This chapter will be focused on epigenetic mechanisms known to affect self-renewal and developmental potency of embryonic-like stem cells, and germ cells which mimic similar epigenetic signatures as pluripotent stem cells. Examples of epigenetic regulation have proven crucial for defining the stem cell state. In particular, a wealth of knowledge regarding stem cell-specific epigenetic modifications has occurred over the past decade with discoveries that include describing unique stem cell-specific chromosome structure, DNA and histone modifications and noncoding RNAs. The impact of these findings and the better understanding of epigenetic regulation in pluripotent stem cells provides a foundation for discovering mechanisms which regulate human development and differentiation in addition to those that can facilitate cellular reprogramming.
In eukaryotes, chromosomes consist of repeating chromatin units called nucleosomes, which encompass segments of DNA (~147 bp) wound around a central core of eight histone (
In mammals, heterochromatin is associated with high levels of some methylation marks, including lysine (
2. Epigenetic control in pluripotent stem cells
2.1. Changes in chromatin ultrastructure in pluripotent stem cells
With the discovery of culturing embryonic stem cells (ESCs), several groups have been able to show the progression of global changes in the chromatin architecture of these cells. Through these studies, it has been shown that undifferentiated pluripotent stem cells contain less heterochromatic regions and express less chromatin structural proteins. Moreover, binding of these proteins (i.e. HP1α, lamin B) to heterochromatic regions is weaker compared to lineage-committed cells . Additionally, pluripotent transcription factors and chromatin remodeling proteins are overexpressed in ESCs compared to more differentiated progenitor cells . One study further showed that chromatin remodeler Chd1 knockdown results with heterochromatin accumulation and skewed differentiation in mouse ESCs, which suggests functional relevancy to the ‘open’ chromatin structure . Together, these studies show that pluripotent ESCs has an open and hyperdynamic chromatin structure which transforms into a more compact, repressive-like, chromatin state during differentiation.
As ESC chromatin is more transcriptionally permissive, it is also more sensitive to nuclease activity. This may also be in part due to differences that are seen in the chromatin localization in the nucleus. For instance, one study using the DamID (DNA adenine methyltransferase identification) technique showed that pluripotency genes, including Oct4 and Nanog, move to the nuclear lamina and are silenced while lineage-specific genes disassociate from the lamina and are expressed. This was specifically shown during the differentiation of mouse ESCs into terminal astrocytes which demonstrated cell type-specific relocations of these areas during differentiation . These areas near the nuclear periphery were called Lamina Associated Domains (
Genome-wide ChIP analyses have also described other lamina associated domains with significant overlap with the LADS domains. These regions referred as
Since the discovery of generating induced pluripotent stem (
In embryonic stem cells, lineage-specific gene expression program regulators are repressed, but poised for a rapid response to differentiate . These areas of chromatin, have so called bivalent domains, consist of opposing chromatin marks; i.e. H3K4me for activation and H3K27me for silencing. In ESCs, these domains are believed to be responsible for preventing the transcription responsible for their early differentiation to a specific lineage while priming the area for activation when the appropriate cues are expressed. Consistent with this belief is the findings that the bulk of the protein-encoding genes of human ESCs, including transcriptionally inactive genes have H3K4me, H3K9ac and H3K14ac rich promoter regions in areas of the nucleosome adjacent and downstream of transcription start sites [19, 20]. Moreover, in ESCs, genes with bivalent gene promoters tend to have unmethylated CpG islands . The initial step of active DNA demethylation in mammals occurs by the conversion of 5-methylcytosine of DNA (5mC) to 5-hydroxymethylcytosine (5hmC). A prime example of this in pluripotent stem cells has been shown in regulating the expression of the stem cell transcription factor, Nanog. Here, the demethylated state is critical for the upregulation of Nanog which is an essential regulator of ESC pluripotency and self-renewal, while its downregulation attributed to methylation of its promoter is required for ICM specification . Recent studies demonstrate that demethylation of Nanog is in part contributed to the expression of the Tet methylcytosine dioxygenase 1 (TET1) enzyme which is a TET family member of enzymes that catalyze the conversion of 5mC to 5hmC. This enzyme has been found to demethylate Nanog promoter sites in mouse ES cells [23, 24]. Both TET1 and TET2 expression have also been shown to be regulated by Oct4 expression in mouse ES cells, downregulated following differentiation alongside other stem cell markers, and is induced concomitantly with 5-hmC during fibroblast reprogramming into iPS cells .
In addition to promoter regulation, methylC-Seq genome-wide analysis has also discovered novel types of DNA methylation regulation at non-CG sites (CHG and CHH sites where H = A, C, or T residues). These analyses showed that non-CG methylation accounted for 25% of the total ESC methylome and that these sites were more commonly found within gene bodies than within promoter sites . Furthermore, the methylation of these sites was lost when differentiation was induced in ESCs, and restored during the generation of in induced pluripotent stem cells. This included many differentially methylated regions associated with genes involved in pluripotency and differentiation.
2.3. Polycomb and trithorax group proteins in pluripotent stem cells
Recent studies have established that developmental gene priming and bivalency are crucial for pluripotency whereby the chromatin of pluripotent stem cells are transcriptionally permissive, with normally silent DNA repeat regions, transcriptionally related histone modifications such as H3K9ac, H3K4me3, H3K36me3 and low stochastic transcription of lineage-restricted genes [8, 9]. The poised state is believed to inhibit the activity of RNA Polymerase II (
PcG, TrxG, and BAF complex associated genes are conserved from fly to man and are important in the regulation of organogenesis and development. PcG proteins were initially discovered as repressors of the Hox or homoeotic genes in
PcG proteins produce two distinct protein complexes that act sequentially to regulate gene expression – the “Bmi-1 complex” also known as Polycomb Repressive Complexes (
Polycomb repressive complexes have been shown associated with many developmental regulator regions in ESCs, and many of the PcG repressed targets of ESCs are also ‘bivalent’ [30, 39]. For instance, PRC2 target genes have been shown to be preferentially turned on during ESC differentiation and that the pluripotent stem cell regulating genes Oct4, Sox2, and Nanog co-occupy a significant subset of these genes. Therefore, it has been suggested that the PRC2 complex represses a distinct group of developmental genes that have to be repressed to maintain pluripotency. This would promote a poised or primed state which could be readily activated during early differentiation . For example, the histone methyltransferase Ezh2 is known to catalyze H3K27me3. In fact, bivalency domains at PRC2 regulated promoters are roughly five times more likely to become DNA methylated during differentiation than those with non-PRC2 regulated promoters  suggesting that the PRC2 complex plays a pivotal role in the switch for early lineage commitment . Jarid2, a member of the Jumonji family of histone demethylases, has also been shown to play an important role in properly recruiting PRC1 and PRC2 and initiating the RNA Polymerase II activating form (Ser5P-RNAPII)  to bivalent loci to promote differentiation [43-45]. While Jarid2 is enzymatically inactive in ESCs, recent evidence has shown that Jarid2 is regulated by pluripotency factors in ESCs . In null ESCs lacking Jarid2 expression were able to self-renew but unable to differentiate despite expressing appropriate PRC2 target genes demonstrating that transcriptional priming of bivalent genes in ESCs was dependent on Jarid2 expression.
In addition to the bivalent marks associated with PRC2 associated H3 modifications in pluripotent stem cells, bivalent genes in stem cells also exhibit repressive marks of H2AK119Ub1 at their promoter and throughout the coding region. For this reason, members of the PRC1 complex Ring1A and Ring1B proteins which catalyze H2AK119ub1 have also reveal a role in regulating pluripotency [30, 46]. For instance, in ESCs, double mutants of Ring1A/B demonstrate reduced levels of H2AK119Ub1, repression of known stemness genes (including Oct4 targets), increased expression of developmental regulator targets, and spontaneous differentiation. Furthermore, upon differentiation, Ring1A/B lost binding to their target loci suggesting that a Ring 1/B mediated complex functions downstream of the stem cell core transcriptional machinery to maintain the ESC state .
In addition to PcG complexes, core members of the TrxG and BAF chromatin remodeling complexes have also been shown to contribute to the bivalent mark in stem cells by acting in concert to establish and preserve H3K4me3 [48, 49]. Another core member, WD repeat domain 5 (
3. Epigenetic control in primordial germ cells and pluripotent embryonic germ cells
Primordial germ cells (
Key initiators of PGC induction in the epiblast include the Blimp1 (
In addition to pluripotent associated genes, early germ-cell development and imprinted genes also undergo demethylation during this time. These include well-established postmigratory germ cell genes Mvh (also known as Ddx4), Sycp3 (synaptonemal complex protein 3) and Dazl (deleted in azoospermia-like). These genes are demethylated in germ cells and repressed in somatic cells. This demethylation occurs during the migration of PGCs into the gonad at CpG islands of their promoters as well as at differentially methylated regions (
Another important epigenetic process required for germ cell development and cellular reprogramming to the pluripotent state involves the X chromosome. In female adult cells, one of the two X chromosomes is inactivated to compensate for the differences in gene expression between sexes. For this purpose, X chromosome inactivation is initiated in early embryos by noncoding X-inactive specific transcript (Xist) RNA followed by chromatin modifications on the inactive X chromosome which leads to stable gene repression in somatic cells. Likewise, reactivation of the X chromosome is required for the totipotency of the female blastocyst and germ cell development. Reactivation of the X chromosome also occurs to establish pluripotency in iPS cells. During development, epigenetic reprogramming or re-activation of the inactive X-chromosome commences in PGCs during their migration through the hindgut along their route to the developing gonads where imprint erasure is completed . In mouse PGCs, decreased Xist expression, and the displacement of PcG repressor proteins EED and SUZ12, results in the loss of the inactive X associated histone modification, H3K27me3 . In humans, PcG proteins YY1, EZH2, and EED have also been found in the ovarian follicles, oocytes and preimplantation embryos. YY1 and EZH2 transcripts were additionally detected in human metaphase II oocytes suggesting they may be play a similar role in human germ cell reprogramming .
4. MicroRNAs and stem cells
Studies in mice have shown that induction of neural differentiation in mouse ESCs with retinoic acid results in increased miR-134, miR-296, and miR-470 which in turn interact with the coding sequences of the pluripotency transcription factors Oct4, Sox2, and Nanog. These results suggest that through interaction of the miRNAs these pluripotent stem cells genes are downregulated thereby permitting differentiation to proceed . Additionally, the ESC-specific miR-290 cluster has also been shown to regulate Oct4 methylation in differentiating ESCs . Other studies have shown that mouse ESCs deficient in proteins of the miRNA processing apparatus such as Dicer, Drosha, DGCR8, and Ddx5 exhibit differentiation and developmental defects [95-97].
Interestingly, PcG proteins have been shown to be both regulators of miRNA expression as well as their targets. For instance, miRNA-101 has been shown to directly regulate the expression of the PRC protein EZH2 in highly aggressive cancers [98, 99].
5. Epigenetic regulation in progenitor and adult stem cells
Progenitor cells and adult stem cells are thought to be predecessors of pluripotent or multipotent stem cells that are generated during early differentiation. During their transition in development, bivalently marked stem cell genes can become either active, or inactive, or remain bivalent, dependent in part, on the activity of key enzymes which drive these chromatin modifications such as lysine demethylases (
Specific differences occur in the chromatin states between pluripotent stem cells, progenitor cells and more differentiated cell types which include active, repressed and poised states of chromatin. Several lines of evidence suggest that priming in the poised state enables genes to respond rapidly when differentiation cues are presented . For example, during neural induction, several hundred genes including those required to maintain stem cell-ness become de novo mCG and therefore transcriptionally silenced. Furthermore, the observation was made that neural precursors that are derived from ESCs acquired more mCG than terminal neurons, suggesting that the transition from pluripotent to lineage-committed cells is associated with these changes [17, 21, 101, 102].
Polycomb group proteins also appear to play a unique role in defining the progenitor or adult stem cell state. It has been shown that the PRC1 complex protein Bmi-1 activates multiple pathways that are important for regulating the stem cell-like state. For example, it has been shown that Bmi-1 is potentially upregulated via the pluripotent stem cell marker SALL4 signaling and has been shown to regulate stem cell self-renewal by repressing Hox genes, as well as INK4a locus genes, p16INK4a and p19ARF. BMI1 has also been shown to facilitate stem cell-like features in adult stem cells such as increased telomerase activity, transcriptional factor GATA3, and NF-kB pathways. These pathways are associated with the prevention of senescence, differentiation and apoptosis, while promoting immortalization and proliferation (for review see ).
6. Epigenetic dysregulation in cancer stem cells
Cancer stem/initiating cells (CSC) have been defined as a subset of cancer cells that have clonal ability or self-renewal and are resilient against cancer therapies [104, 105]. As such CSCs are implicated in cancer initiation, metastasis, and recurrence of some cancers . Although the most well established pluripotent stem cell genes OCT4, NANOG, cMYC and SOX2 are implicated in many poorly differentiated or metastatic cancers [107-109], they are not expressed in all and they are not all elevated concordantly. In addition, targets of NANOG, OCT4, SOX2, and c-MYC are often overexpressed in tumors that are poorly differentiated, more so than in those that are well differentiated . These genes also play a significant role in the induction of pluripotency into iPS cells from differentiated cell types and are thus involved in regulating epigenetic reprogramming [111-113]. More specifically, it is found that c-MYC, which is also an oncogene is sufficient for the reactivation of ESC-like transcriptional program in both, normal and cancer cells . Additionally, studies have shown that one of the inherent issues with generating iPS cells is their propensity to become cancer stem cell-like [115, 116]. Taken together, these results indicate that aberrant activation of an ESC or iPS-like transcriptional program might cause induction of pathological self-renewal in adult differentiated cells, characteristic of cancer stem cells.
Aberrant function of PcG proteins has also been established in the malignancy of various cancers . This is not surprising as it is well known that polycomb complexes contribute to the epigenetic regulation of key networks associated with self-renewal , differentiation, and proliferation [92, 119-123]. These roles for polycombs have been demonstrated in cancer cells and normal stem cells  and more recently studied for their targeted function in CSCs . For instance, there is much evidence that overexpression of the EZH2 polycomb gene occurs in multiple human malignancies (see [117, 126]). One study showed that this may in part be atributed to a genomic loss of miR-101 which has been shown to lead to increased EZH2 levels [99, 127]. Although how EZH2 contributes to carcinogenesis remains poorly defined, recent evidence suggests that overexpression of EZH2 can contribute to improper silencing of tumor suppressor genes . In this case, EZH2 was shown to target a pro-differentiation tumor suppressor gene, retinoic acid receptor β2 (
The pluripotent stem cells have a chromatin that is hyperdynamic, with a preponderance of modified histones and chromatin remodelers that ensures low-level transcription and tight regulation. Losing pluripotency is accompanied with a more compact, repressive, chromatin structure, which leads to cellular differentiation. Chromatin architecture is regulated at multiple levels in conjunction with known pluripotent genes to constitute an interwoven pluripotency network. Although there are many gaps in our knowledge of how epigenetic modifications regulate the pluripotent state, it is known that PcG repressor proteins prevent the precocious expression of lineage-restricted gene expression in pluripotent stem cells and germ cells by contributing to a unique ‘primed’ bivalent state of the chromatin. Future studies will provide mechanistic insights into the signaling cues required to maintain this state and inhibit differentiation while iPS cells and adult stem cells provide a renewed opportunity to study the role of chromatin architecture for controlling the pluripotent state. This will include understanding the mechanisms that interplay between pluripotent transcription factors, epigenetic regulators, and miRNAs to balance self-renewal and differentiation, properties which regulate reprogramming and carcinogenesis.
cdk, cyclin-dependent kinase; H2A-K119-Ub, ubiquitinylated histone H2A lysine 119; H3K27me3, tri-methylated histone H3 lysine K27; PcG, Polycomb group genes; ESC, embryonic stem cells; EGC, embryonic germ cells; PGC, primordial germ cells; iPS, induced pluripotent stem cells; CSC, cancer stem cells; RARβ2, retinoic acid receptor β2; Hh, Hedghog; KDMs, lysine demethylases; DUBs, histone deubiquitylases; DNMT, DNA methyltransferases; YY1, Ying Yang 1; EZH2 Enhancer of Zeste-2; EED, embryonic ectoderm development; GDF3, growth differentiation factor 3; DMR, differentially methylated regions; DAZL. deleted in azoospermia-like; Mvh, deadhead box 4; Sycp3, synaptonemal complex protein 3; E, embryonic day; RNAP II, RNA Polymerase II; trxG, trithorax group proteins; AID, activation-induced cytidine deaminase;
This work was supported by NIH grants R01 AR053851 and R01 CA131074 to R Eckert and R21HD057487 awarded to C Kerr as well as by the State of Maryland Stem Cell Research Fund 2010-MSCRFI-0110-00 to R Eckert and 2007-MSCRFII-0159-00 awarded to C Kerr.
Kouzarides T. Chromatin modifications and their function. Cell. 2007 Feb 23;128(4):693-705.
Vermeulen M, Eberl HC, Matarese F, Marks H, Denissov S, Butter F, et al. Quantitative interaction proteomics and genome-wide profiling of epigenetic histone marks and their readers. Cell. 2010 Sep 17;142(6):967-80.
Lee JS, Smith E, Shilatifard A. The language of histone crosstalk. Cell. 2010 Sep 3;142(5):682-5.
Joffe B, Leonhardt H, Solovei I. Differentiation and large scale spatial organization of the genome. Curr Opin Genet Dev. 2010 Oct;20(5):562-9.
Fisher CL, Fisher AG. Chromatin states in pluripotent, differentiated, and reprogrammed cells. Curr Opin Genet Dev. 2011 Apr;21(2):140-6.
Kloc A, Martienssen R. RNAi, heterochromatin and the cell cycle. Trends Genet. 2008 Oct;24(10):511-7.
Strahl BD, Allis CD. The language of covalent histone modifications. Nature. 2000 Jan 6;403(6765):41-5.
Mattout A, Meshorer E. Chromatin plasticity and genome organization in pluripotent embryonic stem cells. Curr Opin Cell Biol. 2010 Jun;22(3):334-41.
Efroni S, Duttagupta R, Cheng J, Dehghani H, Hoeppner DJ, Dash C, et al. Global transcription in pluripotent embryonic stem cells. Cell Stem Cell. 2008 May 8;2(5):437-47.
Gaspar-Maia A, Alajem A, Polesso F, Sridharan R, Mason MJ, Heidersbach A, et al. Chd1 regulates open chromatin and pluripotency of embryonic stem cells. Nature. 2009 Aug 13;460(7257):863-8.
Peric-Hupkes D, Meuleman W, Pagie L, Bruggeman SW, Solovei I, Brugman W, et al. Molecular maps of the reorganization of genome-nuclear lamina interactions during differentiation. Mol Cell. 2010 May 28;38(4):603-13.
Guelen L, Pagie L, Brasset E, Meuleman W, Faza MB, Talhout W, et al. Domain organization of human chromosomes revealed by mapping of nuclear lamina interactions. Nature. 2008 Jun 12;453(7197):948-51.
Pickersgill H, Kalverda B, de Wit E, Talhout W, Fornerod M, van Steensel B. Characterization of the Drosophila melanogaster genome at the nuclear lamina. Nat Genet. 2006 Sep;38(9):1005-14.
Wen B, Wu H, Shinkai Y, Irizarry RA, Feinberg AP. Large histone H3 lysine 9 dimethylated chromatin blocks distinguish differentiated from embryonic stem cells. Nat Genet. 2009 Feb;41(2):246-50.
Yokochi T, Poduch K, Ryba T, Lu J, Hiratani I, Tachibana M, et al. G9a selectively represses a class of late-replicating genes at the nuclear periphery. Proc Natl Acad Sci U S A. 2009 Nov 17;106(46):19363-8.
Cedar H, Bergman Y. Linking DNA methylation and histone modification: patterns and paradigms. Nat Rev Genet. 2009 May;10(5):295-304.
Trowbridge JJ, Orkin SH. DNA methylation in adult stem cells: New insights into self-renewal. Epigenetics. 2010 Apr 31;5(3).
Bernstein BE, Mikkelsen TS, Xie X, Kamal M, Huebert DJ, Cuff J, et al. A bivalent chromatin structure marks key developmental genes in embryonic stem cells. Cell. 2006 Apr 21;125(2):315-26.
Guenther MG, Levine SS, Boyer LA, Jaenisch R, Young RA. A chromatin landmark and transcription initiation at most promoters in human cells. Cell. 2007 Jul 13;130(1):77-88.
Roelen BA, Lopes SM. Of stem cells and gametes: similarities and differences. Curr Med Chem. 2008;15(13):1249-56.
Mohn F, Weber M, Rebhan M, Roloff TC, Richter J, Stadler MB, et al. Lineage-specific polycomb targets and de novo DNA methylation define restriction and potential of neuronal progenitors. Mol Cell. 2008 Jun 20;30(6):755-66.
Ito S, D'Alessio AC, Taranova OV, Hong K, Sowers LC, Zhang Y. Role of Tet proteins in 5mC to 5hmC conversion, ES-cell self-renewal and inner cell mass specification. Nature. 2010 Aug 26;466(7310):1129-33.
Ito S, Shen L, Dai Q, Wu SC, Collins LB, Swenberg JA, et al. Tet proteins can convert 5-methylcytosine to 5-formylcytosine and 5-carboxylcytosine. Science. 2010 Sep 2;333(6047):1300-3.
Tahiliani M, Koh KP, Shen Y, Pastor WA, Bandukwala H, Brudno Y, et al. Conversion of 5-methylcytosine to 5-hydroxymethylcytosine in mammalian DNA by MLL partner TET1. Science. 2009 May 15;324(5929):930-5.
Koh KP, Yabuuchi A, Rao S, Huang Y, Cunniff K, Nardone J, et al. Tet1 and Tet2 regulate 5-hydroxymethylcytosine production and cell lineage specification in mouse embryonic stem cells. Cell Stem Cell. 2011 Feb 4;8(2):200-13.
Lister R, Pelizzola M, Dowen RH, Hawkins RD, Hon G, Tonti-Filippini J, et al. Human DNA methylomes at base resolution show widespread epigenomic differences. Nature. 2009 Nov 19;462(7271):315-22.
Simon JA, Kingston RE. Mechanisms of polycomb gene silencing: knowns and unknowns. Nat Rev Mol Cell Biol. 2009 Oct;10(10):697-708.
Sauvageau M, Sauvageau G. Polycomb group genes: keeping stem cell activity in balance. PLoS Biol. 2008 Apr 29;6(4):e113.
Cole MF, Young RA. Mapping key features of transcriptional regulatory circuitry in embryonic stem cells. Cold Spring Harb Symp Quant Biol. 2008;73:183-93.
Surface LE, Thornton SR, Boyer LA. Polycomb group proteins set the stage for early lineage commitment. Cell Stem Cell. 2010 Sep 3;7(3):288-98.
Ho L, Crabtree GR. Chromatin remodelling during development. Nature. 2010 Jan 28;463(7280):474-84.
Pietersen AM, van Lohuizen M. Stem cell regulation by polycomb repressors: postponing commitment. Curr Opin Cell Biol. 2008 Apr;20(2):201-7.
Singhal N, Graumann J, Wu G, Arauzo-Bravo MJ, Han DW, Greber B, et al. Chromatin-Remodeling Components of the BAF Complex Facilitate Reprogramming. Cell. 2010 Jun 11;141(6):943-55.
Sauvageau M, Sauvageau G. Polycomb group proteins: multi-faceted regulators of somatic stem cells and cancer. Cell Stem Cell. 2010 Sep 3;7(3):299-313.
Wu H, D'Alessio AC, Ito S, Wang Z, Cui K, Zhao K, et al. Genome-wide analysis of 5-hydroxymethylcytosine distribution reveals its dual function in transcriptional regulation in mouse embryonic stem cells. Genes Dev. 2011 Apr 1;25(7):679-84.
Fischle W, Wang Y, Jacobs SA, Kim Y, Allis CD, Khorasanizadeh S. Molecular basis for the discrimination of repressive methyl-lysine marks in histone H3 by Polycomb and HP1 chromodomains. Genes Dev. 2003 Aug 1;17(15):1870-81.
Jacobs SA, Khorasanizadeh S. Structure of HP1 chromodomain bound to a lysine 9-methylated histone H3 tail. Science. 2002 Mar 15;295(5562):2080-3.
Orlando V. Polycomb, epigenomes, and control of cell identity. Cell. 2003 Mar 7;112(5):599-606.
Spivakov M, Fisher AG. Epigenetic signatures of stem-cell identity. Nat Rev Genet. 2007 Apr;8(4):263-71.
Lee TI, Jenner RG, Boyer LA, Guenther MG, Levine SS, Kumar RM, et al. Control of developmental regulators by Polycomb in human embryonic stem cells. Cell. 2006 Apr 21;125(2):301-13.
Landeira D, Fisher AG. Inactive yet indispensable: the tale of Jarid2. Trends Cell Biol. 2011 Feb;21(2):74-80.
Brookes E, Pombo A. Modifications of RNA polymerase II are pivotal in regulating gene expression states. EMBO Rep. 2009 Nov;10(11):1213-9.
Landeira D, Sauer S, Poot R, Dvorkina M, Mazzarella L, Jorgensen HF, et al. Jarid2 is a PRC2 component in embryonic stem cells required for multi-lineage differentiation and recruitment of PRC1 and RNA Polymerase II to developmental regulators. Nat Cell Biol. 2010 Jun;12(6):618-24.
Pasini D, Cloos PA, Walfridsson J, Olsson L, Bukowski JP, Johansen JV, et al. JARID2 regulates binding of the Polycomb repressive complex 2 to target genes in ES cells. Nature. 2010 Mar 11;464(7286):306-10.
Shen X, Kim W, Fujiwara Y, Simon MD, Liu Y, Mysliwiec MR, et al. Jumonji modulates polycomb activity and self-renewal versus differentiation of stem cells. Cell. 2009 Dec 24;139(7):1303-14.
Eskeland R, Leeb M, Grimes GR, Kress C, Boyle S, Sproul D, et al. Ring1B compacts chromatin structure and represses gene expression independent of histone ubiquitination. Mol Cell. 2010 May 14;38(3):452-64.
Endoh M, Endo TA, Endoh T, Fujimura Y, Ohara O, Toyoda T, et al. Polycomb group proteins Ring1A/B are functionally linked to the core transcriptional regulatory circuitry to maintain ES cell identity. Development. 2008 Apr;135(8):1513-24.
Ho L, Jothi R, Ronan JL, Cui K, Zhao K, Crabtree GR. An embryonic stem cell chromatin remodeling complex, esBAF, is an essential component of the core pluripotency transcriptional network. Proc Natl Acad Sci U S A. 2009 Mar 31;106(13):5187-91.
Lessard JA, Crabtree GR. Chromatin regulatory mechanisms in pluripotency. Annu Rev Cell Dev Biol. 2010 Nov 10;26:503-32.
Ang YS, Tsai SY, Lee DF, Monk J, Su J, Ratnakumar K, et al. Wdr5 mediates self-renewal and reprogramming via the embryonic stem cell core transcriptional network. Cell. 2010 Apr 15;145(2):183-97.
Ho L, Ronan JL, Wu J, Staahl BT, Chen L, Kuo A, et al. An embryonic stem cell chromatin remodeling complex, esBAF, is essential for embryonic stem cell self-renewal and pluripotency. Proc Natl Acad Sci U S A. 2009 Mar 31;106(13):5181-6.
Fazzio TG, Huff JT, Panning B. An RNAi screen of chromatin proteins identifies Tip60-p400 as a regulator of embryonic stem cell identity. Cell. 2008 Jul 11;134(1):162-74.
Schaniel C, Ang YS, Ratnakumar K, Cormier C, James T, Bernstein E, et al. Smarcc1/Baf155 couples self-renewal gene repression with changes in chromatin structure in mouse embryonic stem cells. Stem Cells. 2009 Dec;27(12):2979-91.
Liang J, Wan M, Zhang Y, Gu P, Xin H, Jung SY, et al. Nanog and Oct4 associate with unique transcriptional repression complexes in embryonic stem cells. Nat Cell Biol. 2008 Jun;10(6):731-9.
Pardo M, Lang B, Yu L, Prosser H, Bradley A, Babu MM, et al. An expanded Oct4 interaction network: implications for stem cell biology, development, and disease. Cell Stem Cell. 2010 Apr 2;6(4):382-95.
van den Berg DL, Snoek T, Mullin NP, Yates A, Bezstarosti K, Demmers J, et al. An Oct4-centered protein interaction network in embryonic stem cells. Cell Stem Cell. 2010 Apr 2;6(4):369-81.
Hayashi K, Surani MA. Resetting the epigenome beyond pluripotency in the germline. Cell Stem Cell. 2009 Jun 5;4(6):493-8.
Surani MA, Hayashi K, Hajkova P. Genetic and epigenetic regulators of pluripotency. Cell. 2007 Feb 23;128(4):747-62.
Monk M, Boubelik M, Lehnert S. Temporal and regional changes in DNA methylation in the embryonic, extraembryonic and germ cell lineages during mouse embryo development. Development. 1987 Mar;99(3):371-82.
Tada M, Tada T, Lefebvre L, Barton SC, Surani MA. Embryonic germ cells induce epigenetic reprogramming of somatic nucleus in hybrid cells. Embo J. 1997 Nov 3;16(21):6510-20.
Hajkova P, Ancelin K, Waldmann T, Lacoste N, Lange UC, Cesari F, et al. Chromatin dynamics during epigenetic reprogramming in the mouse germ line. Nature. 2008 Apr 17;452(7189):877-81.
Ohinata Y, Payer B, O'Carroll D, Ancelin K, Ono Y, Sano M, et al. Blimp1 is a critical determinant of the germ cell lineage in mice. Nature. 2005 Jul 14;436(7048):207-13.
Vincent SD, Dunn NR, Sciammas R, Shapiro-Shalef M, Davis MM, Calame K, et al. The zinc finger transcriptional repressor Blimp1/Prdm1 is dispensable for early axis formation but is required for specification of primordial germ cells in the mouse. Development. 2005 Mar;132(6):1315-25.
Yamaji M, Seki Y, Kurimoto K, Yabuta Y, Yuasa M, Shigeta M, et al. Critical function of Prdm14 for the establishment of the germ cell lineage in mice. Nat Genet. 2008 Aug;40(8):1016-22.
Gillich A, Bao S, Grabole N, Hayashi K, Trotter MW, Pasque V, et al. Epiblast stem cell-based system reveals reprogramming synergy of germline factors. Cell Stem Cell. 2012 Apr 6;10(4):425-39.
Nagamatsu G, Kosaka T, Kawasumi M, Kinoshita T, Takubo K, Akiyama H, et al. A germ cell-specific gene, Prmt5, works in somatic cell reprogramming. J Biol Chem. 2011 Mar 25;286(12):10641-8.
Ancelin K, Lange UC, Hajkova P, Schneider R, Bannister AJ, Kouzarides T, et al. Blimp1 associates with Prmt5 and directs histone arginine methylation in mouse germ cells. Nat Cell Biol. 2006;8(6):623-30.
Maatouk DM, Kellam LD, Mann MR, Lei H, Li E, Bartolomei MS, et al. DNA methylation is a primary mechanism for silencing postmigratory primordial germ cell genes in both germ cell and somatic cell lineages. Development. 2006 Sep;133(17):3411-8.
Reik W, Dean W. Back to the beginning. Nature. 2002 Nov 14;420(6912):127.
Popp C, Dean W, Feng S, Cokus SJ, Andrews S, Pellegrini M, et al. Genome-wide erasure of DNA methylation in mouse primordial germ cells is affected by AID deficiency. Nature. 2010 Feb 25;463(7284):1101-5.
Morgan HD, Dean W, Coker HA, Reik W, Petersen-Mahrt SK. Activation-induced cytidine deaminase deaminates 5-methylcytosine in DNA and is expressed in pluripotent tissues: implications for epigenetic reprogramming. J Biol Chem. 2004 Dec 10;279(50):52353-60.
Reik W. Stability and flexibility of epigenetic gene regulation in mammalian development. Nature. 2007 May 24;447(7143):425-32.
Hackett JA, Sengupta R, Zylicz JJ, Murakami K, Lee C, Down TA, et al. Germline DNA Demethylation Dynamics and Imprint Erasure Through 5-Hydroxymethylcytosine. Science. 2012 Dec 13.
de Napoles M, Nesterova T, Brockdorff N. Early loss of Xist RNA expression and inactive X chromosome associated chromatin modification in developing primordial germ cells. PLoS One. 2007;2(9):e860.
Hinkins M, Huntriss J, Miller D, Picton HM. Expression of Polycomb-group genes in human ovarian follicles, oocytes and preimplantation embryos. Reproduction. 2005 Dec;130(6):883-8.
Labosky PA, Barlow DP, Hogan BL. Mouse embryonic germ (EG) cell lines: transmission through the germline and differences in the methylation imprint of insulin-like growth factor 2 receptor (Igf2r) gene compared with embryonic stem (ES) cell lines. Development. 1994 Nov;120(11):3197-204.
Tada T, Tada M, Hilton K, Barton SC, Sado T, Takagi N, et al. Epigenotype switching of imprintable loci in embryonic germ cells. Dev Genes Evol. 1998 Feb;207(8):551-61.
Onyango P, Jiang S, Uejima H, Shamblott MJ, Gearhart JD, Cui H, et al. Monoallelic expression and methylation of imprinted genes in human and mouse embryonic germ cell lineages. Proc Natl Acad Sci U S A. 2002 Aug 6;99(16):10599-604.
Matsui Y, Zsebo K, Hogan BL. Derivation of pluripotential embryonic stem cells from murine primordial germ cells in culture. Cell. 1992;70(5):841-7.
Stewart CL, Gadi I, Bhatt H. Stem cells from primordial germ cells can reenter the germ line. Dev Biol. 1994 Feb;161(2):626-8.
Shamblott MJ, Axelman J, Wang S, Bugg EM, Littlefield JW, Donovan PJ, et al. Derivation of pluripotent stem cells from cultured human primordial germ cells. Proceedings of the National Academy of Sciences of the United States of America. 1998;95(23):13726-31.
Hiller M, Liu C, Blumenthal PD, Gearhart JD, Kerr CL. Bone morphogenetic protein 4 mediates human embryonic germ cell derivation. Stem Cells Dev. 2011 Feb;20(2):351-61.
Kashyap V, Rezende NC, Scotland KB, Shaffer SM, Persson JL, Gudas LJ, et al. Regulation of stem cell pluripotency and differentiation involves a mutual regulatory circuit of the NANOG, OCT4, and SOX2 pluripotency transcription factors with polycomb repressive complexes and stem cell microRNAs. Stem Cells Dev. 2009 Sep;18(7):1093-108.
Bartel DP. MicroRNAs: target recognition and regulatory functions. Cell. 2009 Jan 23;136(2):215-33.
Gangaraju VK, Lin H. MicroRNAs: key regulators of stem cells. Nat Rev Mol Cell Biol. 2009 Feb;10(2):116-25.
Houbaviy HB, Murray MF, Sharp PA. Embryonic stem cell-specific MicroRNAs. Dev Cell. 2003 Aug;5(2):351-8.
Barroso-delJesus A, Romero-Lopez C, Lucena-Aguilar G, Melen GJ, Sanchez L, Ligero G, et al. Embryonic stem cell-specific miR302-367 cluster: human gene structure and functional characterization of its core promoter. Mol Cell Biol. 2008 Nov;28(21):6609-19.
Letzen B, Liu C, Thakor N, Gearhart J, All A, Kerr C. MicroRNA Expression Profiling of Oligodendrocyte Differentiation from Human Embryonic Stem Cells. PLoS one. 2010;5(5):e10480 http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2864763/.
Lakshmipathy U, Love B, Goff LA, Jornsten R, Graichen R, Hart RP, et al. MicroRNA Expression Pattern of Undifferentiated and Differentiated Human Embryonic Stem Cells. Stem Cells Dev. 2007 Dec;16(6):1003-16.
Marson A, Levine SS, Cole MF, Frampton GM, Brambrink T, Johnstone S, et al. Connecting microRNA genes to the core transcriptional regulatory circuitry of embryonic stem cells. Cell. 2008 Aug 8;134(3):521-33.
Tay Y, Zhang J, Thomson AM, Lim B, Rigoutsos I. MicroRNAs to Nanog, Oct4 and Sox2 coding regions modulate embryonic stem cell differentiation. Nature. 2008 Oct 23;455(7216):1124-8.
Pasini D, Bracken AP, Helin K. Polycomb group proteins in cell cycle progression and cancer. Cell Cycle. 2004 Apr;3(4):396-400.
Wang H, Garzon R, Sun H, Ladner KJ, Singh R, Dahlman J, et al. NF-kappaB-YY1-miR-29 regulatory circuitry in skeletal myogenesis and rhabdomyosarcoma. Cancer Cell. 2008 Nov 4;14(5):369-81.
Sinkkonen L, Hugenschmidt T, Berninger P, Gaidatzis D, Mohn F, Artus-Revel CG, et al. MicroRNAs control de novo DNA methylation through regulation of transcriptional repressors in mouse embryonic stem cells. Nat Struct Mol Biol. 2008 Mar;15(3):259-67.
Kanellopoulou C, Muljo SA, Kung AL, Ganesan S, Drapkin R, Jenuwein T, et al. Dicer-deficient mouse embryonic stem cells are defective in differentiation and centromeric silencing. Genes Dev. 2005 Feb 15;19(4):489-501.
Wang Y, Medvid R, Melton C, Jaenisch R, Blelloch R. DGCR8 is essential for microRNA biogenesis and silencing of embryonic stem cell self-renewal. Nat Genet. 2007 Mar;39(3):380-5.
Fukuda T, Yamagata K, Fujiyama S, Matsumoto T, Koshida I, Yoshimura K, et al. DEAD-box RNA helicase subunits of the Drosha complex are required for processing of rRNA and a subset of microRNAs. Nat Cell Biol. 2007 May;9(5):604-11.
Banerjee R, Mani RS, Russo N, Scanlon CS, Tsodikov A, Jing X, et al. The tumor suppressor gene rap1GAP is silenced by miR-101-mediated EZH2 overexpression in invasive squamous cell carcinoma. Oncogene. 2011 Oct 20;30(42):4339-49.
Varambally S, Cao Q, Mani RS, Shankar S, Wang X, Ateeq B, et al. Genomic loss of microRNA-101 leads to overexpression of histone methyltransferase EZH2 in cancer. Science. 2008 Dec 12;322(5908):1695-9.
Cui K, Zang C, Roh TY, Schones DE, Childs RW, Peng W, et al. Chromatin signatures in multipotent human hematopoietic stem cells indicate the fate of bivalent genes during differentiation. Cell Stem Cell. 2009 Jan 9;4(1):80-93.
Collas P. Programming differentiation potential in mesenchymal stem cells. Epigenetics. 2010 Aug 16;5(6):476-82.
Meissner A, Mikkelsen TS, Gu H, Wernig M, Hanna J, Sivachenko A, et al. Genome-scale DNA methylation maps of pluripotent and differentiated cells. Nature. 2008 Aug 7;454(7205):766-70.
Jiang L, Li J, Song L. Bmi-1, stem cells and cancer. Acta Biochim Biophys Sin (Shanghai). 2009 Jul;41(7):527-34.
Clarke MF, Fuller M. Stem cells and cancer: two faces of eve. Cell. 2006 Mar 24;124(6):1111-5.
Hill RP, Perris R. "Destemming" cancer stem cells. J Natl Cancer Inst. 2007 Oct 3;99(19):1435-40.
Dalerba P, Cho RW, Clarke MF. Cancer stem cells: models and concepts. Annu Rev Med. 2007;58:267-84.
Mongan NP, Martin KM, Gudas LJ. The putative human stem cell marker, Rex-1 (Zfp42): structural classification and expression in normal human epithelial and carcinoma cell cultures. Mol Carcinog. 2006 Dec;45(12):887-900.
Chiou SH, Yu CC, Huang CY, Lin SC, Liu CJ, Tsai TH, et al. Positive correlations of Oct-4 and Nanog in oral cancer stem-like cells and high-grade oral squamous cell carcinoma. Clin Cancer Res. 2008 Jul 1;14(13):4085-95.
Raman JD, Mongan NP, Liu L, Tickoo SK, Nanus DM, Scherr DS, et al. Decreased expression of the human stem cell marker, Rex-1 (zfp-42), in renal cell carcinoma. Carcinogenesis. 2006 Mar;27(3):499-507.
Ben-Porath I, Thomson MW, Carey VJ, Ge R, Bell GW, Regev A, et al. An embryonic stem cell-like gene expression signature in poorly differentiated aggressive human tumors. Nat Genet. 2008 May;40(5):499-507.
Takahashi K, Tanabe K, Ohnuki M, Narita M, Ichisaka T, Tomoda K, et al. Induction of pluripotent stem cells from adult human fibroblasts by defined factors. Cell. 2007 Nov 30;131(5):861-72.
Yu J, Vodyanik M, Smuga-Otto K, Antosiewicz-Bourget J, Frane J, Tian S, et al. Induced pluripotent stem cell lines derived from human somatic cells. Science. 2007;318(5858):1917.
Wernig M, Meissner A, Foreman R, Brambrink T, Ku M, Hochedlinger K, et al. In vitro reprogramming of fibroblasts into a pluripotent ES-cell-like state. Nature. 2007 Jul 19;448(7151):318-24.
Wong DJ, Liu H, Ridky TW, Cassarino D, Segal E, Chang HY. Module map of stem cell genes guides creation of epithelial cancer stem cells. Cell Stem Cell. 2008 Apr 10;2(4):333-44.
Ohm J, Mali P, Van Neste L, Berman D, Liang L, Pandiyan K, et al. Cancer-Related Epigenome Changes Associated with Reprogramming to Induced Pluripotent Stem Cells. Cancer Research. 2010;70(19):7662.
Mali P, Chou BK, Yen J, Ye Z, Zou J, Dowey S, et al. Butyrate greatly enhances derivation of human induced pluripotent stem cells by promoting epigenetic remodeling and the expression of pluripotency-associated genes. Stem Cells. 2010 Apr;28(4):713-20.
Varambally S, Dhanasekaran SM, Zhou M, Barrette TR, Kumar-Sinha C, Sanda MG, et al. The polycomb group protein EZH2 is involved in progression of prostate cancer. Nature. 2002 Oct 10;419(6907):624-9.
Kamminga LM, Bystrykh LV, de Boer A, Houwer S, Douma J, Weersing E, et al. The Polycomb group gene Ezh2 prevents hematopoietic stem cell exhaustion. Blood. 2006 Mar 1;107(5):2170-9.
Pasini D, Bracken AP, Jensen MR, Lazzerini Denchi E, Helin K. Suz12 is essential for mouse development and for EZH2 histone methyltransferase activity. Embo J. 2004 Oct 13;23(20):4061-71.
Bracken AP, Dietrich N, Pasini D, Hansen KH, Helin K. Genome-wide mapping of Polycomb target genes unravels their roles in cell fate transitions. Genes Dev. 2006 May 1;20(9):1123-36.
Bracken AP, Kleine-Kohlbrecher D, Dietrich N, Pasini D, Gargiulo G, Beekman C, et al. The Polycomb group proteins bind throughout the INK4A-ARF locus and are disassociated in senescent cells. Genes Dev. 2007 Mar 1;21(5):525-30.
Dietrich N, Bracken AP, Trinh E, Schjerling CK, Koseki H, Rappsilber J, et al. Bypass of senescence by the polycomb group protein CBX8 through direct binding to the INK4A-ARF locus. Embo J. 2007 Mar 21;26(6):1637-48.
Bracken AP, Pasini D, Capra M, Prosperini E, Colli E, Helin K. EZH2 is downstream of the pRB-E2F pathway, essential for proliferation and amplified in cancer. Embo J. 2003 Oct 15;22(20):5323-35.
Widschwendter M, Fiegl H, Egle D, Mueller-Holzner E, Spizzo G, Marth C, et al. Epigenetic stem cell signature in cancer. Nat Genet. 2007 Feb;39(2):157-8.
Liu S, Dontu G, Mantle ID, Patel S, Ahn NS, Jackson KW, et al. Hedgehog signaling and Bmi-1 regulate self-renewal of normal and malignant human mammary stem cells. Cancer Res. 2006 Jun 15;66(12):6063-71.
Raman JD, Mongan NP, Tickoo SK, Boorjian SA, Scherr DS, Gudas LJ. Increased expression of the polycomb group gene, EZH2, in transitional cell carcinoma of the bladder. Clin Cancer Res. 2005 Dec 15;11(24 Pt 1):8570-6.
Friedman JM, Liang G, Liu CC, Wolff EM, Tsai YC, Ye W, et al. The putative tumor suppressor microRNA-101 modulates the cancer epigenome by repressing the polycomb group protein EZH2. Cancer Res. 2009 Mar 15;69(6):2623-9.