List of oligomers for EMSA.
Abstract
An R-loop is a triple-stranded nucleic acid structure consisting of a DNA–RNA hybrid and a displaced single-stranded DNA. R-loops are associated with diverse biological reactions, such as immune responses and gene regulation, and dysregulated R-loops can cause genomic instability and replication stress. Therefore, investigating the formation, regulation, and elimination of R-loops is important for understanding the molecular mechanisms underlying biological processes and diseases related to R-loops. Existing research has primarily focused on R-loop detection. In this chapter, we introduce a variety of biochemical and biophysical techniques for R-loop sensing and visualization both in vivo and in vitro, including single-molecule imaging. These methods can be used to investigate molecular mechanisms underlying R-loop search and identification.
Keywords
- R-loop
- genetic instability
- R-loop sensing
- and single-molecule imaging
1. Introduction
1.1 History of R-loops
R-loops are three-stranded nucleic acid structures consisting of a DNA–RNA hybrid and a displaced single-stranded (ss) DNA. They were first described in 1976 by Thomas
1.2 Biological functions of R-loops
RNA–DNA hybrids can be formed from GC-rich clusters during transcription or primer synthesis of DNA replication [2, 8]. Because nucleic acid strands are stabilized when they form a double-stranded conformation, the nascent RNA is hybridized to the template DNA strand when the double-stranded (ds)DNA is denatured during replication or transcription [2]. Therefore, R-loops can form at any time when there is a chance that RNA can be annealed with its template DNA. The thread-back model proposes that R-loop formation stems from the annealing of RNA with DNA when the DNA left behind the transcriptome is negatively supercoiled and unwound [9]. Previous studies support this model [10, 11, 12, 13]. Incomplete transcription elongation and termination also induce RNA–DNA hybrid formation, and the denaturation of duplex DNA by negative supercoiling increases R-loop formation.
R-loops have multiple roles in diverse biological reactions (Figure 1). First, R-loops induce genetic rearrangements in B-cells during immunoglobulin class switching [14]. R-loop formation is promoted by transcription through switched immunoglobulin loci, and the R-loop provides a ssDNA substrate for activation-induced deaminase (AID), which converts cytosine to uracil in both DNA strands. Uracil is subsequently removed by uracil glycosylase, and apurinic/apyrimidinic endonuclease makes nicks at the abasic sites and induces DNA double-strand breaks. During DNA double-strand break repair, the immunoglobulin locus is rearranged to change the level of antibodies generated. R-loops can also regulate both the activation and termination of transcription. Most human promoters are associated with CpG islands [15]. Ginno
1.3 R-loops, genomic instability, and human diseases
Despite the multiple roles of R-loops in normal cellular processes described above, they are also considered a form of DNA damage that can threaten genomic maintenance and integrity. In particular, the displaced ssDNA in an R-loop can increase genomic instability because it is a good endonuclease substrate [13, 27]. R-loops also induce replication stress. When the displaced ssDNA is broken, the replication fork stops at the R-loop. The RNA–DNA hybrid itself can block the progression of replication forks, and DNA polymerases may become trapped at R-loops [13, 28, 29]. Such replication stresses will activate DNA repair pathways, which might cause chromosome rearrangement [29].
Genomic instability that stems from R-loops may also contribute to some human diseases. Although there is no apparent evidence that R-loops are directly associated with disease, efforts to show causality between R-loops and disease have increased [30]. Some genetic disorders are caused by gene-specific repeats. R-loop formation is highly probable in tandem repeat sequences with high GC content and could change the repeat length. In particular, trinucleotide repeat expansion is a major cause of neurological and neuromuscular diseases, such as Huntington’s disease and fragile X syndrome [31, 32]. It has been proposed that R-loops are associated with other neurological disorders, including amyotrophic lateral sclerosis, Aicardi-Goutières syndrome, and Prader-Willi syndrome [33, 34, 35]. R-loops also appear to be associated with cancer.
1.4 R-loop prevention and elimination
As described above, R-loops can cause genomic instability unless they are resolved, so they must be properly regulated. Several proteins are involved in R-loop prevention or elimination, such as RNase H, DNA TOP1, and Sen1 [38]. For example, RNase H directly removes R-loops by specifically degrading the RNA in RNA–DNA hybrid structures [39]. RNA helicases also resolve R-loops by unwinding RNA–DNA hybrid structures [40]. Because negative supercoiling promotes R-loop formation, topoisomerases play a key role in preventing R-loops [41]. In the case of replication fork stalling due to R-loops, FANCD2 recruits RNA processing enzymes such as hnRNP U and DDX47 to resolve R-loops at the stalled fork [42].
2. In vivo R-loop assays
Visualizing R-loop formation is important for understanding R-loop metabolism. Because R-loops basically consist of nucleic acids, distinguishing R-loop from ds- and ss-DNA or RNA using existing DNA staining or visualization methods is challenging. S9.6 is an antibody specific to an RNA–DNA hybrid, which was developed in 1986 and rapidly advanced R-loop-related research [43]. This antibody is commonly used to detect R-loops both
Currently, the most popular R-loop characterization technique is DNA–RNA immunoprecipitation sequencing (DRIP-seq), in which RNA–DNA hybrid strands are immunoprecipitated with S9.6 and then sequenced (Figure 2, [47, 48]). DRIP-seq was first adopted for profiling CpG island promoters, where R-loops are predominantly formed [16]. This method revealed that genes containing terminal GC-rich sequences form R-loops at their 3′-end, suggesting that R-loops contribute to efficient transcription termination [20]. The DRIP-seq technique has been further improved; S1 nuclease treatment prior to DRIP-seq can stabilize the DNA–RNA hybrid because S1 removes the displaced ssDNA, thus improving the resolution [49]. In conventional DRIP-seq, it is assumed that the content of R-loops or RNA–DNA hybrids does not vary depending on cell type and growth condition. For appropriate comparison, quantitative differential DNA–RNA immunoprecipitation sequence (qDRIP-seq) uses synthetic RNA–DNA hybrids as internal standards and facilitates comparison between different conditions with high resolution and sensitivity [50]. Although DRIP-seq is a very robust and well-characterized technique, it can only measure the ensemble average level of R-loops. However, single-molecule R-loop footprinting (SMRF-seq) can reveal the R-loop population via chemical reactivity of ssDNA at the single-molecule level. Malig
Fluorescently labeled S9.6 can be used as an R-loop probe in microscope imaging at the cellular level (Figure 3a). The brief procedure is following. K562 cells were pelleted after trypsinization for detaching cells from the plate. Supernatant was discarded to approximately 300 ul, and cell pellets were resuspended. 5 ml of 37°C pre-warmed 75 mM KCl solution was added in a drop-wise manner while the resuspended cells were slowly agitated. After the cells were incubated at 37°C for 14 min, five or six drops of fresh ice-cold fixative solution (3,1 methanol:acetic acid) were added to the cells, which were centrifuged again. Supernatant was discarded to approximately 300 ul, and cell pellets were resuspended. The cells were treated on ice with 5 ml of ice-cold fixative solution in a drop-wise manner. After washed once with fixative solution, the cells were spread onto a clean slide followed by 1 min incubation in 95°C steam for drying. The slide was immediately treated with blocking buffer (1x PBS, 5% BSA, 0.5% Triton X-100) and incubated at room temperature for 1 hr. The slide was successively treated with S9.6 antibody (1500) in blocking buffer at 4°C overnight. After residual S9.6 antibody was washed three times with washing buffer (1x PBS supplemented with 0.1% Triton X-100), the slide was treated with mouse AlexaFluor 594-conjugated secondary antibody at room temperature for 1 hr. The unbound secondary antibody was washed three times with washing buffer, and then the cells were stained with 4,6 diamidino-2-phenylindole (DAPI) and mounted using Vectashield (Vector Laboratories). Finally, the cells were imaged using a fluorescence microscope.
The use of immunofluorescence with S9.6 can allow visualization of the intracellular locations of RNA–DNA hybrids, even in mitochondria [54, 55, 56]. Furthermore, R-loop detection by S9.6 is ensured by RNase H1 overexpression (Figure 3b). R-loops can also be visualized via R-loop associated proteins with diverse modifications. Prendergast
3. In vitro approaches
In addition to
Oligomer name | Sequences |
---|---|
5’-GCC GTC GCA TGA CGC TGC CGA ATT CTA CCA CGC GAT TCA TAC CTG TCG TGC CAG CTG CTT TGC CCA CCT GCA GGT TCA CCT CGT CCC TGG C-3′ | |
5′-[Cy3]-GCC AGG GAC GAG GTG AAC CTG CAG GTG GGC AAA GCA GCT GGC ACG ACA GGT ATG AAT CGC GTG GTA GAA TTC GGC AGC GTC ATG CGA CGG C-3’ | |
5′-[Cy3]-GCC AGG GAC GAG GTG AAC CTG CAG GTG GGC GGC TAC TAC TTA GAT GTC ATC CGA GGC TTA TTG GTA GAA TTC GGC AGC GTC ATG C GA CGG C-3’ | |
5′-[Cy5]-GCA GCU GGC ACG ACA GGU AUG AAU C-3’ |
Substrate name | Mixture recipe (total 20 μl in reaction buffer) |
---|---|
Purified RBD-DsRed specifically binds to RNA-containing structures, enabling its use as a probe of R-loops (Figure 4b). DNA fibers can be spread on a surface to distinguish the positions of R-loop regions with the purified RBD-DsRed. Various tags combining the RBD of RNase H1 have been used in microscopic fluorescent imaging, EMSA, and DRIP-seq to identify R-loops [63]. Crossely
Atomic force microscopy (AFM) scans a sample on a mica surface using a cantilever to yield a topographic image of the sample [64]. AFM has revealed diverse types of nucleic acids structures and DNA-protein complex formations [65, 66, 67]. AFM is also applied for visualizing R-loop formation. Carrasco-Salas
4. Single-molecule approaches for R-loop studies
Although R-loop formation, function, and fate have been extensively studied using biochemical assays and cell-based imaging as described above, those approaches still have limitations related to probing molecular details due to the ensemble average effect. Such hurdles can be overcome with single-molecule techniques that enable researchers to 1) observe individual molecules without an ensemble average effect, 2) mechanically manipulate biomolecules, and 3) directly observe biomolecular interactions [69]. Several single-molecule techniques have been utilized for R-loop studies. Lee
In addition to PIFE, single-molecule FRET (smFRET) has been widely used for probing the conformational dynamics of biomolecules (Figure 5a) [73, 74]. FRET requires two dyes (donor and acceptor) with spectral overlap for donor emission and acceptor absorption. In FRET, only the donor dye is excited, while the acceptor dye emits fluorescence through energy transfer when both dyes are in close proximity, as the energy transfer efficiency depends on the distance between them. R-loops are also studied using smFRET, during which the target DNA or RNA and RNA polymerases are fluorescently labeled with FRET donors and acceptors (Figure 5a, [75]). For smFRET experiments, one DNA oligomer with both FRET donor (Cy3) and acceptor (Cy5) and its complementary oligomer with biotin were hybridized. The hybridized DNA was anchored on the surface of a quartz slide coated with polyethylene glycol (PEG) via biotin-streptavidin interaction. Transcription was initiated by injecting 8 nM T7 RNA polymerases and 2 mM of rNTPs in imaging buffer (40 mM Tris–HCl [pH 8.0], 50 mM KCl, 5 mM NaOH, 20 mM MgCl2, 1 mM DTT, 2 mM spermidine, 3 mM Trolox, 5 mM PCA, and 4 units/ml PCD). Total internal reflection fluorescence (TIRF) microscopy equipped with an electron-multiplying CCD camera was used for fluorescence imaging. Donor (Cy3) and acceptor (Cy5) dyes were excited by 532-nm and 633-nm lasers, respectively. smFRET experiments revealed that R-loop formation precedes and facilitates G-quadruplex formation, which is extremely stable even after R-loop resolution. Using smFRET, we can examine R-loop formation induced by dsDNA denaturation, collision between RNAP and obstacles such as protein roadblocks or DNA lesions, and G-quadruplex formation of displaced ssDNA during R-loop formation [70, 75].
In addition to R-loop formation, sensing R-loops is important for downstream processes, including R-loop resolution. In particular, how R-loop-binding proteins recognize R-loops in long genomic DNA is unclear. R-loop search mechanisms have been investigated with a novel single-molecule fluorescence imaging technique called DNA curtain (Figure 5b, [76, 77]). In this assay, DNA molecules are anchored on a lipid bilayer and aligned at nanometric diffusion barriers. Owing to the fluidity of the surface lipid bilayer, DNA molecules are unidirectionally stretched under hydrodynamic flow. DNA curtains can be used to identify sequence-dependent binding of proteins to DNA. Moreover, they allow us to visualize the movement of a protein along a single DNA molecule in real time. To study the search mechanism, an R-loop is inserted into a specific location of lambda phage DNA and fluorescently imaged with Cy5-labeled RNA in the R-loop. Then, the R-loop-binding protein is tagged with a fluorescent nanoparticle called a quantum dot (Qdot), which has a different emission wavelength from Cy5. Two-color imaging of both Cy5 and Qdot in the DNA curtain allows the R-loop search mechanism of the R-loop-binding protein. Kang
Magnetic tweezers assay can measure both the tension and topological features of a single supercoiled DNA. In this approach, a linear DNA molecule is torsionally constrained by tethering the DNA ends to the slide surface and a magnetic bead that is rotated to induce DNA supercoiling (Figure 5c). Portmen
With advances in single-molecule imaging technology, we can investigate R-loops and related factors that cannot be observed in traditional ensemble assays. The convergence of single-molecule techniques and R-loop research will pave the way to more thorough investigation of R-loops with higher spatiotemporal resolution.
5. Conclusions
R-loops are involved in various cellular activities but can threaten genomic stability. Detecting these structures is important for understanding their metabolism and underlying mechanism. This chapter described the formation, roles, and regulation of R-loops and related diseases and explored
Acknowledgments
This work was supported by the National Research Foundation (grant number: NRF-2020R1A2B5B01001792) and the Institute for Basic Science (IBS-R022-D1).
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