carboxy-terminal domain (CTD) [5], which is subjected to numerous post-translational modifications of extraordinary importance in gene expression regulation [6-8].RNAPII transcription plays a central role in gene expression and is highly regulated at many steps, such as initiation, elongation and termination. Furthermore, phosphorylation of the Rpb1 CTD is known to regulate all of the transcription steps and coordinate these steps with other nuclear events. Prior to mRNA biosynthesis, RNAPII proceeds through several steps, such as promoter recognition, preinitiation complex (PIC) assembly, open complex formation, initiation and promoter escape. This sequence of events is initiated by the binding of gene-specific activators and coactivators, which results in the recruitment of basal transcription machinery (i.e., general transcription factors (GTFs): TFIIA, TFIIB, TFIID, TFIIE, TFIIF, and TFIIH) and RNAPII to promoters [9-11]. Basal transcription factors position RNAPII on promoters to form the PIC but also function at later steps, such as promoter melting and initiation site selection. Thereafter, initiation proceeds, and RNAPII leaves the promoter during promoter clearance and proceeds into processive transcript elongation. Finally, when the gene has been fully transcribed, transcriptional termination occurs, and RNAPII is released and recycled to reinitiate a new round of transcription [12-14].

During its passage across a gene, RNAPII must overcome challenges. Initially, the polymerase needs to escape from the promoter, and the synthesis of the pre-mRNAs must be tightly coupled to its subsequent processing (i.e., capping, splicing, and polyadenylation). Then, initiation factors must be exchanged for elongation factors [15], which are thought to increase the transcription rate and RNAPII processivity. In fact, recently, there has been an extraordinary increase in the number of proteins known to influence transcription elongation by avoiding transcriptional arrest, facilitating chromatin passage and mRNA processing [16-21], allowing mRNA packaging into a mature ribonucleoprotein (mRNP) and controlling mRNP quality and mRNA export [13, 22-28]. Therefore, the discovery of all of these factors has provided further evidence that the elongation phase is also highly regulated in eukaryotic cells and strictly coordinated with other nuclear processes [12-14].


2. RNAPII CTD phosphorylation: The CTD code

During the last two decades, gene expression studies have provided further evidence that many steps in gene expression, originally considered distinct and independent, are, in fact, highly coordinated, linked and regulated in a complex web of connections [29-30]. The central coordinator that directs this regulatory network (i.e., from transcription initiation to termination and with pre-mRNA processing) in combination with many other nuclear functions is RNAPII, and the carboxy-terminal domain (CTD) of its largest subunit is of remarkable importance. CTD phosphorylation regulates and coordinates the entire transcription cycle with pre-mRNA processing, mRNA transport and with chromatin remodeling and modification [13]. The CTD, therefore, has a critical integrating role in essentially all of the mRNA biogenesis steps, thus, it is subject to a dynamic regulation during the transcription cycle (i.e., [21, 31-32]). Therefore, RNAPII phosphorylation is one of the key processes in the regulation of transcription specifically and gene expression in general; consequently, deciphering the mechanisms that underlie RNAPII phosphorylation regulation has become one of the most studied issues in the field of gene expression.

RNAPII is comprised of 12 subunits (Rpb1-12) that are structurally and functionally conserved from yeast to mammals [33-34]. In 1985, the largest subunit of RNAPII, Rpb1, from mouse and Saccharomyces cerevisiae, was cloned [4, 35], and its sequence revealed that it contained a highly conserved carboxy-terminal domain (CTD). This domain has been extensively studied since then and, although it is a simple repetition in tandem of the heptapeptide consensus sequence Tyr1-Ser2-Pro3-Thr4-Ser5-Pro6-Ser7 (YSPTSPS); Figure 1), the CTD has an extremely complex functionality. The consensus sequence is present in animals, plants, yeast, and in many protists [5, 36-37], and it has been hypothesized that the CTD structure has originated through amplifications of a repetitive DNA sequence and that the number of repeats appears directly correlated with genomic complexity (Figure 1A; [38]). For example, mouse and human CTDs contain 52 repeats [35, 39-40]; the Drosophila CTD contains 45 repeats [41]; 25-27 repeats are found in the yeast CTD (Figure 1A; [4]); and 15 repeats are found in protozoan CTDs [5, 38]. Although the CTD is completely dispensable for in vitro transcription, it is required for efficient RNA processing [17, 42]. In fact, the CTD is essential for cell viability because its deletion is lethal in mice, Drosophila and yeast, and partial truncations or site-specific mutations cause specific growth defects [5, 42].

Figure 1.

Human and Saccharomyces cerevisiae Rpb1-CTDs.

Original studies showed that two RNAPII forms can be differentiated in SDS-PAGE gels because of the different mobility of Rpb1 [43]. These two forms were termed RNAPIIA and RNAPIIO, and they differ in the extent of CTD phosphorylation. RNAPIIA is hypophosphorylated [44], and RNAPIIO is hyperphosphorylated [45]. Moreover, both forms, IIA and IIO, are functionally distinct because the IIA form is preferentially recruited to the promoter and associated with preinitiation complexes [46], whereas RNAPIIO functions during elongation, is highly phosphorylated [44] and thus requires de-phosphorylation to stimulate its recruitment into the PIC complexes and to reinitiate a new round of transcription [47]. We currently know that this earlier two-step transcription cycle model that is based on the two RNAPII forms is overly simple. Different phosphorylated forms of RNAPII are specific and characteristic of the different steps that occur during the transcription cycle [48], and the correct progression of RNAPII through the transcription cycle is dependent on changes in the CTD phosphorylation status. Differential CTD phosphorylation promotes the exchange of initiation and elongation factors during promoter clearance [15], the exchange of elongation and 3’-end processing factors at termination [49], as well as RNAPII recycling [50] and, moreover, links pre-mRNA processing and other nuclear events with transcription [17, 42]. Therefore, the CTD phosphorylation cycle is very complex. It is widely known that the three serines (i.e., Ser2, Ser5, and Ser7) [7, 51], the tyrosine [52-53] and the threonine [54] in each repeat can be phosphorylated. Additionally, both proline residues can be isomerized by a prolyl isomerase [55]. Moreover, glycosylation of serines and threonine can also occur [8], and in human cells, the CTD can be methylated at some of the degenerate repeat sites [56]. The multitude of possible CTD modifications, especially Ser phosphorylations, in combination with the numerous repetitions, gives rise to a wide range of variations (i.e., phosphorylation patterns) that have been termed the “CTD code” (Figure 2) [6-8].

Figure 2.

The CTD Code. Only Ser (S) and Thr (T) phosphorylation sites have been considered. CTD glycosylation has not been considered [57] because this modification is mutually exclusive of phosphorylation [8]. n: number of consensus repetitions.

The RNAPII CTD code determines and coordinates the timely sequential recruitment of required specific factors during the transcription cycle. Therefore, the CTD functions as a scaffold that coordinates mRNA biogenesis, such as transcription initiation [58], promoter clearance [59], elongation [60], and termination [31, 61-62], as well as RNA processing [17, 21, 30] and snRNA and snoRNA gene expression [63-65] by recruiting the appropriate set of factors when required during active transcription. These factors recognize CTD phosphorylation patterns either indirectly or directly by contacting phosphorylated residues. Among the CTD-associated factors are export and histone modifier factors and DNA repair factors [21].

2.1. Ser2P and Ser5P, and to a lesser extent, Ser7P, are the main determinants of the CTD code

To determine precisely which serine residues are phosphorylated in a particular repeat has been challenging because of the numbers of phospho-acceptor amino acid residues and consensus motif repetitions (Figure 1). However, studies involving chromatin immunoprecipitation with specific monoclonal antibodies have provided evidence that differential phosphorylation of the Ser residues coincides with the temporal and spatial recruitment of different factors [8, 32, 48, 66-67]. In fact, these antibodies have been largely used to decipher and characterize the role of CTD phosphorylation during the transcription cycle and in gene expression regulation [8, 32, 68]. Antibodies that selectively recognize either Ser2 or Ser5 phosphorylation (i.e., Ser2P or Ser5P, respectively) were the first residues to be described [66]; phosphorylation of these two residues has been extensively studied, and they have been considered as the two main determinants of the CTD code [6]. It is widely known that CTD phosphorylation switch from Ser5 to Ser2 during the course of transcription and is subject to a dynamic regulation during the whole transcription cycle [69-71]. The level of Ser5 phosphorylation peaks early in the transcription cycle and remains constant or decreases as RNAPII progresses to the 3′ end of the gene (Figure 3); [48, 67, 72]). In contrast, Ser2 phosphorylation is the predominant modification in the coding and 3′-end gene regions and occurs simultaneously with productive elongation [31, 48, 73]. On the other hand, de-phosphorylation of Ser5 occurs during the initiation-elongation transition and throughout the entire elongation step, whereas Ser2 de-phosphorylation occurs at the end of transcription to recycle the polymerase and reinitiate a new round of transcription. Therefore, reversible phosphorylation/de-phosphorylation of the CTD plays a significant role in modulating the transcription cycle [31-32].

Most recently, the use of new anti-CTD monoclonal antibodies has demonstrated that Ser7, which is the most degenerate position of the CTD [41], can be phosphorylated during the transcription of snRNA genes and protein-coding genes [64, 68, 74]. Subsequently, this mark increases the complexity of the CTD code [7-8]. Ser7 phosphorylation is mediated by the same kinase [74-75], although, at least in Saccharomyces cerevisiae, Ser7P appears not to be dephosphorylated by the same Ser5 phosphatase (see below) [76].The first study on Ser7 phosphorylation provided further evidence that this modification is functionally important for transcription and processing of snRNAs [8, 64] and hypothesized that the CTD code could be gene-transcription dependent. In mammals, Ser7P peaks at the promoter region of snRNA genes but is enhanced toward the 3′ end of protein-coding genes [68]. Recent genome-wide distribution studies in yeast have provided further evidence that Ser7P in protein coding genes occurs early during transcription initiation and is maintained during the entire transcription cycle. In fact, Ser7P is not only maintained, but it is also generated de novo during transcription elongation. Additionally, it has been hypothesized that Ser7 phosphorylation could facilitate elongation and suppress cryptic transcription [77].

Figure 3.

RNAPII CTD phosphorylation profile in Sacharomyces cerevisiae. During transcription initiation and promoter escape RNAPII CTD is phosphorylated on Ser5 (Ser5P) [48, 78]. Concurrently, Ser7 is phosphorylated (Ser7P), establishing a bivalent mark at both protein-coding and noncoding genes [74-76]. Shortly after promoter dissociation, Ser5P is rapidly removed while phosphorylated Ser2 (Ser2P) and Ser7P continue to accumulate [70, 77]. Finally, all CTD marks are rapidly removed at the end of transcription, and the hypophosphorylated RNAPII (in grey) is ready to assemble into the pre-initiation complex and re-initiate transcription [73, 79-80]. Small circles represent phosphorylated serine residues (green cirlces for Ser5P, blue circles for Ser7P and red circles for Ser2P). Differently colored big circles represent the distinct phosphorylated forms of RNAPII during initiation, elongation and termination. TSS: transcription start site; p(A): polyadenylation site.

2.2. Tyrosine 1 and Threonine 4 can also be phosphorylated

Tyrosine 1 (Tyr1) is evolutionarily conserved and present in all of the 52 repeats of the mammalian CTD, and in all of the 26-27 repeats of the yeast CTD. Although, it is well known that Tyr1 is susceptible to phosphorylation by tyrosine kinases in vivo [52-53] and that Tyr1 mutations are lethal in yeast [81], the function of this modification is unknown. Additionally, threonine 4 (Thr4) is also subjected to phosphorylation, at least in mammalian and in yeast cells [54, 82], and recently it has been demonstrated that phosphorylation of the Thr4 residues is required specifically for histone mRNA 3' end processing, which facilitates the recruitment of 3' processing factors to histone genes, and is evolutionarily conserved from yeast to human [54].

In mammals, there is an important degeneracy at some positions in the CTD, mainly in most of the carboxy-terminal repeats. Thus, the last repeat of the CTD is followed by a conserved 10 amino acid extension (Figure 1; [5]) that contains a constitutive site for the casein kinase (CK) II site [83]. Though deletion of this extension results in degradation of the CT, and effects in transcription and pre-mRNA processing [83-84], mutation of the CKII target site does not affect RNAPII CTD stability. Additionally, this extension is required for the phosphorylation of Tyr1 by c-Abl in mammals and it has been suggested that Tyr1 phosphorylation could be involved in functions specific of these higher eukaryotes [85]. Finally, non-consensus residues, such as lysine and arginine, are also present in the CTD, and they could be potentially modified by acetylation, ubiquitylation, sumoylation (lysine residues) and methylation (lysine and arginine residues) [86]. Therefore, the possibilities of CTD modifications are enormous, and only some of the modifications have been demonstrated to influence, while interacting with numerous factors, different aspects of gene expression.


3. Modifying enzymes: Kinases and phosphatases

Most of what is known concerning CTD-protein interactions, and in particular RNAPII CTD modifying enzymes, is derived from animal and yeast models, especially Saccharomyces cerevisiae, since the consensus sequence and repetitive structure of the CTD in addition to the CTD-modifying enzymes are highly conserved across a wide range of organisms. A number of kinases and phosphatases that target the CTD have been described and extensively studied (Tables 1 and 2, and reference therein). Recent genome-wide distribution studies of the CTD modifications in yeast have provided further evidence that complex interplay exists between these enzymes (i.e., kinases, phosphatases and isomerase), which coordinate a universal RNAPII CTD cycle [69]. These modifying enzymes alter specific serine residues within the CTD repeats and have distinct and specific functions along the transcription cycle. Although the catalytic mechanisms of CTD kinases and phosphatases are known, the basis for their specificity remains incompletely understood [87-88].

Below, in figure 4, we will highlight the most relevant features and functions of CTD kinases and phosphatases, with special emphasis on the budding yeast enzymes because extensive studies on RNAPII CTD phosphorylation have been performed on that organism, and most of these enzyme complexes are evolutionarily conserved.

3.1. RNAPII CTD kinases

The CTD is phosphorylated by members of the cyclin-dependent kinase (CDK) family, which usually consists of a catalytic and a cyclin subunit. Although CDKs are cell cycle regulators, several members of this family have direct functions in RNAPII activity regulation [39, 88]. All these kinases are members of multiprotein transcription regulatory complexes and, in mammals, the best known are Cdk7/CycH, Cdk8/CycC and Cdk9/CycT; recently, Cdk12/CycK has been characterized as a new CTD kinase [89]. These kinases are evolutionarily conserved, and the following four complexes with kinase activity have been identified in the well-known yeast model Saccharomyces cerevisae: Kin28/Ccl1, Srb10/Srb11, Bur1/Bur2 and Ctk1/Ctk2 (Table 1).

ySrb10 / Srb11
hCdk8 / CycC

Other substrates
Bdf1 and Taf2, Med2
Gcn4, Msn2, Ste12, Gal4
TFIIH inhibition
PIC inhibition / activation
Scaffold complex formation
SAGA-dependent transcription
yKin28 / Ccl1-Tfb3
hCdk7 / CycH

Other substrates
Promoter scape
Scaffold complex formation
Capping complex recruitment
Bur1 activity stimulation
Set1/COMPASS recruitment
Elongation factor Paf1C recruitment
SAGA complex recruitment
snRNA 3’ processing
Gene looping
[64, 72, 74-76, 90, 94-100]
yBur1 / Bur2
hCdk9 / CycT

Other Substrates
hDSIF (ySpt5), Rad6/Bre1
Ctk1 activity stimulation
PAF complex recruitment
H3K4 methylation
H2B monoubiquitination
Histone genes 3’-end processing
[54, 99, 101-104]
yCtk1 / Ctk2-Ctk3
hCdk12 / CycK

Other Substrates
RNAPII release from basal initiation factors
3’-processing factors recruitment
Transcription termination
Spt6 recruitment
H3K36 methylation
Translation elongation
[16, 49, 89, 105-112]

Table 1.

RNAPII CTD kinases. Mammalian and Saccharomyces cerevisiae kinases are shown.

Figure 4.

The levels of CTD phosphorylation are precisely modulated during the whole transcription cycle by the action of evolutionary conserved kinases and phosphatases. The level of Ser5 phosphorylation peaks early in the transcription cycle due to the action of Kin28 (Cdk7 in human) and remains constant or decreases as RNAPII progresses to the 3′ end of the gene [48, 67, 72]. In contrast, Ser2 phosphorylation is the predominant modification in the gene body and towards the 3′ end, and occurs concurrently with productive elongation [31, 48]. Ctk1 is the principal kinase responsible for Ser2 phosphorylation in the body of the genes [16, 73]. In addition to Ctk1, the Bur1/Bur2 kinase complex phosphorylates Ser2 when RNAPII is near the promoter and stimulates Ser2 phosphorylation by Ctk1 during elongation [99]. Several CTD-phosphatases have been shown to specifically de-phosphorylate Ser5P (Ssu72 and Rtr1), Ser2P (Fcp1) and Ser7 (Ssu72) to promote the initiation-elongation transition, elongation, termination, and RNAPII recycling [50, 73, 79, 167, 182]. Srb10 was demonstrated to phosphorylate the RNAPII CTD prior to PIC assembly, negatively regulating transcription initiation [92].

3.1.1. Pre-initiation and Initiation RNAPII CTD kinases

Cdk8/CycC. and Srb10/Srb11

Human Cdk8/CycC and yeast Srb10/Srb11 are part of the CDK-module of Mediator [113], a large complex of 25-30 proteins that is structured in 4 sub-complexes or modules that act as a molecular bridge between DNA-binding transcription factors and RNAPII [114-115]. Mediator is required for the expression of nearly all RNAPII transcribed genes [116]. Cdk8/Srb10 is part of the CDK-module (Cdk8, cyclin C, MED12 and MED13 in mammals; Srb8, 9, 10 and 11 in yeast), which dynamically associates with Mediator [93, 117]. Although Cdk8/Srb10 can phosphorylate Ser2 and Ser5 of the CTD repeats in vitro [90, 92-94, 109, 113], the in vivo relevance of Cdk8/Srb10 remains to be defined. In fact, several studies have provided evidence that Srb10/11 can have both negative [116] and positive [118] effects on gene expression in vivo. Srb10 was demonstrated to phosphorylate the RNAPII CTD prior to PIC assembly, negatively regulating transcription initiation (Figure 4; [92]). Notably, human Cdk8 represses transcription via phosphorylation and inactivation of the cyclin H subunit of TFIIH, which is the Cdk7 partner [90]. However, subsequent work showed that Srb10 functions in association with Kin28 (hCdk7) to promote RNAPII re-initiation [94]. Following PIC formation and an initial round of transcription, it is thought that subsequent rounds of RNAPII binding and promoter clearance are facilitated via a “scaffold complex” that is composed of a subset of Mediator subunits and GTFs (except TFIIB and TFIIF) that remains bound at the promoter [119]. Therefore, Kin28 and Srb10 have overlapping positive functions in promoting transcription and in the formation of the scaffold complex [94]. Srb10 phosphorylates two subunits of the general transcription factor TFIID (Bdf1 and Taf2) at the PIC; however, the role of these phosphorylation events has not yet been defined. Moreover, Srb10 phosphorylates and inactivates some transcription factors [120-122] by triggering their nuclear export or degradation [123-124] and phosphorylates and enhances the activity of others (Table 1). In summary, the in vivo relevance of RNAPII phosphorylation by Cdk8/Srb10 and its role in gene expression have yet to be elucidated.

Cdk7/CycH. and Kin28/Ccl1-Tfb3

The Cdk7/cyclin H complex in mammals and its homolog in Saccharomyces cerevisiae, Kin28/Ccl1, are part of the TFIIH general transcription factor. In yeast, Kin28 is found associated with a third subunit (Tfb3) to form a trimer, called TFIIK (Kin28-Ccl1-Tfb3) within TFIIH [125]. Mammalian Cdk7 was isolated as a RNAPII CTD kinase that possesses Cdk-activating kinase (CAK) activity [126-128], whereas in yeast, Kin28 lacks this activity [129]. The CAK activity is fulfilled by a different kinase, Cak1 [130-131]. Cdk7 and Kin28 are both essential for cell viability [132], and the in vivo function of Kin28 has been extensively studied in yeast. Cdk7/Kin28 is the primary kinase that phosphorylates the CTD within a transcription initiation complex (Figure 4). Cdk7/Kin28 has been demonstrated to phosphorylate both Ser5 and Ser7 in vitro and in vivo [72, 74-76, 92]. Phosphorylation on Ser5 by Cdk7/Kin28 is thought to disrupt the stable interactions between the CTD and PIC components, thereby permitting the polymerase to release from the promoter and commence productive transcript elongation [92, 133-134]. Ser5 phosphorylation by Cdk7/Kin28 is required for the recruitment of the mRNA-capping complex [72, 135-137] and nuclear cap-binding complex (CBC) [100] to nascent transcripts and for co-transcriptional recruitment of elongation factor Paf1C [138], histone H3-lysine 4 methyltransferase complex (SET1/COMPASS) [98], and histone acetyltransferase complex SAGA [97].

Additionally, yeast Kin28 phosphorylates two subunits of Mediator (i.e., Med4 and Rgr1/Med14), and although the functionally of these modifications is unknown, it has been demonstrated that Mediator significantly enhances the phosphorylation of RNAPII CTD by Kin28 [94, 96]. In fact, in vitro assembly of TFIIH into a pre-initiation complex requires Mediator [139], and following transcription initiation, phosphorylation of Ser5 by Kin28 parallels with the release of Mediator from the CTD of RNAPII as promoter clearance occurs [80].

As discussed above, in yeast, Kin28 and Srb10 have overlapping functions in promoting transcription, PIC dissociation and subsequent scaffold complex formation [94]. Genetic analysis has provided further evidence that Kin28 and Srb10 are not redundant because only Kin28 is essential for growth, and Srb10 is much less processive in terms of phosphorylation than Kin28 [140]. It is clear that Kin28 is the primary kinase responsible for the high level of phosphorylation of RNAPII during initiation [48, 67, 94, 141]. In fact, one essential role of Kin28 that Srb10 does not have is the stimulation of pre-mRNA processing. However, what appears clear, at least in yeast, is that PIC dissociation is dependent on the kinase activities of Kin28 and Srb10. Additionally, another function of RNAPII CTD Ser5 phosphorylation by Kin28 is the enhancement of Bur1/Bur2 recruitment and Ser2 CTD phosphorylation near the promoters [99]. Moreover, it has recently been demonstrated that TFIIH kinase places bivalent marks on the CTD, thereby phosphorylating Ser7 during transcription initiation [74-75].

3.1.2. RNAPII CTD elongating kinases

Cdk9/CycT. and Cdk12/CycK

Eukaryotic organisms possess many factors that regulate transcriptional elongation; among these factors is Cdk9 kinase, which is the catalytic subunit of the positive transcription elongation factor b (P-TEFb) that controls the elongation phase of transcription by RNAPII in mammals and Drosophila melanogaster [12]. Cdk9 is the major Ser2 kinase, but it also contributes to Ser5 phosphorylation in vitro and in vivo during the initiation-elongation transition and the polymerase release of promoter-proximal pausing [109, 142]. Cdk9 activity is also required for efficient coupling of transcription with pre-mRNA processing [108]. Additionally, very recently, it has been shown that Thr4 is phosphorylated by Cdk9 [54].

In higher eukaryotes, the transcription factor P-TEFb not only regulates CTD phosphorylation, but it also inhibits the action of transcriptional repressors and is required for the association of several elongation factors with the transcribing polymerase. P-TEFb also targets DRB sensitivity-inducing factor (DSIF) and negative elongation factor (NELF) [142-144] (Table 1). Thus, P-TEFb promotes transcription by the following two different mechanisms: inhibiting the action of transcriptional repressors and phosphorylating the CTD during transcription elongation. Until recently, it was believed that Cdk9 was the only CTD Ser2 kinase in higher eukaryotes. In fact, Cdk9 can reconstitute the activity of both S. cerevisiae Ser2 CTD kinases, Bur1 and Ctk1. However, it has recently been demonstrated that Drosophila have one ortholog of yeast Ctk1, Cdk12, whereas humans have two, Cdk12 and Cdk13; only Cdk12 has been clearly demonstrated to be an elongating CTD kinase [89, 145]. Notably and similarly, fission yeast Schizosaccharomyces pombe has the following two Ser2 elongating kinases: Lsk1 (ScCtk1) and Cdk9 (ScBur1) [146].


Bur1 kinase and its cyclin, Bur2, form an essential CDK in S. cerevisiae involved in transcription elongation [147-148]. Although Bur1 and Ctk1 kinase complexes appear to functionally reconstitute the activity of P-TEFb in yeast [149], Bur1 is more related in sequence and functionally to mammalian P-TEFb than Ctk1 [147, 149], and as we have discussed, it is clear that Cdk12 is the functional equivalent of yeast Ctk1 [89, 145]. Bur1 can phosphorylate Ser2 and Ser5 [99, 147, 150] [151], and although it was first demonstrated to show some preference for Ser5 and to be less active than Ctk1 or Kin28 [147], later studies provided evidence that Bur1 interacts with the RNAPII CTD and phosphorylates at Ser2. In fact, Bur1 phosphorylates elongating RNAPII molecules that have been previously phosphorylated at Ser5 and are located near the promoter during early transcription elongation (Figure 4, and [99]. Thus, it has been hypothesized that Bur1/Bur2 is recruited to RNAPII, whose repeats are phosphorylated on Ser5 to enhance phosphorylation on Ser2 by Ctk1. Consistent with it, Bur1 produces the Ser2 phosphorylated residues that remains when Ctk1 is inactivated [152]. Bur1 also stimulates transcription elongation as its mammalian homologue P-TEFb [150, 152], and mutations on BUR1 cause sensitivity to drugs that are known to affect transcription elongation (e.g., 6-azauracil) [147, 150]. More recently, a chemical-genomic analysis has provided further evidence that Bur1 also phosphorylates Ser7 in the body of the genes [77].

Bur1 shares another function with the mammalian and Schizosaccharomyces pombe Cdk9 [142, 153]. Bur1 kinase activity is important for the in vivo phosphorylation of the elongation factor Spt5 (mammalian DSIF) [102, 154]. Spt5 contains a carboxy-terminal domain that consists of approximately 15 repeats (CTR) that are similar to the RNAPII CTD [102], which is subject to phosphorylation. The Spt5-CTR is required for efficient elongation by RNAPII and for chromatin modifications in transcribed regions (see below). Thus, Spt5 phosphorylation mediates, at least in part, Bur1 kinase roles on transcription elongation and histone modifications [154].


Ctk1 was originally identified as the kinase subunit of the yeast CTDK-I complex that catalyzes phosphorylation of the RNAPII CTD [155]. Ctk2 is the cyclin, and the Ctk3 function remains unknown. Ctk1 is the principal kinase that is responsible for CTD-Ser2P during transcription elongation, which is coincident with reduced Ser5P [73, 156]. Although Ctk1 is not directly involved in transcription elongation [16, 18, 157], it associates with RNAPII throughout elongation [49], and the kinase activity of Ctk1 is required for the association of polyadenylation and termination factors [16] and histone modification factors [158]. Additionally, Ctk1 interacts genetically as well as biochemically with the TREX complex [159], which couples transcription elongation to mRNA export [160]. Moreover, Ctk1 promotes the dissociation of basal transcription factors from elongating RNAPII, early during transcription, however, kinase activity is not required [105].

In addition to its functions in transcribing gene coding proteins, Ctk1 is involved in RNAPI transcription, interacts with RNAPI in vivo [161], and it is required for the integrity of the rDNA tandem array [162]. All of these studies suggest that Ctk1 might participate in the regulation of distinct nuclear transcriptional machineries. Additionally, it has been demonstrated that Ctk1 is required for DNA damage-induced transcription [163], and notably, that Ctk1 has a role in the fidelity of translation elongation in the cytoplasm [110, 164].

3.2. RNAPII CTD phosphatases

Dynamic de-phosphorylation of Ser2P and Ser5P make a significant contribution to changes in CTD phosphorylation patterns during the transcription cycle and is essential for RNAPII recycling [8, 31]. Dephosphrylation is achieved by several CTD phosphatases (Table 2). Initially, only one phosphatase was identified, Fcp1, which is required for Ser2P de-phosphorylation, transcription elongation and RNAPII recycling to initiate new rounds of transcription [47, 165]. Two other CTD phosphatase were later identified in yeast, Ssu72, a component of the mRNA 3' end processing machinery [79, 88, 166] and Rtr1 [167]. In mammals, in addition to Fcp1, there are other CTD phosphatases, i.e., the small phosphatase SCP1 [168] and RPAP2, which is the human homolog of Rtr1 [169]. Briefly, Fcp1 dephosphorylates Ser2P [73]; Ssu72 dephosphorylates Ser5P and Ser7P [50, 69]; and Rtr1 in yeast and SCP1 in mammals specifically dephosphorylate Ser5P [79, 167-168].

Rtr1. / RPAP2

Chromatin immunoprecipitation studies have provided further evidence that the increase in Ser2P occurs as transcription progresses through the gene and follows Ser5P de-phosphorylation. Rtr1 in yeast was identified as the RNAPII CTD phosphatase driven the Ser5-Ser2P transition at the 5’ regions of the transcribed genes. Rtr1 genetically interacts with the RNAPII machinery, and Rtr1 deletion provokes global Ser5P accumulation in whole-cell extracts and Ser5P association throughout the coding regions [167, 171]. RPAP2 was identified in a systematic analysis carried out to determine the composition and organization of the soluble RNAPII machinery [169], and as in the case of Rtr1, Ser5P levels increase in vivo when RPAP2 is knocked down. Additionally, RPAP2 depletion affects snRNA gene expression as it does mutations of the Ser7 residue [64]. In fact, Ser7P recruits the 3’-end processing Integrator complex and RPAP2 to drive Ser5 de-phosphorylation of RNAPII CTD during the transcription of snRNA genes [170, 183]. Recently, a model has been proposed in which RPAP2 recruitment to snRNA genes through CTD-Ser7P triggers a cascade of events that are critical for proper gene expression [170].

CTD-Ser5PPromote Ser5P to Ser2P transition
Association of Integrator with snRNA genes
[167, 169-171]
CTD-Ser5P, Ser7P
Transcription initiation/elongation
Transcription termination and 3’-end processing
Facilitate Fcp1 activity
Gene looping and RNAPII recycling
[50, 69, 79, 166, 172-176]
y/h Fcp1
Positive regulator of RNAPII transcription
Transcription elongation
Transcription termination and RNAPII recycling
[47, 73, 165, 177-182]
hSCP1CTD-Ser5PTransition from initiation / capping to processive transcript elongation.[168]

Table 2.

RNAPII CTD phosphatases. Human and Saccharomyces cerevisiae phosphatases are shown.


Ssu72 was first described as a Ser5P phosphatase and recently as a Ser7P phosphatase [50, 69]. In fact, Ssu72 was originally identified as functionally interacting with the general transcription factor TFIIB [184-185]. Afterward, it was demonstrated that Ssu72 is part of the cleavage and polyadenylation factor (CPF) with a role at the 3’-end of genes [166, 175]. In fact, Ssu72 is crucial for transcription-coupled 3’-end processing and termination of protein-coding genes [175, 186-187]. Later, Ssu72 was characterized as a Ser5P phosphatase [79] and a potential tyrosine phosphatase [188] and, most recently, it has been demonstrated that Ssu72 is also a Ser7 phosphatase [50, 69]. A genome-wide distribution analysis of Ssu72 has demonstrated two peaks of association (Figure 4): a low peak at the 5’-end of genes and a higher peak at the cleavage and polyadenylation site or immediately after it [50]. In agreement with it, Ssu72 dephosphorylates RNAPII CTD following cleavage and polyadenylation and recycles the terminating RNAPII, giving rise to a hypophosphorylated polymerase. In fact, inactivation of Ssu72 leads to the accumulation of Ser7P marks that avoids RNAPII recruitment to the PIC, and therefore inhibits transcription initiation, which results in cell death [50]. In other words, Ssu72 is critical for transcription termination, 3’-end processing and RNAPII recycling to restart a new round of transcription. Additionally, it has been shown that Ssu72 has a function in gene looping [172]. In a screen looking for mammalian retinoblastoma tumor suppressors, a human homolog of yeast Ssu72 was identified. As in yeast, mammalian Ssu72 associates with TFIIB and the yeast cleavage/polyadenylation factor Pta1, and exhibits intrinsic phosphatase activity [176]. The crystal complex structure that is formed by human symplekin (Pta1 in yeast), hSsu72 and a CTD phosphopeptide has been elucidated, and hSsu72 was demonstrated to have a function in coupling transcription to pre-mRNA 3'-end processing [187].

Fcp1. / SCP1

Fcp1 was the first discovered CTD phosphatase and is highly conserved among eukarya [177, 189-191]. It directly de-phosphorylates RNAPII, and its activity is stimulated in vitro by TFIIF and inhibited by TFIIB [73, 177-178]. Fcp1 is essential for cell viability and for transcription in yeast [177-178] and preferentially dephosphorylates Ser2P [73, 192]. Fcp1 has two essential domains: an FCP homologous domain near the amino-terminus and a downstream BRCA1 carboxy-terminal (BRCT) domain [87]. Higher eukaryotes have additional small CTD phosphatases (SCPs) that contain only the FCPH domain characteristic of the Fcp1 proteins. However, SCP1 preferentially catalyzes Ser5P de-phosphorylation and is especially active on RNAPII molecules that have been phosphorylated by TFIIH [168].

Gene transcription is decreased in cells lacking Fcp1 function, and fcp1 mutants exhibited a general accumulation of hyperphosphorylated RNAPII in whole-cell extracts, and specifically in the gene coding regions [178]. Fcp1 also has the ability to stimulate RNAPII transcript elongation in vitro independent of its phosphatase activity [182], which suggests that it associates with and modulates elongating RNAPII. In agreement with this, chromatin immunoprecipitation studies have demonstrated that Fcp1 associates with the promoter and coding region of active genes in vivo [73]. Recent genome-wide studies have provided further evidence that Fcp1 associates with genes from promoter to 3’-end regions, showing the highest association of Fcp1 with the cleavage and polyadenylation site. This association occurs after Bur1 and Ctk1 have dissociated, which permits Fcp1 to completely dephosphorylate all the remaining Ser2P residues ([50], Figure 4). Fcp1 is also responsible for de-phosphorylation of RNAPII following its release from DNA [165]. Fcp1 association with genes at the cleavage polyadenylation site overlaps with Ssu72 association, whereas this overlapping does not exist at the 5’ and coding regions (Figure 4). This fact indicates that CTD de-phosphorylation may be coupled at the 3’-ends, and it has been hypothesized that Ssu72 activity may be important for Fcp1 function, thereby coupling Ser2P de-phosphorylation to the removal of Ser5P and Ser7P [69].


4. Other factors influencing RNAPII CTD phosphorylation

Although many factors can have effects on CTD phosphorylation, we will highlight the following two that we believe are of significant relevance: the prolyl isomerases hPin1/yEss1 and the structure of the RNAPII itself. In addition, we will describe the role of ySub1 in CTD phosphorylation, because it has been extensively studied by us.

4.1. hPin1 / yEss1

The CTD can adopt either cis- or trans-conformations, which can significantly affect its modification, especially its phosphorylation. Peptidyl prolyl isomerases (PPIases) are enzymes that accelerate the rates of rotation about the peptide bond preceding proline and are important for protein folding and regulation of dynamic cellular processes [193-194]. Pin1 in mammals and Ess1 in S. cerevisiae are RNAPII CTD PPIases. Phosphorylated Ser2 and Ser5 match with the pSer-Pro sequence that is recognized by Pin1, and the CTD appears to be its principal target of regulation [195-196]. Pin1 has specificity for phosphorylated Ser/Thr-Pro sequences, and it modulates RNAPII activity during cell cycle at least in part by regulating RNAPII CTD phosphorylation levels [195]. Yeast Ess1 physically interacts with the CTD [55, 197], and it preferentially binds and isomerizes in vitro Ser5P residues [198]. Although Pin1 stimulates RNAPII CTD hyperphosphorylation, which results in transcription repression and inhibition of mRNA splicing [195-196], in vivo studies have proposed that Ess1 promotes RNAPII CTD de-phosphorylation. In any case, both isomerases have important functions in transcription. Therefore, initiation-elongation transition is inhibited by Pin1 [196], whereas Ess1 affects multiple steps, such as initiation, elongation, 3′-end processing, and termination [197, 199-201]. In fact, it has been demonstrated that Ess1 promotes Ssu72-dependent function by creating the CTD structural conformation that is recognized by Ssu72 [202], and recently it has been confirmed that isomerization is a key regulator of RNAPII CTD de-phosphorylation at the end of genes [69].

4.2. RNAPII structure and Rpb1-CTD localization

The structure of the complete 12-subunit RNAPII (Rpb1-12) is known [203-204]. Rpb4 and Rpb7 subunits form a conserved sub-complex that is conserved in all three eukaryotic RNA polymerases and archaea RNAP [205-206]. Crystal structures of the Rpb4/7 heterodimer in the context of the complete RNAPII complex localized it in the proximity of the Rpb1-CTD [203, 207], and biochemical and genetic studies suggest that Rpb4/7 might have a function in the recruitment of some CTD-binding proteins to transcribing RNAPII. Moreover, it is possible that this sub-complex, Rpb4/7, would regulate the access of CTD modifying enzymes during the whole transcription cycle [203, 207, 209-212]. Actually, structural studies have provided further evidence that the CTD extends from the RNAPII core enzyme near the RNA exit channel [204], where it is ideally located to bind and be affected by the action of a multitude of factors, among them kinases, phosphatases and isomerases. In fact, in yeast, the isopropylisomerase Ess1 and the phosphatase Fcp1 are associated with Rpb7 and Rpb4, respectively [55, 87, 208].

4.3. The ssDNA binding protein Sub1 as a general regulator of transcription

Sub1 is an ssDNA binding protein that has been implicated in several steps of mRNA metabolism, such as initiation, transcription termination and 3’-end processing [186, 213-215]. Sub1 was originally described as a transcriptional stimulatory protein that is homologous to the human positive coactivator PC4, which physically interacts with activators and components of the RNAPII basal transcription machinery [216-220]. Sub1 genetically and physically interacts with TFIIB [214-215, 221], and several functions have been proposed for Sub1 that include stimulating PIC recruitment and promoter escape. In fact, most recently, using a quantitative proteomic screen to identify promoter-bound PIC components, Sub1 was identified as a functional PIC component that is associated with RNAPII complexes [225]. In addition, we have recently demonstrated that Sub1 globally regulates RNAPII CTD phosphorylation (Figure 5, [222]) and that it is a bona fide elongation factor that influences transcription elongation rates (García and Calvo, unpublished results). Although it has been broadly studied, and several functions have been hypothesized for Sub1 [213, 215, 222-225]; however, the exact mechanism by which Sub1 functions in transcription remains unclear. Sub1 globally regulates RNAPII-CTD phosphorylation during the entire transcription cycle by modulating, albeit differentially, the activity and recruitment of CTD modifying enzymes [222, 224]. We have proposed a model showing how Sub1 might function to globally regulate RNAPII CTD phosphorylation (Figure 5). In wild-type cells (wt), non-phosphorylated Sub1 joins the promoter (possibly via TFIIB; [214-215, 221]), contacting the promoter via its DNA binding domain. At that point, Sub1 interacts with the Cdk8-Mediator complex, helping to maintain the PIC in a stable but inactive conformation. Sub1 is then phosphorylated (possibly by the action of kinases at the PIC, similarly to PC4, its human homolog), losing its DNA binding capacity and promoting clearance of TFIIB [214-215, 226]. The PIC next changes conformation such that Kin28 can be activated, and with the help of Srb10 promotes PIC dissociation into the scaffold complex as well as the recruitment of elongating kinases Ctk1 and Bur1. In contrast, in the absence of Sub1 (sub1Δ), Srb10 activity and recruitment are decreased, while Kin28 recruitment and activity increases, in agreement with TFIIH being negatively regulated by Cdk8-containing Mediator complexes [90, 227]. As a result, Ser5P levels are increased, and consequently Bur1 and Ctk1 association with chromatin is also enhanced [99, 228]. Furthermore, in sub1Δ cells there is a reduction on Fcp1 phosphatase levels and its association with chromatin, which induces an additional increase in Ser2P, impairing RNAPII recycling after transcription termination. Thus, a decrease in RNAPII recruitment is observed in cells lacking Sub1 [224]. Additionally, Sub1 also influences Spt5 elongation factor phosphorylation by Bur1 (García and Calvo, unpublished results). We currently do not understand the biochemical basis for these effects. We have not found evidence that Sub1 associates with any of the CTD kinases or evidence that Sub1 influences the CTD kinase activities by influencing post-translational modifications of the kinases. Therefore, we currently consider two possible explanations for the effects of Sub1 on the activities of the CTD kinases. One explanation is that Sub1 enhances the association (or dissociation) of an unidentified, common regulator with the kinases, whereas the other is that Sub1 in some manner influences kinase accessibility to the CTD.

Figure 5.

Model showing how Sub1 might function to globally regulate RNAPII CTD phosphorylation [222]. Different font sizes in the figure text indicate the increase or decrease of the corresponding CTD modifying enzymes in sub1Δ versus wt cells.


5. RNAPII CTD phosphorylation and pre-mRNA processing

The CTD is an unordered structure that extends from the RNAPII core enzyme, near the RNA exit channel [204, 209]. This localization is convenient to interact with a plethora of factors, such as the CTD-modifying enzymes and binding factors involved in distinct nuclear processes, for example, components of the RNA processing machinery [32, 88]. Furthermore, its length and the ability to adopt numerous conformations permit it to interact with different factors at the same time [31-32], and it is currently clear that these interactions depends on the CTD phosphorylation patterns during the transcription cycle [8, 21].

As transcription progresses the nascent RNA is capped to protect the 5′ end, intron sequences are removed, and a polyadenylated tail is added to the 3’ end. Coupling mRNA processing to transcription increases processing efficiency and allows multiple regulatory pathways to guarantee that only correctly modified mRNAs are exported. For more than a decade, numerous studies have provided evidence that the CTD serves as a scaffold for the assembly of an enormous variety of protein complexes to coordinate not only transcription of non-coding and protein-coding genes [8, 58-62, 64-65], but also pre-mRNA processing [21, 31-32]: capping [42, 135, 137], splicing [229], and 3’-end cleavage and polyadenylation [42]. All of these functions are achieved through the recognition and reading of the CTD code during the transcription cycle [6-8, 31]. Thus, co-transcriptional CTD-mediated processing of nascent RNA plays a crucial role in both recruitment of RNA processing machineries and regulation of their activities. Indeed, a functional CTD is not required for in vitro transcription by RNAPII, but it is essential for efficient pre-mRNA processing [42, 230-231].


The capping reaction consists in the addition of an inverted 7-methylguanosine cap to the first RNA residue by a 5'-5' triphosphate bridge. It is a characteristic of all RNAPII transcripts and is added to the 5’-end of nascent transcripts when they are only 25-50 bases long. The capping complex contains the following three enzymatic activities: RNA 5'-triphosphatase, guanylyl transferase and RNA (guanine-7) methyltransferase [17, 67]. In yeast, these activities are achieved by three enzymes (i.e., Cet1, Ceg1 and Abd1, respectively), whereas in metazoans, these activities are performed by two enzymes (i.e., HCE and MT) because guanylyl transferase and RNA 5'-triphosphatase are two functionally domains of HCE protein [17]. Following Ser5 phosphorylation by TFIIH, the mRNA capping complex binds directly and specifically to Ser5P residues through the Ceg1 subunit in yeast or the guanylyl transferase domain in metazoans [48, 67, 78, 95, 137]. Furthermore, phosphorylated CTD interaction with the capping complex allosterically stimulates the capping enzyme activity and in response, enhances early transcription [136, 232]. Because the CTD is located near the RNA exit channel, its interaction with the capping complex permits its positioning for rapid processing of the mRNA 5’-end as the nascent transcript emerges from the polymerase. This is thought to protect the RNA from degradation and promote RNAPII to proceed into productive transcription elongation. In fact, by coupling capping and early transcription, only capped RNA will be elongated [67, 136, 232-233].

3’-end processing

Not only capping and transcription are linked at the 5’-end regions of protein coding-genes, but also polyadenylation and transcription termination at the 3’-end regions. In brief, 3’-end processing consists of the following two-step reaction: endonucleolytic cleavage of the pre-mRNA and subsequent addition of a poly(A) tail [17]. Both enzymatic reactions require a functional CTD [42, 230]. In fact, deletion of the CTD or absence of CTD phosphorylation negatively affects 3’-end processing [16, 30, 106, 157, 234]. Furthermore, the CTD binds 3′-end processing factors and stimulates cleavage/polyadenylation in vivo and in vitro [42, 230]. The cleavage is achieved by a complex that consists of CstF, CPSF, CF1, and CF2 in higher eukaryotes and CF1A, CF1B, and CFII in yeast, whereas the polyadenylation reaction is performed by a poly(A) polymerase in both cases [17]. Cleavage/polyadenylation factors CPSF and CstF can specifically bind to CTD affinity columns and are copurified with RNAPII [42]. In yeast, several 3’-end factors preferentially binds phosphorylated CTD [72, 106-107, 235]. Furthermore, yeast 3'-end processing factors are recruited depending on Ser2 phosphorylation by Ctk1 when RNAPII reaches the 3’-end regions of the transcribed genes. Therefore, regulation of CTD phosphorylation as the polymerase transcribes facilitates coordination of the assembly of the 3′-end processing machinery with transcription [16]. Additionally, the polyadenylation signals are required for proper transcription termination in mammals and yeast [236-237]. In fact, Rtt103, which is a 3'-end mRNA processing factor, interacts with the CTD phosphorylated on Ser2 and recruits a 5’-3’ RNA exonuclease, thereby promoting the release of RNAPII from the DNA [238-239]. In summary, Ser5 phosphorylation by TFIIH kinase (Kin28/Cdk7) is required to recruit the RNA-capping machinery to RNAPII [48, 67, 72], whereas Ser2 phosphorylation is required for the recruitment of 3’-end processing complexes and for transcription termination [16, 30, 106, 238-239] (Figure 7). However, it is unknown whether phosphorylation of Ser5 and Ser2 of all of the repeats or only some of the repeats is required to enhance capping and cleavage/polyadenylation, respectively.

Ser7 phosphorylation has been functionally related with 3’-end processing of snRNA in higher eukaryotes. Human snRNA genes, contrary to protein-coding genes, are not polyadenylated, and instead of a poly(A) signal, they contain a conserved 3′ box RNA-processing element that is recognized by the snRNA gene-specific Integrator RNA 3′ end-processing complex. This complex binds to RNAPII CTD and links transcription and 3’-end processing [63-64, 240-241]. Therefore, in metazoans, Ser7P, in combination with Ser2P, is a major determinant for the recruitment of the Integrator complex to snRNA genes during its transcription [64, 240-241]. In yeast, the Integrator-like complex recruitment depends on Ser7 phosphorylation, the promoter elements and the specialized PIC that binds those elements [74]. After promoter escape, the RNA processing complex travels with the elongating phosphorylated polymerase up to the 3’-end box at the end of the snRNA transcription unit, where it associates with the nascent transcript in a co-transcriptional-dependent manner.


As in the case of capping and cleavage/polyadenylation, a number of studies performed in vivo and in vitro during the last decades have demonstrated the existence of a functional interaction between the transcriptional machinery and the splicing apparatus [21, 242]. However, this functional interaction and the underlying mechanism are less accurately understood. The most complex pre-mRNA processing reaction is splicing, which is carried out by a large complex, the spliceosome, consisting of at least 150 protein components and five snRNAs [242]. The first indication of a coupling between transcription and splicing came from studies demonstrating that truncation of the CTD severely altered splicing in vitro [42]. Later it was shown that the CTD directly affects splicing, and that a phosphorylated CTD is required for the efficient splicing reaction [231, 243]. These data provided evidence that an elongating RNAPII with phosphorylated CTD is an active component of the splicing reaction. A number of physical links between the phosphorylated CTD and the splicing apparatus have been established, and chromatin immunoprecipitation analysis have shown that the direct binding of the splicing machinery to the nascent RNA is responsible in a large part for the co-transcriptional splicing in yeast and mammals [244-245]. Hyperphosphorylated, but not hypophosphorylated RNAPII, has been found associated with splicing factors and detected in active spliceosomes [246-248]. For instance, in yeast, the splicing factor Prp40 binds to phosphorylated CTD [249]; in mammals, Spt6 binds selectively to the CTD-Ser2P [112], and the spliceosome-associated protein CA150 interacts with phosphorylated CTD while interacting with the SF1 splicing factor [250-251]. Therefore, all these studies led to the idea that the phosphorylated CTD acts as a scaffold, binding multiple splicing factors, and directly enhancing the spliceosome assembly. Corroborating this idea, a recent study identified a splicing factor, U2AF65, that interacts directly with the CTD to activate splicing and likely plays a role in spliceosome assembly [242, 252]. Another recent study provided evidence that coupling transcription and splicing through CTD phosphorylation can be a regulatory point in the control of gene expression. For instance, it has been described that a set of inducible genes can be actively transcribed by RNAPII phosphorylated on Ser5, but not on Ser2, under non-inducing conditions, giving rise to a full length unspliced transcript. However, after induction, Cdk9 is recruited, phosphorylates the CTD on Ser2 and the generated transcript is properly spliced [253]. This fact strongly implicates Ser2P as a key in the integration of splicing and transcription. In addition to constitutive splicing, functional links between the CTD and alternative splicing have also been provided [86]. Thus, it has been suggested that the CTD may regulate the choice of alternative exons by increasing the local concentration of splicing factors [229], and that possibility participate in the physical modulation of alternative splicing.


6. RNAPII CTD phosphorylation coordinates transcription to other nuclear processes

6.1. Coupling the CTD code and the histone code

The nucleosome is the basic element of chromatin and consists of a histone octamer composed of two copies of histone 2A (H2A), H2B, H3 and H4, wrapped by 146 bp of DNA [254]. The histones carry numerous post-translational modifications, and some of these are associated with transcription. In fact, a general view is that histone post-translational modifications draw parallel with either positive or negative transcriptional states. Numerous discoveries have led to the idea that such modifications regulate transcription either directly by causing structural changes to chromatin (e.g., histone acetylation) or indirectly by recruiting protein complexes (e.g., histone methylation) [255-257]. Therefore, chromatin not only plays an essential role in packaging the DNA, but also in regulating gene expression. Most histone modifications reside in their amino- and carboxy-terminal tails, and a few of them in their globular domains. As in the case of CTD phosphorylation, where Ser5P triggers Ser2 phosphorylation, some histone modifications mark the deposition of another, thus creating a complex epigenetic signal code, the “histone code”, that governs chromatin organization and DNA-dependent processes such as transcription. Therefore, the histone code is responsible for an active or inactive chromatin state with respect to transcription, because it coordinates the recruitment of various chromatin modifying and remodeling complexes to regulate chromatin structure and, consequently, transcription [258-259]. Because this review focuses on RNAPII CTD phosphorylation, only certain histone modifications, which are functionally related to the CTD code and transcription, will be discussed. There are excellent reviews that discuss all the histone modifications and their roles in different nuclear processes [255, 258, 260-261].

Lysine is a key substrate residue because it undergoes many exclusive modifications important for transcription regulation (i.e., acetylation, methylation, ubiquitination and SUMOylation [255, 261]. The lysine residues can be mono-, di- or trimethylated, and each level of modification can result in distinct biological effects. In brief, with respect to transcription, acetylation activates and sumoylation appears to be repressive, and both modifications may mutually interfere. On the other hand, methylation can have distinct effects; thus, lysine 4 in histone H3 (H3K4me3) is trimethylated at the 5’-ends of genes during activation, whereas trimethylation of H3K9 occurs in transcriptionally silent regions. Arginine residues of H3 and H4 can also be mono- or dimethylated, which activate transcription. Serine/threonine phosphorylation of H3 in specific sites also marks activated transcription, and ubiquitination of H2B and H2A are associated with active and repressed transcription, respectively (reviewed by [255-257]. All histone modifications are removable by specific enzymes (e.g., histone deacetylases (HDACs), phosphatases, and ubiquitin proteases ([255-257], and references therein). In fact HDACs play important regulatory roles during active transcription [262].

Methylation of H3K4 and K36 are the most well characterized histone modifications with roles in active transcription [263], and whose functions are directly linked to RNAPII CTD phosphorylation (Figure 6). H3K4 is methylated by the Set1/COMPASS complex, while K36 is mediated by the Set2 complex. The profile of H3K4 tri-methylation (H3K4me3) strongly correlates with the distribution pattern of the RNAPII CTD-Ser5P. It is mainly found around the transcriptional start site (TSS) contributing to transcription initiation, elongation and RNA processing [264]. Set1 recruitment and H3K4 tri-methylation usually peaks at the promoter and 5’ region of a gene, depending on Kin28/Cdk7 activity (Figure 7) and Paf1 complex, a RNAPII-associated complex [265], and contributes to transcription initiation, elongation and RNA processing [264] [98]. H3K4 mono and di-methylation tend to expand along the coding regions compared to try-methylation. On the other hand, H3K36 methylation by Set2 is observed across the entire coding region with an increase toward the 3’-ends of actively transcribed genes. Ctk1 also regulates H3K4 methylation [158, 266]. Thereby, differently phosphorylated CTD by Kin28 and Ctk1 is responsible for the characteristic distribution of H3K4 tri-methylation in the coding region [158]. In contrast to Set1, the recruitment of Set2 and H3K36 methylation depends on a CTD-Ser2P/Ser5P double mark (Figure 6), and therefore, on Ctk1 kinase activity [158, 266]. Interestingly, the other Ser2 kinase complex, Bur1/2, also promotes Set2 recruitment and assists H3-K36 methylation, particularly at the 5′ ends of genes and is required for the histone 2B ubiquitination activity of the Rad6/Bre1 complex [101, 103, 152].

Figure 6.

Histone H3 tri-, di-, and mono-methylation and acetylation during RNAPII transcription in S. cerevisiae.

H3 acetylation / deacetylation is also relevant during active transcription. Thus, histone acetyl and deacetyl transferase complexes (HAT and HDACs, respectively) are recruited to the transcriptional machinery during elongation through the interaction with RNAPII. Indeed, they modulate histone occupancy in the coding regions of actively transcribed genes, and this depends on CTD phosphorylation status [267-268]. HAT acetylates nucleosomes promoting nucleosomes eviction and allowing RNAPII to pass through. Afterward, the nucleosomes are immediately reassembled behind the polymerase and HDACs are co-transcriptionally recruited to rapidly and efficiently deacetylate the reassembled nucleosomes behind the polymerase. Altogether, this avoids cryptic transcription and maintains active transcription [262]. Methylation of histone H3 by Set1 and Set2 is required for deacetylation of nucleosomes in coding regions by the histone deacetylase complexes (HDACs) Set3C and Rpd3C(S), respectively. HDACs’ recruitment is triggered by H3K4 methylation at promoters and within coding regions to restrict hyperactetylated histones to promoters and to maintain transcription activity. Set1-H3K4me2 can be recognized by two different HDACs, RPD3S or SET3C [264]. The Set1-SET3C pathway preferentially affects actively transcribed genes with promoters configured for efficient initiation/re-initiation [269]. In contrast, Set1-RPD3S pathway is active at loci subjected to cryptic and weak transcription encompassing repressed promoters of coding genes. Related to this, phosphorylation of the CTD by Kin28/Cdk7 is important for the initial recruitment of the Rpd3S and Set3 HDACs to coding sequences ([268], Figure 7). In fact, it has been reported that Set3C and Rpd3C(S) are co-transcriptionally recruited in the absence of Set1 and Set2, but stimulated by the CTD kinase Kin28/Cdk7. Hence, the Rpd3C(S) and Set3C co-transcriptional recruitment is stimulated by CTD Ser5P to achieve the deacetylation of H3 residues. This, together with evidence that the RNAPII CTD recruits additional chromatin modifying complexes, histone chaperones and elongation factors, suggest that phosphorylated RNAPII is crucial in coordinating the activities of the many factors required for regulating histone dynamics and consequently transcription elongation at actively transcribing genes ([262], and references therein).

6.2. Transport

In addition to the complexes involved in mRNA processing, several other proteins bind to the RNAs as soon as their 5’-end emerges from the RNAPII, packaging them into a messenger ribonucleoparticle (mRNP). This set of interactions of packaging and export factors play a dual function of protecting the RNA from degradation and preparing it to be exported. Although interactions between the CTD and many mRNA processing factors have been characterized, this is not the case for mRNA packaging and export factors. However, packaging and export seems to be also coupled to transcription through RNAPII CTD interactions because defects in transcription elongation, splicing, and 3′-end processing affect export [270]. In yeast, mRNA export is linked to transcription through the TREX (transcription export) complex, which is composed of the THO complex (Tho2, Hpr1, Mft1, and Thp2) and the evolutionally conserved RNA export proteins, Sub2 (UAP56 in human) and Yra1 (REF/Aly in human), and a novel protein termed Tex1 [271-272]. Deletions of the individual THO components causes defects on transcription, transcription-dependent hyper-recombination, and on mRNA export [160, 273]. In addition, the Sub2/Yra1 complex is directly recruited to the actively transcribed regions via the THO complex [272, 274]. Although it has been shown that the TREX complex and Ctk1 are functionally related [159], recruitment of the TREX complex to transcribed genes is not dependent on Ctk1 in yeast [16], and the association of the human TREX complex to transcript might be coupled to transcription indirectly through splicing [275]. Then, the potential role of the CTD and CTD phosphorylation in this process remains unclear, however in a very recent study, the mRNA export factor Yra1 was identified as a CTD phosphorylated-binding protein [276]. Then, this study provides strong support for the idea that the phosphorylated CTD is directly involved in the cotranscriptional recruitment of export factors to active genes. In summary, many aspects of the mRNA metabolism from the 5' capping to the export occur co-transcriptionally and are coordinated through transcription, with the RNAPII CTD and its phosphorylation being the main coordinator in most cases (Figure 7).

Figure 7.

RNAPII CTD phosphorylation/ de-phosphorylation is co-transcriptionally connected and coordinated with other nuclear processes: pre-mRNA processing; histone modifications and mRNA export. The main complexes required for co-transcriptional processes occurring during the expression of a regular protein coding-gene are shown. See text for details.


7. RNAPII CTD phosphorylation and transcription regulation

The levels of CTD phosphorylation/de-phosphorylation are precisely modulated during the entire transcription cycle, which regulates the association of many important factors with initiating and elongating RNAPII, such as transcription and pre-mRNA processing factors, chromatin modifiers and mRNA export factors [21]. The interplay of all of these factors is essential to regulating transcription and, consequently, gene expression. Subsequently, in a regular protein-coding gene, the following set of coordinated nuclear events must occur for it to be properly transcribed in a functional mRNA before it is exported to the cytoplasm and translated (Figure 7). Unphosphorylated RNAPII is recruited to the pre-initiation complex (PIC); then, after its binding to the promoters, it is phosphorylated on Ser5 by yKin28 (hCdk7). Ser5 phosphorylation is required for RNAPII dissociation from the PIC and consequently promotes transcription initiation. Simultaneously, Ser5 phosphorylation targets capping and splicing factor recruitment, the Set1 methyltransferase complex, and the Set3C and Rpd3S histone deacetylase complexes. During early elongation, Ser5P levels are decreased, whereas Ser2P levels increase due to the kinase activity of yBur1 (hCdk9) near the promoters, and by the kinase activity of yCtk1 (hCdk12) at the forward coding and 3’-ends, which leads to the recruitment of the histone methyltransferase Set2 and the activation of the Rpd3S complex, which prevents cryptic transcription within the genes. When RNAPII arrives at and recognizes the termination site, the 3’-end-processing factors that are associated with the CTD achieve cleavage and polyadenylation of the nascent mRNA, which also requires proper phosphorylation of the polymerase. During the termination process, the CTD is de-phosphorylated by Ssu72 and Fcp1, and the polymerase is recycled to initiate a new round of transcription. All along the gene, packaging and export factors (TREX complexes) are incorporated into the transcriptional machinery protecting the transcript from degradation and preparing it for export to the cytoplasm.


8. Therapeutic potential

Cellular differentiation, morphogenesis, development and adaptability of all organisms are subjected to proper gene expression and, therefore, variations in gene regulation can have profound effects on protein function, challenging the viability of the organisms. Currently, it is clear that RNAPII phosphorylation has an important role on gene expression, and therefore, in all the processes mentioned above. Consequently, over the last decade CTD phosphorylation has attracted the attention of biomedical research, especially due to the fact that the CTD kinase Cdk9 has been involved in several physiological cell processes, whose deregulation may be associated with cancer, and also due to the fact that Cdk9 activity is required for human immunodeficiency virus type 1 (HIV-1) replication. Related to it, many studies have shown the enormous potential of Cdk9 kinase inhibition as a treatment of several kinds of tumors, HIV infection, and cardiac hypertrophy.

The human immunodeficiency virus type 1 (HIV-1) requires host cell factors for all steps of the viral replication, among them the transcription elongation factor P-TEFb. Transcription of HIV-1 viral genes is achieved by host RNAPII and is induced by a viral trans-activator protein, Tat. When bound to the TAR viral RNA region, Tat activates HIV-1 transcription by early recruiting of host transcriptional activators including P-TEFb, which phosphorylates RNAPII CTD promoting viral transcript elongation [280]. Thus, treatment with drugs that inhibit Cdk9, such as flavopiridol, has been used as a retroviral therapy on AIDS patients [281]. Therefore, from the point of view of basic research, the study of the functions of Cdk9 and RNAPII CTD phosphorylations are of great interest in understanding the mechanisms that regulate HIV replication, which consequently lead to progress on AIDS biomedical research. Further evidence has been provided of a deregulated Cdk9 function in several tumors such as lymphoma, neuroblastoma, primary neuroectodermal tumor, rhabidomiosarcoma or prostate cancer [282-284]. The Cdk9 inhibition by chemotherapeutic agents, such as flavopiridol or CY-202, has shown to reduce transcription in malignant cells, mainly affecting the short half-lives RNAs. Most of these RNAs code for anti-apoptotic proteins, for instance onco-protein Mcl-1, which is necessary in tumor proliferation maintenance. Unfortunately, they only have a modest activity in patients although promising studies continue at present [285]. Cardiac hypertrophy consists of an increased size of cardiomyocytes, associated to some cardiac diseases as hypertension or diminished heart function. Hypertrophy is a physiological response to a stress stimulus that results in an increase of the cell size, and that may eventually produce a heart failure. Increased cell size produces increased mRNAs transcription, which requires Cdk9 activity. Thus, it has been shown that therapy with Cdk9 inhibitors benefits patients with cardiovascular disorders [286].


9. Concluding remarks

The primary function of the RNAPII CTD phosphorylation in eukaryotes is the integration of transcription with distinct nuclear processes. Thus, CTD phosphorylation operates as a fine-tuning regulatory mechanism during the whole transcription cycle and is consequently of extraordinary importance for proper gene expression. Since the late 1980’s, an overwhelming number of laboratories have tried to decipher the mechanism underlying the creation of a CTD code and how this code is translated during transcription to coordinate mRNA processing, export and chromatin modifications. Although great progress has been achieved, most recently due to wide-genomic analysis techniques, a number of issues remained unsolved. For instance, it is very challenging to determine the exact phosphorylation state of specific residues within specific repeats during each step of transcription, as well as to determine the exact number of repeats that are phosphorylated within the CTD at every step of transcription, and how this is related to CTD specific roles in gene expression. Moreover, it needs to be determined if phosphorylation of the repeats with non-consensus sequences is regulated in the same manner as the consensus repeats, and if this is achieved by the same set of CTD modifying enzymes. In addition, other residues such as lysine and arginine can be potentially modified; therefore, further increasing the complexity of the CTD, and suggesting that if they are transcriptionally modified, may further elucidate the CTD functions or discover new ones. Finally, detailed understanding of RNAPII CTD phosphorylation is very relevant and will add insight into the processes that alter gene expression, such as HIV infection and cancer, and will help to investigate if other human CTD modifying enzymes, in addition to Cdk9, may be good candidates for therapy. In conclusion, research has made much progress, but further progress is still needed, and the new massive techniques in genomics and proteomics will help to advance complete understanding much faster.


This work was supported by a grant from the Spanish Ministerio de Ciencia e Innovación (BFU 2009-07179) to OC. AG was supported by a fellowship from the Junta de Castilla y León. The IBFG acknowledges support from “Ramón Areces Foundation”.


  1. 1. JunS. H.MJReichlenTajiri. M.MurakamiK. S.2011Archaeal RNA polymerase and transcription regulationCrit Rev Biochem Mol Biol. 462740
  2. 2. WernerF.GrohmannD.2011Evolution of multisubunit RNA polymerases in the three domains of lifeNat Rev Microbiol. 98598
  3. 3. GrohmannD.WernerF.2011Cycling through transcription with the RNA polymerase F/E (RPB4/7) complex: structure, function and evolution of archaeal RNA polymeraseRes Microbiol. 1621018
  4. 4. AllisonL. A.MoyleM.ShalesM.InglesC. J.1985Extensive homology among the largest subunits of eukaryotic and prokaryotic RNA polymerases.Cell42599610
  5. 5. Corden JL1990Tails of RNA polymerase II.Trends Biochem Sci. 15383387
  6. 6. BuratowskiS.2003The CTD code.Nat Struct Biol. 10679680
  7. 7. Corden JL2007Transcription. Seven ups the code. Science. 31817351736
  8. 8. EgloffS.MurphyS.2008Cracking the RNA polymerase II CTD codeTrends Genet. 24280288
  9. 9. HahnS.YoungE. T.2011Transcriptional regulation in Saccharomyces cerevisiae: transcription factor regulation and function, mechanisms of initiation, and roles of activators and coactivatorsGenetics189705736
  10. 10. SikorskiT. W.BuratowskiS.2009The basal initiation machinery: beyond the general transcription factorsCurr Opin Cell Biol. 21344351
  11. 11. Thomas MC, Chiang CM2006The general transcription machinery and general cofactors.Crit Rev Biochem Mol Biol. 41105178
  12. 12. SaundersA.CoreL. J.LisJ. T.2006Breaking barriers to transcription elongation.Nat Rev Mol Cell Biol. 7557567
  13. 13. SelthL. A.SigurdssonS.SvejstrupJ. Q.2010Transcript Elongation by RNA Polymerase IIAnnu Rev Biochem. 79271293
  14. 14. ShilatifardA.ConawayR. C.ConawayJ. W.2003The RNA polymerase II elongation complex.Annu Rev Biochem. 72693715
  15. 15. Pokholok DK, Hannett NM, Young RA2002Exchange of RNA polymerase II initiation and elongation factors during gene expression in vivo.Mol Cell. 9799809
  16. 16. AhnS. H.KimM.BuratowskiS.2004Phosphorylation of serine 2 within the RNA polymerase II C-terminal domain couples transcription and 3’ end processing.Mol Cell. 136776
  17. 17. HiroseY.ManleyJ. L.2000RNA polymerase II and the integration of nuclear events.Genes Dev. 1414151429
  18. 18. MasonP. B.StruhlK.2005Distinction and relationship between elongation rate and processivity of RNA polymerase II in vivo.Mol Cell. 17831840
  19. 19. OrphanidesG.ReinbergD.2000RNA polymerase II elongation through chromatin.Nature407471475
  20. 20. OrphanidesG.ReinbergD.2002A unified theory of gene expression.Cell108439451
  21. 21. PeralesR.BentleyD.2009Cotranscriptionality": the transcription elongation complex as a nexus for nuclear transactions. Mol Cell. 36178191
  22. 22. Carmody SR, Wente SR2009mRNA nuclear export at a glanceJ Cell Sci. 12219331937
  23. 23. ChanaratS.SeizlM.StrasserK.2011The Prp19 complex is a novel transcription elongation factor required for TREX occupancy at transcribed genesGenes Dev. 2511471158
  24. 24. la CruzJ.LunaR.AguileraA.2011Nab2 functions in the metabolism of RNA driven by polymerases II and IIIMol Biol Cell. 2227292740
  25. 25. IglesiasN.StutzF.2008Regulation of mRNP dynamics along the export pathwayFEBS Lett. 58219871996
  26. 26. KomiliS.SilverP. A.2008Coupling and coordination in gene expression processes: a systems biology viewNat Rev Genet. 93848
  27. 27. KrukJ. A.DuttaA.FuJ.DSGilmourReese. J. C.2011The multifunctional Ccr4-Not complex directly promotes transcription elongation. Genes Dev. 25581593
  28. 28. Svejstrup JQ2007Elongator complex: how many roles does it play? Curr Opin Cell Biol. 19331336
  29. 29. ManiatisT.ReedR.2002An extensive network of coupling among gene expression machines.Nature416499506
  30. 30. ProudfootN. J.FurgerA.MJDye2002Integrating mRNA processing with transcription.Cell108501512
  31. 31. BuratowskiS.2009Progression through the RNA polymerase II CTD cycleMol Cell. 36541546
  32. 32. Phatnani HP, Greenleaf AL2006Phosphorylation and functions of the RNA polymerase II CTD.Genes Dev. 2029222936
  33. 33. CramerP.2002Multisubunit RNA polymerases.Curr Opin Struct Biol. 128997
  34. 34. CramerP.2002Common structural features of nucleic acid polymerases.Bioessays. 24724729
  35. 35. Corden JL, Cadena DL, Ahearn JM, Jr., Dahmus ME1985A unique structure at the carboxyl terminus of the largest subunit of eukaryotic RNA polymerase II.Proc Natl Acad Sci U S A. 8279347938
  36. 36. LiuP.GreenleafA. L.StillerJ. W.2008The essential sequence elements required for RNAPII carboxyl-terminal domain function in yeast and their evolutionary conservation. Mol Biol Evol. 25719727
  37. 37. LiuP.KenneyJ. M.StillerJ. W.GreenleafA. L.2010Genetic organization, length conservation, and evolution of RNA polymerase II carboxyl-terminal domain. Mol Biol Evol. 2726282641
  38. 38. ChapmanR. D.HeidemannM.HintermairC.EickD.2008Molecular evolution of the RNA polymerase II CTDTrends Genet. 24289296
  39. 39. PrelichG.2002RNA polymerase II carboxy-terminal domain kinases: emerging clues to their function.Eukaryot Cell. 1153162
  40. 40. WintzerithM.AckerJ.VicaireS.VigneronM.KedingerC.1992Complete sequence of the human RNA polymerase II largest subunit.Nucleic Acids Res. 20: 910.
  41. 41. AllisonL. A.WongJ. K.FitzpatrickV. D.MoyleM.InglesC. J.1988The C-terminal domain of the largest subunit of RNA polymerase II of Saccharomyces cerevisiae, Drosophila melanogaster, and mammals: a conserved structure with an essential function.Mol Cell Biol. 8321329
  42. 42. Mc CrackenS.FongN.YankulovK.BallantyneS.PanG.GreenblattJ.PattersonS. D.WickensM.BentleyD. L.1997The C-terminal domain of RNA polymerase II couples mRNA processing to transcription. Nature. 385357361
  43. 43. Schwartz LB, Roeder RG1975Purification and subunit structure of deoxyribonucleic acid-dependent ribonucleic acid polymerase II from the mouse plasmacytoma, MOPC 315.J Biol Chem. 25032213228
  44. 44. Cadena DL, Dahmus ME1987Messenger RNA synthesis in mammalian cells is catalyzed by the phosphorylated form of RNA polymerase II.J Biol Chem. 2621246812474
  45. 45. ZhangJ.CordenJ. L.1991Phosphorylation causes a conformational change in the carboxyl-terminal domain of the mouse RNA polymerase II largest subunit.J Biol Chem. 26622972302
  46. 46. LuH.FloresO.WeinmannR.ReinbergD.1991The nonphosphorylated form of RNA polymerase II preferentially associates with the preinitiation complex.Proc. Natl. Acad. Sci. U S A. 881000410008
  47. 47. ChoH.KimT. K.ManceboH.LaneW. S.FloresO.ReinbergD.1999A protein phosphatase functions to recycle RNA polymerase IIGenes Dev. 1315401552
  48. 48. KomarnitskyP.ChoE. J.BuratowskiS.2000Different phosphorylated forms of RNA polymerase II and associated mRNA processing factors during transcriptionGenes Dev. 1424522460
  49. 49. KimM.AhnS. H.KroganN. J.GreenblattJ. F.BuratowskiS.2004Transitions in RNA polymerase II elongation complexes at the 3’ ends of genes.EMBO J. 23354364
  50. 50. Zhang DW, Mosley AL, Ramisetty SR, Rodriguez-Molina JB, Washburn MP, Ansari AZ2012Ssu72 Phosphatase-dependent Erasure of Phospho-Ser7 Marks on the RNA Polymerase II C-terminal Domain Is Essential for Viability and Transcription TerminationJ Biol Chem. 28785418551
  51. 51. PalancadeB.BensaudeO.2003Investigating RNA polymerase II carboxyl-terminal domain (CTD) phosphorylationEur J Biochem. 27038593870
  52. 52. BaskaranR.ChiangG. G.MysliwiecT.KruhG. D.WangJ. Y.1997Tyrosine phosphorylation of RNA polymerase II carboxyl-terminal domain by the Abl-related gene product.J Biol Chem. 2721890518909
  53. 53. BaskaranR.MEDahmusWang. J. Y.1993Tyrosine phosphorylation of mammalian RNA polymerase II carboxyl-terminal domainProc Natl Acad Sci U S A. 901116711171
  54. 54. HsinJ. P.ShethA.ManleyJ. L.2011RNAPII CTD phosphorylated on threonine-4 is required for histone mRNA 3’ end processing. Science. 334683686
  55. 55. WuX.WilcoxC. B.DevasahayamG.HackettR. L.Arevalo-RodriguezM.MECardenasHeitman. J.HanesS. D.2000The Ess1 prolyl isomerase is linked to chromatin remodeling complexes and the general transcription machineryEMBO J. 1937273738
  56. 56. SimsR. J.3rd RojasL. A.BeckD.BonasioR.SchullerR.DruryW. J.3rd EickD.ReinbergD.2011The C-terminal domain of RNA polymerase II is modified by site-specific methylation. Science. 33299103
  57. 57. Kelly WG, Dahmus ME, Hart GW1993RNA polymerase II is a glycoprotein. Modification of the COOH-terminal domain by O-GlcNAc.J Biol Chem. 2681041610424
  58. 58. KimY. J.BjorklundS.LiY.SayreM. H.KornbergR. D.1994A multiprotein mediator of transcriptional activation and its interaction with the C-terminal repeat domain of RNA polymerase II.Cell77599608
  59. 59. Corden JL1993RNA polymerase II transcription cycles.Curr Opin Genet Dev. 3213218
  60. 60. CordenJ. L.PatturajanM.1997A CTD function linking transcription to splicing.Trends Biochem Sci. 22413416
  61. 61. GudipatiR. K.VillaT.BoulayJ.LibriD.2008Phosphorylation of the RNA polymerase II C-terminal domain dictates transcription termination choiceNat Struct Mol Biol. 15786794
  62. 62. VasiljevaL.KimM.MutschlerH.BuratowskiS.MeinhartA.2008The Nrd1-Nab3-Sen1 termination complex interacts with the Ser5-phosphorylated RNA polymerase II C-terminal domainNat Struct Mol Biol. 15795804
  63. 63. EgloffS.MurphyS.2008Role of the C-terminal domain of RNA polymerase II in expression of small nuclear RNA genes.Biochem Soc Trans. 36537539
  64. 64. EgloffS.O’ReillyD.ChapmanR. D.TaylorA.TanzhausK.PittsL.EickD.MurphyS.2007Serine-7 of the RNA polymerase II CTD is specifically required for snRNA gene expression.Science. 31817771779
  65. 65. JacobsE. Y.OgiwaraI.WeinerA. M.2004Role of the C-terminal domain of RNA polymerase II in U2 snRNA transcription and 3’ processing.Mol Cell Biol. 24846855
  66. 66. PatturajanM.SchulteR. J.BMSeftonBerezney. R.VincentM.BensaudeO.WarrenS. L.CordenJ. L.1998Growth-related changes in phosphorylation of yeast RNA polymerase II. J Biol Chem. 27346894694
  67. 67. SchroederS. C.SchwerB.ShumanS.BentleyD.2000Dynamic association of capping enzymes with transcribing RNA polymerase IIGenes Dev. 1424352440
  68. 68. ChapmanR. D.HeidemannM.AlbertT. K.MailhammerR.FlatleyA.MeisterernstM.KremmerE.EickD.2007Transcribing RNA polymerase II is phosphorylated at CTD residue serine-7. Science. 31817801782
  69. 69. BatailleA. R.JeronimoC.JacquesP. E.LarameeL.MEFortinForest. A.BergeronM.HanesS. D.RobertF.2012A universal RNA polymerase II CTD cycle is orchestrated by complex interplays between kinase, phosphatase, and isomerase enzymes along genesMol Cell. 45158170
  70. 70. KimH.EricksonB.LuoW.SewardD.GraberJ. H.PollockD. D.MegeeP. C.BentleyD. L.2010Gene-specific RNA polymerase II phosphorylation and the CTD code. Nat Struct Mol Biol. 1712791286
  71. 71. MayerA.LidschreiberM.SiebertM.LeikeK.SodingJ.CramerP.2010Uniform transitions of the general RNA polymerase II transcription complexNat Struct Mol Biol. 1712721278
  72. 72. RodriguezC. R.ChoE. J.KeoghM. C.MooreC. L.GreenleafA. L.BuratowskiS.2000Kin28, the TFIIH-associated carboxy-terminal domain kinase, facilitates the recruitment of mRNA processing machinery to RNA polymerase IIMol Cell Biol. 20104112
  73. 73. ChoE. J.MSKoborKim. M.GreenblattJ.BuratowskiS.2001Opposing effects of Ctk1 kinase and Fcp1 phosphatase at Ser 2 of the RNA polymerase II C-terminal domain.Genes Dev. 1533193329
  74. 74. MSAkhtarHeidemann. M.TietjenJ. R.ZhangD. W.ChapmanR. D.EickD.AnsariA. Z.2009TFIIH kinase places bivalent marks on the carboxy-terminal domain of RNA polymerase IIMol Cell. 34387393
  75. 75. Glover-CutterK.LarochelleS.EricksonB.ZhangC.ShokatK.FisherR. P.BentleyD. L.2009TFIIH-associated Cdk7 kinase functions in phosphorylation of C-terminal domain Ser7 residues, promoter-proximal pausing, and termination by RNA polymerase II. Mol Cell Biol. 2954555464
  76. 76. KimM.SuhH.ChoE. J.BuratowskiS.2009Phosphorylation of the yeast Rpb1 C-terminal domain at serines 2, 5, and 7.J Biol Chem. 2842642126426
  77. 77. TietjenJ. R.ZhangD. W.Rodriguez-MolinaJ. B.WhiteB. E.MSAkhtarHeidemann. M.LiX.ChapmanR. D.ShokatK.KelesS.EickD.AnsariA. Z.2010Chemical-genomic dissection of the CTD code. Nat Struct Mol Biol. 1711541161
  78. 78. GhoshA.ShumanS.LimaC. D.2011Structural insights to how mammalian capping enzyme reads the CTD codeMol Cell. 43299310
  79. 79. KrishnamurthyS.HeX.Reyes-ReyesM.MooreC.HampseyM.2004Ssu72 Is an RNA polymerase II CTD phosphatase.Mol Cell. 14387394
  80. 80. SvejstrupJ. Q.LiY.FellowsJ.GnattA.BjorklundS.KornbergR. D.1997Evidence for a mediator cycle at the initiation of transcriptionProc Natl Acad Sci U S A. 9460756078
  81. 81. West ML, Corden JL1995Construction and analysis of yeast RNA polymerase II CTD deletion and substitution mutationsGenetics. 14012231233
  82. 82. ZhangJ.CordenJ. L.1991Identification of phosphorylation sites in the repetitive carboxyl-terminal domain of the mouse RNA polymerase II largest subunit.J Biol Chem. 26622902296
  83. 83. ChapmanR. D.PalancadeB.LangA.BensaudeO.EickD.2004The last CTD repeat of the mammalian RNA polymerase II large subunit is important for its stabilityNucleic Acids Res. 323544
  84. 84. FongN.BirdG.VigneronM.BentleyD. L.2003A 10 residue motif at the C-terminus of the RNA pol II CTD is required for transcription, splicing and 3’ end processingEMBO J. 2242744282
  85. 85. BaskaranR.EscobarS. R.WangJ. Y.1999Nuclear c-Abl is a COOH-terminal repeated domain (CTD)-tyrosine (CTD)-tyrosine kinase-specific for the mammalian RNA polymerase II: possible role in transcription elongation. Cell Growth Differ. 10387396
  86. 86. MJMunoz laMata. M.KornblihttA. R.2010The carboxy terminal domain of RNA polymerase II and alternative splicingTrends Biochem Sci. 35497504
  87. 87. KamenskiT.HeilmeierS.MeinhartA.CramerP.2004Structure and mechanism of RNA polymerase II CTD phosphatases.Mol Cell. 15399407
  88. 88. MeinhartA.KamenskiT.HoeppnerS.BaumliS.CramerP.2005A structural perspective of CTD function.Genes Dev. 1914011415
  89. 89. BartkowiakB.LiuP.PhatnaniH. P.FudaN. J.CooperJ. J.PriceD. H.AdelmanK.LisJ. T.GreenleafA. L.2010CDK12 is a transcription elongation-associated CTD kinase, the metazoan ortholog of yeast Ctk1. Genes Dev. 2423032316
  90. 90. AkoulitchevS.ChuikovS.ReinbergD.2000TFIIH is negatively regulated by cdk8-containing mediator complexes.Nature407102106
  91. 91. HallbergM.PolozkovG. V.HuG. Z.BeveJ.GustafssonC. M.RonneH.BjorklundS.2004Site-specific Srb10-dependent phosphorylation of the yeast Mediator subunit Med2 regulates gene expression from the 2-microm plasmid.Proc Natl Acad Sci U S A. 10133703375
  92. 92. Hengartner CJ, Myer VE, Liao SM, Wilson CJ, Koh SS, Young RA1998Temporal regulation of RNA polymerase II by Srb10 and Kin28 cyclin-dependent kinases.Mol Cell. 24353
  93. 93. LarschanE.WinstonF.2005The Saccharomyces cerevisiae Srb8-Srb11 complex functions with the SAGA complex during Gal4-activated transcription.Mol Cell Biol. 25114123
  94. 94. LiuY.KungC.FishburnJ.AnsariA. Z.ShokatK. M.HahnS.2004Two cyclin-dependent kinases promote RNA polymerase II transcription and formation of the scaffold complex.Mol Cell Biol. 2417211735
  95. 95. FabregaC.ShenV.ShumanS.LimaC. D.2003Structure of an mRNA capping enzyme bound to the phosphorylated carboxy-terminal domain of RNA polymerase II.Mol Cell. 1115491561
  96. 96. GuidiB. W.BjornsdottirG.HopkinsD. C.LacomisL.Erdjument-BromageH.TempstP.MyersL. C.2004Mutual targeting of mediator and the TFIIH kinase Kin28.J Biol Chem. 2792911429120
  97. 97. GovindC. K.ZhangF.QiuH.HofmeyerK.HinnebuschA. G.2007Gcn5 promotes acetylation, eviction, and methylation of nucleosomes in transcribed coding regionsMol Cell. 253142
  98. 98. NgH. H.RobertF.YoungR. A.StruhlK.2003Targeted recruitment of Set1 histone methylase by elongating Pol II provides a localized mark and memory of recent transcriptional activity.Mol Cell. 11709719
  99. 99. QiuH.HuC.HinnebuschA. G.2009Phosphorylation of the Pol II CTD by KIN28 enhances BUR1/BUR2 recruitment and Ser2 CTD phosphorylation near promotersMol Cell. 33752762
  100. 100. WongC. M.QiuH.HuC.DongJ.HinnebuschA. G.2007Yeast cap binding complex impedes recruitment of cleavage factor IA to weak termination sites.Mol Cell Biol. 2765206531
  101. 101. RNLaribeeKrogan. N. J.XiaoT.ShibataY.HughesT. R.GreenblattJ. F.BDStrahl2005BUR kinase selectively regulates H3 K4 trimethylation and H2B ubiquitylation through recruitment of the PAF elongation complexCurr Biol. 1514871493
  102. 102. LiuY.WarfieldL.ZhangC.LuoJ.AllenJ.LangW. H.RanishJ.ShokatK. M.HahnS.2009Phosphorylation of the transcription elongation factor Spt5 by yeast Bur1 kinase stimulates recruitment of the PAF complex. Mol Cell Biol. 2948524863
  103. 103. WoodA.SchneiderJ.DoverJ.JohnstonM.ShilatifardA.2005The Bur1/Bur2 complex is required for histone H2B monoubiquitination by Rad6/Bre1 and histone methylation by COMPASS.Mol Cell. 20589599
  104. 104. ZhouZ.LinI. J.DarstR. P.BungertJ.2009Maneuver at the transcription start site: Mot1p and NC2 navigate TFIID/TBP to specific core promoter elementsEpigenetics414
  105. 105. AhnS. H.KeoghM. C.BuratowskiS.2009Ctk1 promotes dissociation of basal transcription factors from elongating RNA polymerase IIEMBO J. 28205212
  106. 106. LicatalosiD. D.GeigerG.MinetM.SchroederS.CilliK.Mc NeilJ. B.BentleyD. L.2002Functional interaction of yeast pre-mRNA 3’ end processing factors with RNA polymerase II.Mol Cell. 911011111
  107. 107. MeinhartA.CramerP.2004Recognition of RNA polymerase II carboxy-terminal domain by 3’-RNA-processing factors.Nature430223226
  108. 108. NiZ.SchwartzB. E.WernerJ.SuarezJ. R.LisJ. T.2004Coordination of transcription, RNA processing, and surveillance by P-TEFb kinase on heat shock genes. Mol Cell. 135565
  109. 109. RamanathanY.RajparaS. M.RezaS. M.LeesE.ShumanS.MathewsM. B.Pe’eryT.2001Three RNA polymerase II carboxyl-terminal domain kinases display distinct substrate preferences.J Biol Chem. 2761091310920
  110. 110. RotherS.StrasserK.2007The RNA polymerase II CTD kinase Ctk1 functions in translation elongation.Genes Dev. 2114091421
  111. 111. WoodA.ShuklaA.SchneiderJ.LeeJ. S.JDStantonDzuiba. T.SwansonS. K.FlorensL.WashburnM. P.WyrickJ.BhaumikS. R.ShilatifardA.2007Ctk complex-mediated regulation of histone methylation by COMPASS. Mol Cell Biol. 27709720
  112. 112. YohS. M.ChoH.PickleL.EvansR. M.JonesK. A.2007The Spt6 SH2 domain binds Ser2-P RNAPII to direct Iws1-dependent mRNA splicing and export.Genes Dev. 21160174
  113. 113. LiaoS. M.ZhangJ.JefferyD. A.KoleskeA. J.ThompsonC. M.ChaoD. M.ViljoenM.van VuurenH. J.YoungR. A.1995A kinase-cyclin pair in the RNA polymerase II holoenzyme. Nature. 374193196
  114. 114. Kornberg RD2005Mediator and the mechanism of transcriptional activation.Trends Biochem Sci. 30235239
  115. 115. Taatjes DJ2010The human Mediator complex: a versatile, genome-wide regulator of transcriptionTrends Biochem Sci. 35315322
  116. 116. Holstege FC, Jennings EG, Wyrick JJ, Lee TI, Hengartner CJ, Green MR, Golub TR, Lander ES, Young RA1998Dissecting the regulatory circuitry of a eukaryotic genome. Cell. 95717728
  117. 117. KnueselM. T.MeyerK. D.BerneckyC.TaatjesD. J.2009The human CDK8 subcomplex is a molecular switch that controls Mediator coactivator functionGenes Dev. 23439451
  118. 118. CarlsonM.1997Genetics of transcriptional regulation in yeast: connections to the RNA polymerase II CTD.Annu. Rev. Cell Dev. Biol. 13123
  119. 119. YudkovskyN.RanishJ. A.HahnS.2000A transcription reinitiation intermediate that is stabilized by activator.Nature408225229
  120. 120. HirstM.MSKoborKuriakose. N.GreenblattJ.SadowskiI.1999GAL4 is regulated by the RNA polymerase II holoenzyme-associated cyclin-dependent protein kinase SRB10/CDK8.Mol Cell. 3673678
  121. 121. VincentO.KuchinS.HongS. P.TownleyR.VyasV. K.CarlsonM.2001Interaction of the Srb10 kinase with Sip4, a transcriptional activator of gluconeogenic genes in Saccharomyces cerevisiaeMol Cell Biol. 2157905796
  122. 122. Galbraith MD, Donner AJ, Espinosa JM2010CDK8: a positive regulator of transcriptionTranscription1412
  123. 123. ChiY.MJHuddlestonZhang. X.YoungR. A.AnnanR. S.CarrS. A.DeshaiesR. J.2001Negative regulation of Gcn4 and Msn2 transcription factors by Srb10 cyclin-dependent kinase.Genes Dev. 1510781092
  124. 124. NelsonC.GotoS.LundK.HungW.SadowskiI.2003Srb10/Cdk8 regulates yeast filamentous growth by phosphorylating the transcription factor Ste12.Nature421187190
  125. 125. KeoghM. C.ChoE. J.PodolnyV.BuratowskiS.2002Kin28 is found within TFIIH and a Kin28-Ccl1-Tfb3 trimer complex with differential sensitivities to T-loop phosphorylation.Mol Cell Biol. 2212881297
  126. 126. RoyR.AdamczewskiJ. P.SerozT.VermeulenW.TassanJ. P.SchaefferL.NiggE. A.HoeijmakersJ. H.EglyJ. M.1994The MO15 cell cycle kinase is associated with the TFIIH transcription-DNA repair factor. Cell. 7910931101
  127. 127. SerizawaH.MakelaT. P.ConawayJ. W.ConawayR. C.WeinbergR. A.YoungR. A.1995Association of Cdk-activating kinase subunits with transcription factor TFIIH.Nature374280282
  128. 128. ShiekhattarR.MermelsteinF.FisherR. P.DrapkinR.DynlachtB.WesslingH. C.DOMorganReinberg. D.1995Cdk-activating kinase complex is a component of human transcription factor TFIIH. Nature. 374283287
  129. 129. Cismowski MJ, Laff GM, Solomon MJ, Reed SI1995KIN28 encodes a C-terminal domain kinase that controls mRNA transcription in Saccharomyces cerevisiae but lacks cyclin-dependent kinase-activating kinase (CAK) activity.Mol Cell Biol. 1529832992
  130. 130. EspinozaF. H.FarrellA.NourseJ. L.ChamberlinH. M.GileadiO.DOMorgan1998Cak1 is required for Kin28 phosphorylation and activation in vivoMol Cell Biol. 1863656373
  131. 131. KaldisP.SuttonA.MJSolomon1996The Cdk-activating kinase (CAK)from budding yeast. Cell. 86553564
  132. 132. SimonM.SeraphinB.FayeG.1986KIN28, a yeast split gene coding for a putative protein kinase homologous to CDC28.EMBO J. 526972701
  133. 133. AkoulitchevS.MakelaT. P.WeinbergR. A.ReinbergD.1995Requirement for TFIIH kinase activity in transcription by RNA polymerase II.Nature377557560
  134. 134. JiangY.YanM.JDGralla1996A three-step pathway of transcription initiation leading to promoter clearance at an activation RNA polymerase II promoter.Mol Cell Biol. 1616141621
  135. 135. ChoE. J.TakagiT.MooreC. R.BuratowskiS.1997mRNA capping enzyme is recruited to the transcription complex by phosphorylation of the RNA polymerase II carboxy-terminal domain.Genes Dev. 1133193326
  136. 136. HoC. K.ShumanS.1999Distinct roles for CTD Ser-2 and Ser-5 phosphorylation in the recruitment and allosteric activation of mammalian mRNA capping enzyme.Mol Cell. 3405411
  137. 137. Mc Cracken].FongS.RosoninaN.YankulovE.BrothersK.SiderovskiG.HesselD.FosterA.ShumanS.BentleyS.D. L.1997Capping enzymes are targeted to pre-mRNA by binding to the phosphorylated carboxy-terminal domain of RNA polymerase II. Genes Dev. 1133063318
  138. 138. QiuH.HuC.WongC. M.HinnebuschA. G.2006The Spt4p subunit of yeast DSIF stimulates association of the Paf1 complex with elongating RNA polymerase IIMol Cell Biol. 2631353148
  139. 139. RanishJ. A.YudkovskyN.HahnS.1999Intermediates in formation and activity of the RNA polymerase II preinitiation complex: holoenzyme recruitment and a postrecruitment role for the TATA box and TFIIB.Genes Dev. 134963
  140. 140. BorggrefeT.DavisR.Erdjument-BromageH.TempstP.KornbergR. D.2002A complex of the Srb8,-9,-10, and-11 transcriptional regulatory proteins from yeast. JBiol Chem. 2774420244207
  141. 141. ValayJ. G.SimonM.DuboisM. F.BensaudeO.FaccaC.FayeG.1995The KIN28 gene is required both for RNA polymerase II mediated transcription and phosphorylation of the Rpb1p CTD.J Mol Biol. 249535544
  142. 142. WadaT.TakagiT.YamaguchiY.WatanabeD.HandaH.1998Evidence that P-TEFb alleviates the negative effect of DSIF on RNA polymerase II-dependent transcription in vitro.EMBO J. 1773957403
  143. 143. WadaT.OrphanidesG.HasegawaJ.KimD. K.ShimaD.YamaguchiY.FukudaA.HisatakeK.OhS.ReinbergD.HandaH.2000FACT relieves DSIF/NELF-mediated inhibition of transcriptional elongation and reveals functional differences between P-TEFb and TFIIH. Mol Cell. 510671072
  144. 144. YamaguchiY.TakagiT.WadaT.YanoK.FuruyaA.SugimotoS.HasegawaJ.HandaH.1999NELF, a multisubunit complex containing RD, cooperates with DSIF to repress RNA polymerase II elongation. Cell. 974151
  145. 145. BartkowiakB.GreenleafA. L.2011Phosphorylation of RNAPII: To P-TEFb or not to P-TEFb? Transcription. 2115119
  146. 146. ViladevallL.StAmour. C. V.RosebrockA.SchneiderS.ZhangC.AllenJ. J.ShokatK. M.SchwerB.LeatherwoodJ. K.FisherR. P.2009TFIIH and P-TEFb coordinate transcription with capping enzyme recruitment at specific genes in fission yeast. Mol Cell. 33738751
  147. 147. KeoghM. C.PodolnyV.BuratowskiS.2003Bur1 kinase is required for efficient transcription elongation by RNA polymerase IIMol Cell Biol. 2370057018
  148. 148. YaoS.NeimanA.PrelichG.2000BUR1 and BUR2 encode a divergent cyclin-dependent kinase-cyclin complex important for transcription in vivo.Mol Cell Biol. 2070807087
  149. 149. WoodA.ShilatifardA.2006Bur1/Bur2 and the Ctk complex in yeast: the split personality of mammalian P-TEFb.Cell Cycle. 510661068
  150. 150. MurrayS.UdupaR.YaoS.HartzogG.PrelichG.2001Phosphorylation of the RNA polymerase II carboxy-terminal domain by the Bur1 cyclin-dependent kinase.Mol Cell Biol. 2140894096
  151. 151. Lindstrom DL, Hartzog GA2001Genetic interactions of Spt4-Spt5 and TFIIS with the RNA polymerase II CTD and CTD modifying enzymes in Saccharomyces cerevisiae.Genetics159487497
  152. 152. ChuY.SimicR.WarnerM. H.ArndtK. M.PrelichG.2007Regulation of histone modification and cryptic transcription by the Bur1 and Paf1 complexesEMBO J. 2646464656
  153. 153. PeiY.ShumanS.2003Characterization of the Schizosaccharomyces pombe Cdk9/Pch1 protein kinase: Spt5 phosphorylation, autophosphorylation, and mutational analysis.J Biol Chem. 2784334643356
  154. 154. ZhouK.KuoW. H.FillinghamJ.GreenblattJ. F.2009Control of transcriptional elongation and cotranscriptional histone modification by the yeast BUR kinase substrate Spt5Proc. Natl. Acad. Sci. U S A. 10669566961
  155. 155. Sterner DE, Lee JM, Hardin SE, Greenleaf AL1995The yeast carboxyl-terminal repeat domain kinase CTDK-I is a divergent cyclin-cyclin-dependent kinase complex.Mol Cell Biol. 1557165724
  156. 156. Jones JC, Phatnani HP, Haystead TA, MacDonald JA, Alam SM, Greenleaf AL2004C-terminal repeat domain kinase I phosphorylates Ser2 and Ser5 of RNA polymerase II C-terminal domain repeats.J Biol Chem. 2792495724964
  157. 157. Skaar DA, Greenleaf AL2002The RNA polymerase II CTD kinase CTDK-I affects pre-mRNA 3’ cleavage/polyadenylation through the processing component Pti1p.Mol Cell. 1014291439
  158. 158. XiaoT.ShibataY.RaoB.RNLaribeeO’Rourke. R.MJBuckGreenblatt. J. F.KroganN. J.JDLiebStrahl.BD2007The RNA polymerase II kinase Ctk1 regulates positioning of a 5’ histone methylation boundary along genes.Mol Cell Biol. 27721731
  159. 159. HurtE.MJLuoRother. S.ReedR.StrasserK.2004Cotranscriptional recruitment of the serine-arginine-rich (SR)-like proteins Gbp2 and Hrb1 to nascent mRNA via the TREX complex. Proc Natl Acad Sci U S A. 10118581862
  160. 160. JimenoS.RondonA. G.LunaR.AguileraA.2002The yeast THO complex and mRNA export factors link RNA metabolism with transcription and genome instabilityEMBO J. 2135263535
  161. 161. BouchouxC.HautbergueG.GrenetierS.CarlesC.RivaM.GoguelV.2004CTD kinase I is involved in RNA polymerase I transcriptionNucleic Acids Res. 3258515860
  162. 162. GrenetierS.BouchouxC.GoguelV.2006CTD kinase I is required for the integrity of the rDNA tandem arrayNucleic Acids Res. 3449965006
  163. 163. OstapenkoD.MJSolomon2003Budding yeast CTDK-I is required for DNA damage-induced transcription.Eukaryot Cell. 2274283
  164. 164. HampseyM.KinzyT. G.2007Synchronicity: policing multiple aspects of gene expression by Ctk1.Genes Dev. 2112881291
  165. 165. Kong SE, Kobor MS, Krogan NJ, Somesh BP, Sogaard TM, Greenblatt JF, Svejstrup JQ2005Interaction of Fcp1 phosphatase with elongating RNA polymerase II holoenzyme, enzymatic mechanism of action, and genetic interaction with elongator.J Biol Chem. 28042994306
  166. 166. DichtlB.BlankD.OhnackerM.FriedleinA.RoederD.LangenH.KellerW.2002A role for SSU72 in balancing RNA polymerase II transcription elongation and termination.Mol Cell. 1011391150
  167. 167. MosleyA. L.PattendenS. G.CareyM.VenkateshS.GilmoreJ. M.FlorensL.WorkmanJ. L.WashburnM. P.2009Rtr1 is a CTD phosphatase that regulates RNA polymerase II during the transition from serine 5 to serine 2 phosphorylationMol Cell. 34168178
  168. 168. YeoM.LinP. S.MEDahmusGill. G. N.2003A novel RNA polymerase II C-terminal domain phosphatase that preferentially dephosphorylates serine 5.J Biol Chem. 2782607826085
  169. 169. JeronimoC.ForgetD.BouchardA.LiQ.ChuaG.PoitrasC.TherienC.BergeronD.BourassaS.GreenblattJ.ChabotB.PoirierG. G.HughesT. R.BlanchetteM.PriceD. H.CoulombeB.2007Systematic analysis of the protein interaction network for the human transcription machinery reveals the identity of the 7SK capping enzyme. Mol Cell. 27262274
  170. 170. EgloffS.ZaborowskaJ.LaitemC.KissT.MurphyS.2012Ser7 phosphorylation of the CTD recruits the RPAP2 Ser5 phosphatase to snRNA genesMol Cell. 45111122
  171. 171. GibneyP. A.FriesT.BailerS. M.MoranoK. A.2008Rtr1 is the Saccharomyces cerevisiae homolog of a novel family of RNA polymerase II-binding proteinsEukaryot Cell. 7938948
  172. 172. AnsariA.HampseyM.2005A role for the CPF 3’-end processing machinery in RNAPII-dependent gene looping. Genes Dev. 1929692978
  173. 173. GanemC.DevauxF.TorchetC.JacqC.Quevillon-CheruelS.LabesseG.FaccaC.FayeG.2003Ssu72 is a phosphatase essential for transcription termination of snoRNAs and specific mRNAs in yeastEMBO J. 2215881598
  174. 174. PappasD. L.Jr HampseyM.2000Functional interaction between Ssu72 and the Rpb2 subunit of RNA polymerase II in Saccharomyces cerevisiae.Mol Cell Biol. 2083438351
  175. 175. Steinmetz EJ, Brow DA2003Ssu72 protein mediates both poly(A)-coupled and poly(A)-independent termination of RNA polymerase II transcription. Mol Cell Biol. 2363396349
  176. 176. St-PierreB.LiuX.KhaL. C.ZhuX.RyanO.JiangZ.ZacksenhausE.2005Conserved and specific functions of mammalian ssu72. Nucleic Acids Res. 33464477
  177. 177. ArchambaultJ.ChambersR. S.MSKoborHo. Y.CartierM.BolotinD.AndrewsB.KaneC. M.GreenblattJ.1997An essential component of a C-terminal domain phosphatase that interacts with transcription factor IIF in Saccharomyces cerevisiaeProc Natl Acad Sci U S A. 941430014305
  178. 178. MSKoborArchambault. J.LesterW.HolstegeF. C.GileadiO.JansmaD. B.JenningsE. G.KouyoumdjianF.DavidsonA. R.YoungR. A.GreenblattJ.1999An unusual eukaryotic protein phosphatase required for transcription by RNA polymerase II and CTD dephosphorylation in S. cerevisiae.Mol Cell. 45562
  179. 179. LicciardoP.RuggieroL.LaniaL.MajelloB.2001Transcription activation by targeted recruitment of the RNA polymerase II CTD phosphatase FCP1.Nucleic Acids Res. 2935393545
  180. 180. Lin PS, Dubois MF, Dahmus ME2002TFIIF-associating carboxyl-terminal domain phosphatase dephosphorylates phosphoserines 2 and 5 of RNA polymerase II.J Biol Chem. 2774594945956
  181. 181. Lin PS, Marshall NF, Dahmus ME2002CTD phosphatase: role in RNA polymerase II cycling and the regulation of transcript elongation.Prog Nucleic Acid Res Mol Biol. 72333365
  182. 182. MandalS. S.ChoH.KimS.CabaneK.ReinbergD.2002FCP1, a phosphatase specific for the heptapeptide repeat of the largest subunit of RNA polymerase II, stimulates transcription elongationMol Cell Biol. 2275437552
  183. 183. NiZ.OlsenJ. B.GuoX.ZhongG.RuanE. D.MarconE.YoungP.GuoH.LiJ.MoffatJ.EmiliA.GreenblattJ. F.2011Control of the RNA polymerase II phosphorylation state in promoter regions by CTD interaction domain-containing proteins RPRD1A and RPRD1B. Transcription. 2237242
  184. 184. SunZ. W.HampseyM.1996Synthetic enhancement of a TFIIB defect by a mutation in SSU72, an essential yeast gene encoding a novel protein that affects transcription start site selection in vivo.Mol Cell Biol. 1615571566
  185. 185. WuW. H.PintoI.BSChenHampsey. M.1999Mutational analysis of yeast TFIIB. A functional relationship between Ssu72 and Sub1/Tsp1 defined by allele-specific interactions with TFIIB.Genetics. 153643652
  186. 186. HeX.KhanA. U.ChengH.PappasD. L.Jr HampseyM.MooreC. L.2003Functional interactions between the transcription and mRNA 3’ end processing machineries mediated by Ssu72 and Sub1.Genes Dev. 1710301042
  187. 187. XiangK.NagaikeT.XiangS.KilicT.MMBehManley. J. L.TongL.2010Crystal structure of the human symplekin-Ssu72-CTD phosphopeptide complex. Nature. 467729733
  188. 188. MeinhartA.SilberzahnT.CramerP.2003The mRNA transcription/processing factor Ssu72 is a potential tyrosine phosphatase.J Biol Chem. 2781591715921
  189. 189. Chambers RS, Dahmus ME1994Purification and characterization of a phosphatase from HeLa cells which dephosphorylates the C-terminal domain of RNA polymerase II.J Biol Chem. 2692624326248
  190. 190. Chambers RS, Kane CM1996Purification and characterization of an RNA polymerase II phosphatase from yeast.J Biol Chem. 2712449824504
  191. 191. KimuraM.IshihamaA.2004Tfg3, a subunit of the general transcription factor TFIIF in Schizosaccharomyces pombe, functions under stress conditionsNucleic Acids Res. 3267066715
  192. 192. HausmannS.ShumanS.2002Characterization of the CTD phosphatase Fcp1 from fission yeast. Preferential dephosphorylation of serine 2 versus serine 5.J Biol Chem. 2772121321220
  193. 193. LuK. P.FinnG.LeeT. H.NicholsonL. K.2007Prolyl cis-trans isomerization as a molecular timer.Nat Chem Biol. 3619629
  194. 194. Lu KP, Zhou XZ2007The prolyl isomerase PIN1: a pivotal new twist in phosphorylation signalling and disease.Nat Rev Mol Cell Biol. 8904916
  195. 195. XuY. X.HiroseY.ZhouX. Z.LuK. P.ManleyJ. L.2003Pin1 modulates the structure and function of human RNA polymerase II.Genes Dev. 1727652776
  196. 196. Xu YX, Manley JL2007Pin1 modulates RNA polymerase II activity during the transcription cycleGenes Dev. 2129502962
  197. 197. Morris DP, Phatnani HP, Greenleaf AL1999Phospho-carboxyl-terminal domain binding and the role of a prolyl isomerase in pre-mRNA 3’-End formation.J Biol Chem. 2743158331587
  198. 198. GemmillT. R.WuX.HanesS. D.2005Vanishingly low levels of Ess1 prolyl-isomerase activity are sufficient for growth in Saccharomyces cerevisiae.J Biol Chem. 2801551015517
  199. 199. HaniJ.SchelbertB.BernhardtA.DomdeyH.FischerG.WiebauerK.RahfeldJ. U.1999Mutations in a peptidylprolyl-cis/trans-isomerase gene lead to a defect in 3’-end formation of a pre-mRNA in Saccharomyces cerevisiae.J Biol Chem. 274108116
  200. 200. WilcoxC. B.RossettiniA.HanesS. D.2004Genetic interactions with C-terminal domain (CTD) kinases and the CTD of RNA Pol II suggest a role for ESS1 in transcription initiation and elongation in Saccharomyces cerevisiae.Genetics16793105
  201. 201. WuX.RossettiniA.HanesS. D.2003The ESS1 prolyl isomerase and its suppressor BYE1 interact with RNA pol II to inhibit transcription elongation in Saccharomyces cerevisiae.Genetics16516871702
  202. 202. KrishnamurthyS.MAGhazyMoore. C.HampseyM.2009Functional interaction of the Ess1 prolyl isomerase with components of the RNA polymerase II initiation and termination machineries.Mol Cell Biol. 2929252934
  203. 203. ArmacheK. J.KettenbergerH.CramerP.2003Architecture of initiation-competent 12-subunit RNA polymerase IIProc Natl Acad Sci U S A. 10069646968
  204. 204. CramerP.BushnellD. A.KornbergR. D.2001Structural basis of transcription: RNA polymerase II at 2.8 angstrom resolution.Science. 29218631876
  205. 205. GrohmannD.KloseD.KlareJ. P.KayC. W.SteinhoffH. J.WernerF.2010RNA-binding to archaeal RNA polymerase subunits F/E: a DEER and FRET studyJ Am Chem Soc. 13259545955
  206. 206. Young RA1991RNA polymerase II.Annual Review of Biochemistry60689715
  207. 207. Bushnell DA, Kornberg RD2003Complete, 12-subunit RNA polymerase II at 4.1-A resolution: implications for the initiation of transcription. Proc Natl Acad Sci U S A. 10069696973
  208. 208. KimuraM.SuzukiH.IshihamaA.2002Formation of a carboxy-terminal domain phosphatase (Fcp1)/TFIIF/RNA polymerase II (pol II) complex in Schizosaccharomyces pombe involves direct interaction between Fcp1 and the Rpb4 subunit of pol II.Mol Cell Biol. 2215771588
  209. 209. ArmacheK. J.MitterwegerS.MeinhartA.CramerP.2005Structures of complete RNA polymerase II and its subcomplex, Rpb4/7. J Biol Chem. 28071317134
  210. 210. CaiG.ImasakiT.TakagiY.AsturiasF. J.2009Mediator structural conservation and implications for the regulation mechanismStructure17559567
  211. 211. CaiG.ImasakiT.YamadaK.CardelliF.TakagiY.AsturiasF. J.2010Mediator head module structure and functional interactionsNat Struct Mol Biol. 17273279
  212. 212. SampathV.BalakrishnanB.Verma-GaurJ.OnestiS.SadhaleP. P.2008Unstructured N terminus of the RNA polymerase II subunit Rpb4 contributes to the interaction of Rpb4.Rpb7 subcomplex with the core RNA polymerase II of Saccharomyces cerevisiae.J Biol Chem. 28339233931
  213. 213. CalvoO.ManleyJ. L.2001Evolutionarily conserved interaction between CstF-64 and PC4 links transcription, polyadenylation, and termination.Mol Cell. 710131023
  214. 214. Henry NL, Bushnell DA, Kornberg RD1996A yeast transcriptional stimulatory protein similar to human PC4.J Biol Chem. 2712184221847
  215. 215. 1519331940Knaus R, Pollock R, Guarente L (1996) Yeast SUB1 is a suppressor of TFIIB mutations and has homology to the human co-activator PC4. EMBO J. 15: 1933-1940
  216. 216. GeH.RoederR. G.1994Purification, cloning, and characterization of a human coactivator, PC4, that mediates transcriptional activation of class II genes. Cell. 78513523
  217. 217. KaiserK.StelzerG.MeisterernstM.1995The coactivator 15 PC4) initiates transcriptional activation during TFIIA-TFIID-promoter complex formation.EMBO J. 14: 3520-3527.
  218. 218. KretzschmarM.KaiserK.LottspeichF.MeisterernstM.1994A novel mediator of class II gene transcription with homology to viral immediate-early transcriptional regulators.Cell78525534
  219. 219. 95 21922197 Malik S, Guermah M, Roeder RG (1998) A dynamic model for PC4 coactivator function in RNA polymerase II transcription. Proc. Natl. Acad. Sci. U S A. 95: 2192-2197
  220. 220. WertenS.StelzerG.GoppeltA.LangenF. M.GrosP.TimmersH. T.Van der VlietP. C.MeisterernstM.1998Interaction of PC4 with melted DNA inhibits transcription. EMBO J. 1751035111
  221. 221. 2923082321Rosonina E, Willis IM, Manley JL (2009) Sub1 functions in osmoregulation and in transcription by both RNA polymerases II and III. Mol Cell Biol. 29: 2308-2321
  222. 222. GarciaA.RosoninaE.ManleyJ. L.CalvoO.2010Sub1 globally regulates RNA polymerase II C-terminal domain phosphorylationMol Cell Biol. 3051805193
  223. 223. CalvoO.ManleyJ. L.2003Strange bedfellows: polyadenylation factors at the promoter.Genes Dev. 1713211327
  224. 224. CalvoO.ManleyJ. L.2005The transcriptional coactivator PC4/Sub1 has multiple functions in RNA polymerase II transcription.EMBO J. 2410091020
  225. 225. SikorskiT. W.FicarroS. B.HolikJ.KimT.RandoO. J.MartoJ. A.BuratowskiS.2011Sub1 and RPA Associate with RNA Polymerase II at Different Stages of TranscriptionMol Cell. 44397409
  226. 226. GeH.ZhaoY.ChaitB. T.RoederR. G.1994Phosphorylation negatively regulates the function of coactivator PC4.Proc Natl Acad Sci U S A. 911269112695
  227. 227. OhkuniK.YamashitaI.2000A transcriptional autoregulatory loop for KIN28-CCL1 and SRB10-SRB11, each encoding RNA polymerase II CTD kinase-cyclin pair, stimulates the meiotic development of S. cerevisiae.Yeast. 16829846
  228. 228. Donner AJ, Ebmeier CC, Taatjes DJ, Espinosa JM2010CDK8 is a positive regulator of transcriptional elongation within the serum response networkNat. Struct. Mol. Biol. 17194201
  229. 229. de la MataM.KornblihttA. R.2006RNA polymerase II C-terminal domain mediates regulation of alternative splicing by SRp20.Nat Struct Mol Biol. 13973980
  230. 230. HiroseY.ManleyJ. L.1998RNA polymerase II is an essential mRNA polyadenylation factor.Nature3959396
  231. 231. HiroseY.TackeR.ManleyJ. L.1999Phosphorylated RNA polymerase II stimulates pre-mRNA splicing.Genes Dev. 1312341239
  232. 232. ChoE. J.RodriguezC. R.TakagiT.BuratowskiS.1998Allosteric interactions between capping enzyme subunits and the RNA polymerase II carboxy-terminal domain.Genes Dev. 1234823487
  233. 233. Kim HJ, Jeong SH, Heo JH, Jeong SJ, Kim ST, Youn HD, Han JW, Lee HW, Cho EJ2004mRNA capping enzyme activity is coupled to an early transcription elongation. Mol Cell Biol. 2461846193
  234. 234. FongN.BentleyD. L.2001Capping, splicing, and 3’ processing are independently stimulated by RNA polymerase II: different functions for different segments of the CTD. Genes Dev. 1517831795
  235. 235. BarillaD.BALeeProudfoot. N. J.2001Cleavage/polyadenylation factor IA associates with the carboxyl-terminal domain of RNA polymerase II in Saccharomyces cerevisiaeProc Natl Acad Sci U S A. 98445450
  236. 236. BaurenG.BelikovS.WieslanderL.1998Transcriptional termination in the Balbiani ring 1 gene is closely coupled to 3’-end formation and excision of the 3’-terminal intron.Genes Dev. 1227592769
  237. 237. CEBirse-SebastiaMinvielle.LeeL.BAKellerW.ProudfootN. J.1998Coupling termination of transcription to messenger RNA maturation in yeast.Science. 280298301
  238. 238. KimM.KroganN. J.VasiljevaL.RandoO. J.NedeaE.GreenblattJ. F.BuratowskiS.2004The yeast Rat1 exonuclease promotes transcription termination by RNA polymerase II.Nature432517522
  239. 239. WestS.GromakN.ProudfootN. J.2004Human 5’--> 3’ exonuclease Xrn2 promotes transcription termination at co-transcriptional cleavage sites. Nature. 432522525
  240. 240. BaillatD.MAHakimiNaar. A. M.ShilatifardA.CoochN.ShiekhattarR.2005Integrator, a multiprotein mediator of small nuclear RNA processing, associates with the C-terminal repeat of RNA polymerase II.Cell123265276
  241. 241. EgloffS.SzczepaniakS. A.DienstbierM.TaylorA.KnightS.MurphyS.2010The integrator complex recognizes a new double mark on the RNA polymerase II carboxyl-terminal domain.J Biol Chem. 2852056420569
  242. 242. David CJ, Boyne AR, Millhouse SR, Manley JL2011The RNA polymerase II C-terminal domain promotes splicing activation through recruitment of a U2AF65-Prp19 complexGenes Dev. 25972983
  243. 243. MillhouseS.ManleyJ. L.2005The C-terminal domain of RNA polymerase II functions as a phosphorylation-dependent splicing activator in a heterologous protein.Mol Cell Biol. 25533544
  244. 244. ListermanI.SapraA. K.NeugebauerK. M.2006Cotranscriptional coupling of splicing factor recruitment and precursor messenger RNA splicing in mammalian cells.Nat Struct Mol Biol. 13815822
  245. 245. Moore MJ, Schwartzfarb EM, Silver PA, Yu MC2006Differential recruitment of the splicing machinery during transcription predicts genome-wide patterns of mRNA splicingMol Cell. 24903915
  246. 246. KimE.DuL.BregmanD. B.WarrenS. L.1997Splicing factors associate with hyperphosphorylated RNA polymerase II in the absence of pre-mRNAJ Cell Biol. 1361928
  247. 247. MJMortillaroBlencowe. B. J.WeiX.NakayasuH.DuL.WarrenS. L.SharpP. A.BerezneyR.1996A hyperphosphorylated form of the large subunit of RNA polymerase II is associated with splicing complexes and the nuclear matrix.Proc Natl Acad Sci U S A. 9382538257
  248. 248. YuryevA.PatturajanM.LitingtungY.JoshiR. V.GentileC.GebaraM.CordenJ. L.1996The C-terminal domain of the largest subunit of RNA polymerase II interacts with a novel set of serine/arginine-rich proteinsProc Natl Acad Sci U S A. 9369756980
  249. 249. Morris DP, Greenleaf AL2000The splicing factor, Prp40, binds the phosphorylated carboxyl-terminal domain of RNA polymerase II. J Biol Chem. 2753993539943
  250. 250. CartyS. M.GoldstrohmA. C.SuneC.MAGarcia-BlancoGreenleaf. A. L.2000Protein-interaction modules that organize nuclear function: FF domains of CA150 bind the phosphoCTD of RNA polymerase II.Proc Natl Acad Sci U S A. 9790159020
  251. 251. GoldstrohmA. C.AlbrechtT. R.SuneC.BedfordM. T.MAGarcia-Blanco2001The transcription elongation factor CA150 interacts with RNA polymerase II and the pre-mRNA splicing factor SF1.Mol Cell Biol. 2176177628
  252. 252. David CJ, Manley JL2011The RNA polymerase C-terminal domain: a new role in spliceosome assembly.Transcription2221225
  253. 253. HargreavesD. C.HorngT.MedzhitovR.2009Control of inducible gene expression by signal-dependent transcriptional elongationCell138129145
  254. 254. LugerK.2003Structure and dynamic behavior of nucleosomes.Curr Opin Genet Dev. 13127135
  255. 255. Berger SL2007The complex language of chromatin regulation during transcription.Nature447407412
  256. 256. Cho EJ2007RNA polymerase II carboxy-terminal domain with multiple connections.Exp. Mol. Med. 39247254
  257. 257. HampseyM.ReinbergD.2003Tails of intrigue: phosphorylation of RNA polymerase II mediates histone methylation.Cell113429432
  258. 258. JenuweinT.AllisC. D.2001Translating the histone code.Science. 29310741080
  259. 259. Strahl BD, Allis CD2000The language of covalent histone modifications.Nature4034145
  260. 260. KouzaridesT.2007SnapShot: Histone-modifying enzymesCell
  261. 261. KouzaridesT.2007Chromatin modifications and their functionCell. 128693705
  262. 262. Spain MM, Govind CK2011A role for phosphorylated Pol II CTD in modulating transcription coupled histone dynamicsTranscription27881
  263. 263. KouzaridesT.2002Histone methylation in transcriptional control.Curr Opin Genet Dev. 12198209
  264. 264. PinskayaM.MorillonA.2009Histone H3 lysine 4 di-methylation: a novel mark for transcriptional fidelity? Epigenetics. 4302306
  265. 265. KroganN. J.DoverJ.WoodA.SchneiderJ.HeidtJ.MABoatengDean. K.RyanO. W.GolshaniA.JohnstonM.GreenblattJ. F.ShilatifardA.2003The Paf1 complex is required for histone H3 methylation by COMPASS and Dot1p: linking transcriptional elongation to histone methylation. Mol Cell. 11721729
  266. 266. KizerK. O.PhatnaniH. P.ShibataY.HallH.GreenleafA. L.BDStrahl2005A novel domain in Set2 mediates RNA polymerase II interaction and couples histone H3 K36 methylation with transcript elongationMol Cell Biol. 2533053316
  267. 267. DrouinS.LarameeL.JacquesP. E.ForestA.BergeronM.RobertF.2010DSIF and RNA polymerase II CTD phosphorylation coordinate the recruitment of Rpd3S to actively transcribed genesPLoS Genet. 6: e1001173.
  268. 268. GovindC. K.QiuH.DSGinsburgRuan. C.HofmeyerK.HuC.SwaminathanV.WorkmanJ. L.LiB.HinnebuschA. G.2010Phosphorylated Pol II CTD recruits multiple HDACs, including Rpd3C(S), for methylation-dependent deacetylation of ORF nucleosomes. Mol Cell. 39234246
  269. 269. KimT.BuratowskiS.2009Dimethylation of H3K4 by Set1 recruits the Set3 histone deacetylase complex to 5’ transcribed regionsCell137259272
  270. 270. Brodsky AS, Silver PA2000Pre-mRNA processing factors are required for nuclear export.RNA. 617371749
  271. 271. RondonA. G.JimenoS.AguileraA.2010The interface between transcription and mRNP export: from THO to THSC/TREX-2Biochim Biophys Acta. 1799533538
  272. 272. StrasserK.MasudaS.MasonP.PfannstielJ.OppizziM.Rodriguez-NavarroS.RondonA. G.AguileraA.StruhlK.ReedR.HurtE.2002TREX is a conserved complex coupling transcription with messenger RNA export. Nature. 417304308
  273. 273. RondonA. G.JimenoS.Garcia-RubioM.AguileraA.2003Molecular evidence that the eukaryotic THO/TREX complex is required for efficient transcription elongation.J Biol Chem. 2783903739043
  274. 274. ZenklusenD.VinciguerraP.WyssJ. C.StutzF.2002Stable mRNP formation and export require cotranscriptional recruitment of the mRNA export factors Yra1p and Sub2p by Hpr1pMol Cell Biol. 2282418253
  275. 275. MasudaS.DasR.ChengH.HurtE.DormanN.ReedR.2005Recruitment of the human TREX complex to mRNA during splicingGenes Dev. 1915121517
  276. 276. MacKellar AL, Greenleaf AL2011Cotranscriptional association of mRNA export factor Yra1 with C-terminal domain of RNA polymerase IIJ Biol Chem. 2863638536395
  277. 277. KroganN. J.KimM.TongA.GolshaniA.CagneyG.CanadienV.RichardsD. P.BeattieB. K.EmiliA.BooneC.ShilatifardA.BuratowskiS.GreenblattJ.2003Methylation of histone H3 by Set2 in Saccharomyces cerevisiae is linked to transcriptional elongation by RNA polymerase II. Mol Cell Biol. 2342074218
  278. 278. BMLundeReichow. S. L.KimM.SuhH.LeeperT. C.YangF.MutschlerH.BuratowskiS.MeinhartA.VaraniG.2010Cooperative interaction of transcription termination factors with the RNA polymerase II C-terminal domain. Nat Struct Mol Biol. 1711951201
  279. 279. StewartM.2010Nuclear export of mRNATrends Biochem Sci. 35609617
  280. 280. AmmosovaT.BerroR.JerebtsovaM.JacksonA.CharlesS.KlaseZ.SoutherlandW.GordeukV. R.KashanchiF.NekhaiS.2006Phosphorylation of HIV-1 Tat by CDK2 in HIV-1 transcription. Retrovirology. 3: 78.
  281. 281. ColeyW.Kehn-HallK.Van DuyneR.KashanchiF.2009Novel HIV-1 therapeutics through targeting altered host cell pathwaysExpert Opin Biol Ther. 913691382
  282. 282. BellanC.De FalcoG.LazziS.MicheliP.VicidominiS.SchurfeldK.AmatoT.PalumboA.BagellaL.SabattiniE.BartolommeiS.HummelM.PileriS.TosiP.LeonciniL.GiordanoA.2004CDK9/CYCLIN T1 expression during normal lymphoid differentiation and malignant transformation. J Pathol. 203946952
  283. 283. LeeD. K.DuanH. O.ChangC.2001Androgen receptor interacts with the positive elongation factor P-TEFb and enhances the efficiency of transcriptional elongation.J Biol Chem. 27699789984
  284. 284. SimoneC.GiordanoA.2007Abrogation of signal-dependent activation of the cdk9/cyclin T2a complex in human RD rhabdomyosarcoma cells.Cell Death Differ. 14192195
  285. 285. Shapiro GI2006Cyclin-dependent kinase pathways as targets for cancer treatment.J Clin Oncol. 2417701783
  286. 286. KrystofV.ChamradI.JordaR.KohoutekJ.2010Pharmacological targeting of CDK9 in cardiac hypertrophyMed Res Rev. 30646666

Written By

Olga Calvo and Alicia García

Submitted: December 1st, 2011 Published: September 6th, 2012