R loops: new modulators of genome dynamics and function (original) (raw)
Roberts, R. W. & Crothers, D. M. Stability and properties of double and triple helices: dramatic effects of RNA or DNA backbone composition. Science258, 1463–1466 (1992). CASPubMed Google Scholar
Roy, D., Zhang, Z., Lu, Z., Hsieh, C. L. & Lieber, M. R. Competition between the RNA transcript and the nontemplate DNA strand during R-loop formation in vitro: a nick can serve as a strong R-loop initiation site. Mol. Cell. Biol.30, 146–159 (2010). CASPubMed Google Scholar
Roy, D. & Lieber, M. R. G clustering is important for the initiation of transcription-induced R-loops in vitro, whereas high G density without clustering is sufficient thereafter. Mol. Cell. Biol.29, 3124–3133 (2009). CASPubMedPubMed Central Google Scholar
Duquette, M. L., Handa, P., Vincent, J. A., Taylor, A. F. & Maizels, N. Intracellular transcription of G-rich DNAs induces formation of G-loops, novel structures containing G4 DNA. Genes Dev.18, 1618–1629 (2004). CASPubMedPubMed Central Google Scholar
Aguilera, A. & Garcia-Muse, T. R loops: from transcription byproducts to threats to genome stability. Mol. Cell46, 115–124 (2012). CASPubMed Google Scholar
Huertas, P. & Aguilera, A. Cotranscriptionally formed DNA:RNA hybrids mediate transcription elongation impairment and transcription-associated recombination. Mol. Cell12, 711–721 (2003). This paper provides the first demonstration that R loops cause genome instability and that mRNP biogenesis factors prevent R-loop formation. It shows that R loops accumulate in yeast mutants lacking the Hpr1 subunit of the THO complex and that hyper-recombination in these mutants is partially dependent on the nascent mRNA and R-loop accumulation. CASPubMed Google Scholar
Li, X. & Manley, J. L. Inactivation of the SR protein splicing factor ASF/SF2 results in genomic instability. Cell122, 365–378 (2005). This is the first evidence in vertebrate cells that depletion of a splicing factor causes genome instability in the form of chromosomal rearrangements and mutagenesis mediated by R loops, as shown for chicken DT40 and human HeLa cells depleted of the SRSF1 protein. CASPubMed Google Scholar
Skourti-Stathaki, K., Proudfoot, N. J. & Gromak, N. Human senataxin resolves RNA/DNA hybrids formed at transcriptional pause sites to promote Xrn2-dependent termination. Mol. Cell42, 794–805 (2011). This paper connects RNA:DNA helicase SETX deficiency with R-loop accumulation in human cells. The authors propose that R loops form at G-rich termination pausing sites and are resolved by SETX, which would promote 3′ mRNA degradation by XRN2 and transcription termination. CASPubMedPubMed Central Google Scholar
Castellano-Pozo, M. et al. R loops are linked to histone H3 S10 phosphorylation and chromatin condensation. Mol. Cell52, 583–590 (2013). This work shows a functional link between R loops and the H3S10P chromatin condensation mark. Yeast, worm and human cells depleted of THO subunits show increased levels of H3S10P, which is suppressed by RNase H1 overexpression. Enrichment of the H3K9me2 heterochromatic mark is also shown inC. elegans. It is proposed that chromatin condensation linked to R loops is a strong barrier to replication progression as a major source of replication stress and genome instability. CASPubMed Google Scholar
Wongsurawat, T., Jenjaroenpun, P., Kwoh, C. K. & Kuznetsov, V. Quantitative model of R-loop forming structures reveals a novel level of RNA-DNA interactome complexity. Nucleic Acids Res.40, e16 (2012). CASPubMed Google Scholar
Ginno, P. A., Lim, Y. W., Lott, P. L., Korf, I. & Chedin, F. GC skew at the 5′ and 3 ends of human genes links R-loop formation to epigenetic regulation and transcription termination. Genome Res.23, 1590–1600 (2013). CASPubMedPubMed Central Google Scholar
Ginno, P. A., Lott, P. L., Christensen, H. C., Korf, I. & Chedin, F. R-loop formation is a distinctive characteristic of unmethylated human CpG island promoters. Mol. Cell45, 814–825 (2012). This is the first genome-wide analysis of R-loop locations. It shows that unmethylated human CpG island promoters are characterized by a positive GC skew and by the formation of R loops, which protect fromde novoDNA methylation. CASPubMedPubMed Central Google Scholar
Chan, Y. A. et al. Genome-wide profiling of yeast DNA:RNA hybrid prone sites with DRIP-chip. PLoS Genet.10, e1004288 (2014). PubMedPubMed Central Google Scholar
El Hage, A., Webb, S., Kerr, A. & Tollervey, D. Genome-wide distribution of RNA-DNA hybrids identifies RNase H targets in tRNA genes, retrotransposons and mitochondria. PLoS Genet.10, e1004716 (2014). PubMedPubMed Central Google Scholar
Skourti-Stathaki, K. & Proudfoot, N. J. A double-edged sword: R loops as threats to genome integrity and powerful regulators of gene expression. Genes Dev.28, 1384–1396 (2014). CASPubMedPubMed Central Google Scholar
Cerritelli, S. M. & Crouch, R. J. Ribonuclease H: the enzymes in eukaryotes. FEBS J.276, 1494–1505 (2009). ArticleCASPubMed Google Scholar
Cerritelli, S. M. et al. Failure to produce mitochondrial DNA results in embryonic lethality in Rnaseh1 null mice. Mol. Cell11, 807–815 (2003). CASPubMed Google Scholar
Wahba, L., Amon, J. D., Koshland, D. & Vuica-Ross, M. RNase H and multiple RNA biogenesis factors cooperate to prevent RNA:DNA hybrids from generating genome instability. Mol. Cell44, 978–988 (2011). CASPubMedPubMed Central Google Scholar
Stirling, P. C. et al. R-loop-mediated genome instability in mRNA cleavage and polyadenylation mutants. Genes Dev.26, 163–175 (2012). CASPubMedPubMed Central Google Scholar
Skourti-Stathaki, K., Kamieniarz-Gdula, K. & Proudfoot, N. J. R-loops induce repressive chromatin marks over mammalian gene terminators. Nature516, 436–439 (2014). This paper shows a connection between R loops and chromatin repressive marks in the terminator region of human genes. R loops form at these regions and prime antisense transcription, generating dsRNA that seems to be processed by the RNAi machinery. This event triggers H3K9me2 deposition and heterochromatin formation that facilitates RNA Pol II pausing prior to transcription termination. CASPubMedPubMed Central Google Scholar
Boque-Sastre, R. et al. Head-to-head antisense transcription and R-loop formation promotes transcriptional activation. Proc. Natl Acad. Sci. USA112, 5785–5790 (2015). CASPubMedPubMed Central Google Scholar
Reijns, M. A. et al. Enzymatic removal of ribonucleotides from DNA is essential for mammalian genome integrity and development. Cell149, 1008–1022 (2012). CASPubMedPubMed Central Google Scholar
Hong, X., Cadwell, G. W. & Kogoma, T. Escherichia coli RecG and RecA proteins in R-loop formation. EMBO J.14, 2385–2392 (1995). CASPubMedPubMed Central Google Scholar
Harinarayanan, R. & Gowrishankar, J. Host factor titration by chromosomal R-loops as a mechanism for runaway plasmid replication in transcription termination-defective mutants of Escherichia coli. J. Mol. Biol.332, 31–46 (2003). CASPubMed Google Scholar
Boule, J. B. & Zakian, V. A. The yeast Pif1p DNA helicase preferentially unwinds RNA DNA substrates. Nucleic Acids Res.35, 5809–5818 (2007). CASPubMedPubMed Central Google Scholar
Chakraborty, P. & Grosse, F. Human DHX9 helicase preferentially unwinds RNA-containing displacement loops (R-loops) and G-quadruplexes. DNA Repair (Amst.)10, 654–665 (2011). CAS Google Scholar
Kim, H. D., Choe, J. & Seo, Y. S. The sen1+ gene of Schizosaccharomyces pombe, a homologue of budding yeast SEN1, encodes an RNA and DNA helicase. Biochemistry38, 14697–14710 (1999). CASPubMed Google Scholar
Mischo, H. E. et al. Yeast Sen1 helicase protects the genome from transcription-associated instability. Mol. Cell41, 21–32 (2011). CASPubMedPubMed Central Google Scholar
Becherel, O. J. et al. Senataxin plays an essential role with DNA damage response proteins in meiotic recombination and gene silencing. PLoS Genet.9, e1003435 (2013). CASPubMedPubMed Central Google Scholar
De, I. et al. The RNA helicase Aquarius exhibits structural adaptations mediating its recruitment to spliceosomes. Nat. Struct. Mol. Biol.22, 138–144 (2015). CASPubMed Google Scholar
Sollier, J. et al. Transcription-coupled nucleotide excision repair factors promote R-loop-induced genome instability. Mol. Cell56, 777–785 (2014). This paper provides a mechanism by which R loops accumulated after depletion of human RNA-processing factors such as AQR may be processed into DSBs by the NER nucleases XPG or XPF. Interestingly, this phenomenon seems to be specific to the transcription-coupled NER sub-pathway. CASPubMedPubMed Central Google Scholar
Paulsen, R. D. et al. A genome-wide siRNA screen reveals diverse cellular processes and pathways that mediate genome stability. Mol. Cell35, 228–239 (2009). CASPubMedPubMed Central Google Scholar
Drolet, M. et al. Overexpression of RNase H partially complements the growth defect of an Escherichia coli delta topA mutant: R-loop formation is a major problem in the absence of DNA topoisomerase I. Proc. Natl Acad. Sci. USA92, 3526–3530 (1995). CASPubMedPubMed Central Google Scholar
El Hage, A., French, S. L., Beyer, A. L. & Tollervey, D. Loss of Topoisomerase I leads to R-loop-mediated transcriptional blocks during ribosomal RNA synthesis. Genes Dev.24, 1546–1558 (2010). This work shows that R loops accumulate in the rDNA of yeast Top1 and Top2 mutants and lead to RNA Pol I transcription impairment, truncated rRNA transcripts and reduced rRNA synthesis. In the absence of TOPs, RNase H activity aids in restoring RNA Pol I transcription efficiency. CASPubMedPubMed Central Google Scholar
Stuckey, R., Garcia-Rodriguez, N., Aguilera, A. & Wellinger, R. E. Role for RNA:DNA hybrids in origin-independent replication priming in a eukaryotic system. Proc. Natl Acad. Sci. USA112, 5779–5784 (2015). CASPubMedPubMed Central Google Scholar
Tuduri, S. et al. Topoisomerase I suppresses genomic instability by preventing interference between replication and transcription. Nat. Cell Biol.11, 1315–1324 (2009). This paper shows that TOP1-deficient cells accumulate DNA breaks at transcribed genes all over the genome and have slower replication-fork progression owing to the formation of R loops, suggesting a role for TOP1 in avoiding conflicts between replication and transcription. CASPubMedPubMed Central Google Scholar
Yang, Y. et al. Arginine methylation facilitates the recruitment of TOP3B to chromatin to prevent R loop accumulation. Mol. Cell53, 484–497 (2014). This work shows that human TOP3B reduces both negative supercoiling and R-loop formation by binding to highly transcribed genes through TDRD3, which recognizes histone and RNA Pol II carboxy-terminal domain methylation. Interestingly, TDRD3-deficient cells accumulate R loops at theMYClocus, andTdrd3-null mice show increasedMyc–Ightranslocations, which are common in Burkitt lymphoma. CASPubMedPubMed Central Google Scholar
Wilson-Sali, T. & Hsieh, T. S. Preferential cleavage of plasmid-based R-loops and D-loops by Drosophila topoisomerase IIIβ. Proc. Natl Acad. Sci. USA99, 7974–7979 (2002). CASPubMedPubMed Central Google Scholar
Li, M., Pokharel, S., Wang, J. T., Xu, X. & Liu, Y. RECQ5-dependent SUMOylation of DNA topoisomerase I prevents transcription-associated genome instability. Nat. Commun.6, 6720 (2015). CASPubMed Google Scholar
Castellano-Pozo, M., Garcia-Muse, T. & Aguilera, A. R-loops cause replication impairment and genome instability during meiosis. EMBO Rep.13, 923–929 (2012). CASPubMedPubMed Central Google Scholar
Dominguez-Sanchez, M. S., Barroso, S., Gomez-Gonzalez, B., Luna, R. & Aguilera, A. Genome instability and transcription elongation impairment in human cells depleted of THO/TREX. PLoS Genet.7, e1002386 (2011). CASPubMedPubMed Central Google Scholar
Li, X., Niu, T. & Manley, J. L. The RNA binding protein RNPS1 alleviates ASF/SF2 depletion-induced genomic instability. RNA13, 2108–2115 (2007). CASPubMedPubMed Central Google Scholar
Jimeno, S., Luna, R., Garcia-Rubio, M. & Aguilera, A. Tho1, a novel hnRNP, and Sub2 provide alternative pathways for mRNP biogenesis in yeast THO mutants. Mol. Cell. Biol.26, 4387–4398 (2006). CASPubMedPubMed Central Google Scholar
Wan, Y. et al. Splicing function of mitotic regulators links R-loop-mediated DNA damage to tumor cell killing. J. Cell Biol.209, 235–246 (2015). CASPubMedPubMed Central Google Scholar
Salvi, J. S. et al. Roles for Pbp1 and caloric restriction in genome and lifespan maintenance via suppression of RNA-DNA hybrids. Dev. Cell30, 177–191 (2014). CASPubMed Google Scholar
Gavalda, S., Gallardo, M., Luna, R. & Aguilera, A. R-loop mediated transcription-associated recombination in trf4Δ mutants reveals new links between RNA surveillance and genome integrity. PLoS ONE8, e65541 (2013). CASPubMedPubMed Central Google Scholar
Pefanis, E. et al. RNA exosome-regulated long non-coding RNA transcription controls super-enhancer activity. Cell161, 774–789 (2015). CASPubMedPubMed Central Google Scholar
Sun, Q., Csorba, T., Skourti-Stathaki, K., Proudfoot, N. J. & Dean, C. R-loop stabilization represses antisense transcription at the Arabidopsis FLC locus. Science340, 619–621 (2013). CASPubMedPubMed Central Google Scholar
Kawauchi, J., Mischo, H., Braglia, P., Rondon, A. & Proudfoot, N. J. Budding yeast RNA polymerases I and II employ parallel mechanisms of transcriptional termination. Genes Dev.22, 1082–1092 (2008). CASPubMedPubMed Central Google Scholar
Grzechnik, P., Gdula, M. R. & Proudfoot, N. J. Pcf11 orchestrates transcription termination pathways in yeast. Genes Dev.29, 849–861 (2015). CASPubMedPubMed Central Google Scholar
Porrua, O. & Libri, D. A bacterial-like mechanism for transcription termination by the Sen1p helicase in budding yeast. Nat. Struct. Mol. Biol.20, 884–891 (2013). CASPubMed Google Scholar
Yuce, O. & West, S. C. Senataxin, defective in the neurodegenerative disorder ataxia with oculomotor apraxia 2, lies at the interface of transcription and the DNA damage response. Mol. Cell. Biol.33, 406–417 (2013). CASPubMedPubMed Central Google Scholar
Morales, J. C. et al. Kub5-Hera, the human Rtt103 homolog, plays dual functional roles in transcription termination and DNA repair. Nucleic Acids Res.42, 4996–5006 (2014). CASPubMedPubMed Central Google Scholar
Huang, H. S. et al. Topoisomerase inhibitors unsilence the dormant allele of Ube3a in neurons. Nature481, 185–189 (2012). CAS Google Scholar
Powell, W. T. et al. R-loop formation at Snord116 mediates topotecan inhibition of Ube3a-antisense and allele-specific chromatin decondensation. Proc. Natl Acad. Sci. USA110, 13938–13943 (2013). CASPubMedPubMed Central Google Scholar
Lindahl, T. Instability and decay of the primary structure of DNA. Nature362, 709–715 (1993). CASPubMed Google Scholar
Polak, P. & Arndt, P. F. Transcription induces strand-specific mutations at the 5′ end of human genes. Genome Res.18, 1216–1223 (2008). CASPubMedPubMed Central Google Scholar
Chaudhuri, J. & Alt, F. W. Class-switch recombination: interplay of transcription, DNA deamination and DNA repair. Nat. Rev. Immunol.4, 541–552 (2004). CASPubMed Google Scholar
Meng, F. L. et al. Convergent transcription at intragenic super-enhancers targets AID-initiated genomic instability. Cell159, 1538–1548 (2014). CASPubMedPubMed Central Google Scholar
Qian, J. et al. B cell super-enhancers and regulatory clusters recruit AID tumorigenic activity. Cell159, 1524–1537 (2014). CASPubMedPubMed Central Google Scholar
Gómez-González, B. & Aguilera, A. Activation-induced cytidine deaminase action is strongly stimulated by mutations of the THO complex. Proc. Natl Acad. Sci. USA104, 8409–8414 (2007). PubMedPubMed Central Google Scholar
Kogoma, T. Stable DNA replication: interplay between DNA replication, homologous recombination, and transcription. Microbiol. Mol. Biol. Rev.61, 212–238 (1997). CASPubMedPubMed Central Google Scholar
Ponder, R. G., Fonville, N. C. & Rosenberg, S. M. A switch from high-fidelity to error-prone DNA double-strand break repair underlies stress-induced mutation. Mol. Cell19, 791–804 (2005). CASPubMed Google Scholar
Wimberly, H. et al. R-loops and nicks initiate DNA breakage and genome instability in non-growing Escherichia coli. Nat. Commun.4, 2115 (2013). PubMed Google Scholar
Aguilera, A. & García-Muse, T. Causes of genome instability. Annu. Rev. Genet.47, 1–32 (2013). CASPubMed Google Scholar
Boubakri, H., de Septenville, A. L., Viguera, E. & Michel, B. The helicases DinG, Rep and UvrD cooperate to promote replication across transcription units in vivo. EMBO J.29, 145–157 (2010). CASPubMed Google Scholar
Gan, W. et al. R-loop-mediated genomic instability is caused by impairment of replication fork progression. Genes Dev.25, 2041–2056 (2011). CASPubMedPubMed Central Google Scholar
Wellinger, R. E., Prado, F. & Aguilera, A. Replication fork progression is impaired by transcription in hyperrecombinant yeast cells lacking a functional THO complex. Mol. Cell. Biol.26, 3327–3334 (2006). CASPubMedPubMed Central Google Scholar
Gómez-González, B. et al. Genome-wide function of THO/TREX in active genes prevents R-loop-dependent replication obstacles. EMBO J.30, 3106–3119 (2011). PubMedPubMed Central Google Scholar
Santos-Pereira, J. M. et al. The Npl3 hnRNP prevents R-loop-mediated transcription-replication conflicts and genome instability. Genes Dev.27, 2445–2458 (2013). CASPubMedPubMed Central Google Scholar
Alzu, A. et al. Senataxin associates with replication forks to protect fork integrity across RNA-polymerase-II-transcribed genes. Cell151, 835–846 (2012). This article provides genome-wide evidence that Sen1 (the yeast orthologue of the mammalian RNA–DNA helicase senataxin) accumulates with replication forks at transcribed genes, suggesting that Sen1 protects forks from the formation of recombinogenic damage that can activate the DNA damage checkpoint. CASPubMedPubMed Central Google Scholar
Helmrich, A., Ballarino, M. & Tora, L. Collisions between replication and transcription complexes cause common fragile site instability at the longest human genes. Mol. Cell44, 966–977 (2011). In this work, the authors show that the longest human genes take more than a cell cycle to be transcribed and that collision between transcription and replication machineries is inevitable. This leads to hotspots of DNA breaks called common fragile sites, where R loops form and are responsible for the transcription–replication conflicts that generate genome instability. CASPubMed Google Scholar
Róndon, A. G., Jimeno, S., García-Rubio, M. & Aguilera, A. Molecular evidence that the eukaryotic THO/TREX complex is required for efficient transcription elongation. J. Biol. Chem.278, 39037–39043 (2003). PubMed Google Scholar
Dutta, D., Shatalin, K., Epshtein, V., Gottesman, M. E. & Nudler, E. Linking RNA polymerase backtracking to genome instability in E. coli. Cell146, 533–543 (2011). CASPubMedPubMed Central Google Scholar
Tresini, M. et al. The core spliceosome as target and effector of non-canonical ATM signalling. Nature523, 53–58 (2015). CASPubMedPubMed Central Google Scholar
Bhatia, V. et al. BRCA2 prevents R-loop accumulation and associates with TREX-2 mRNA export factor PCID2. Nature511, 362–365 (2014). This paper shows that depletion of BRCA2 leads to genome instability and accumulation of R loops, as detected by the S9.6 antibody, which specifically recognizes these structures, and by an RNase H1 hybrid-binding domain fused to GFP. The manuscript proposes that R loops are a major source of spontaneous replication stress and that BRCA2 and Fanconi anaemia proteins contribute to the elimination of R loops that block replication-fork progression. CASPubMed Google Scholar
Schlacher, K., Wu, H. & Jasin, M. A distinct replication fork protection pathway connects Fanconi anemia tumor suppressors to RAD51-BRCA1/2. Cancer Cell22, 106–116 (2012). CASPubMedPubMed Central Google Scholar
Britton, S. et al. DNA damage triggers SAF-A and RNA biogenesis factors exclusion from chromatin coupled to R-loops removal. Nucleic Acids Res.42, 9047–9062 (2014). CASPubMedPubMed Central Google Scholar
Luke, B. et al. The Rat1p 5′ to 3′ exonuclease degrades telomeric repeat-containing RNA and promotes telomere elongation in Saccharomyces cerevisiae. Mol. Cell32, 465–477 (2008). CASPubMed Google Scholar
Balk, B. et al. Telomeric RNA-DNA hybrids affect telomere-length dynamics and senescence. Nat. Struct. Mol. Biol.20, 1199–1205 (2013). CASPubMed Google Scholar
Pfeiffer, V., Crittin, J., Grolimund, L. & Lingner, J. The THO complex component Thp2 counteracts telomeric R-loops and telomere shortening. EMBO J.32, 2861–2871 (2013). CASPubMedPubMed Central Google Scholar
Yu, T. Y., Kao, Y. W. & Lin, J. J. Telomeric transcripts stimulate telomere recombination to suppress senescence in cells lacking telomerase. Proc. Natl Acad. Sci. USA111, 3377–3382 (2014). CASPubMedPubMed Central Google Scholar
Arora, R. et al. RNaseH1 regulates TERRA- telomeric DNA hybrids and telomere maintenance in ALT tumour cells. Nat. Commun.5, 5220 (2014).
Nakama, M., Kawakami, K., Kajitani, T., Urano, T. & Murakami, Y. DNA–RNA hybrid formation mediates RNAi-directed heterochromatin formation. Genes Cells17, 218–233 (2012). CASPubMed Google Scholar
Hsu, J. Y. et al. Mitotic phosphorylation of histone H3 is governed by Ipl1/aurora kinase and Glc7/PP1 phosphatase in budding yeast and nematodes. Cell102, 279–291 (2000). CASPubMed Google Scholar
Ivaldi, M. S., Karam, C. S. & Corces, V. G. Phosphorylation of histone H3 at Ser10 facilitates RNA polymerase II release from promoter-proximal pausing in Drosophila. Genes Dev.21, 2818–2831 (2007). CASPubMedPubMed Central Google Scholar
Zippo, A., De Robertis, A., Serafini, R. & Oliviero, S. PIM1-dependent phosphorylation of histone H3 at serine 10 is required for MYC-dependent transcriptional activation and oncogenic transformation. Nat. Cell Biol.9, 932–944 (2007). CASPubMed Google Scholar
El Achkar, E., Gerbault-Seureau, M., Muleris, M., Dutrillaux, B. & Debatisse, M. Premature condensation induces breaks at the interface of early and late replicating chromosome bands bearing common fragile sites. Proc. Natl Acad. Sci. USA102, 18069–18074 (2005). CASPubMedPubMed Central Google Scholar
Groh, M., Lufino, M. M., Wade-Martins, R. & Gromak, N. R-loops associated with triplet repeat expansions promote gene silencing in Friedreich ataxia and fragile X syndrome. PLoS Genet.10, e1004318 (2014). These authors used cells from people with FRDA or FXS, diseases that are characterized by the expansion of trinucleotides in theFXNandFMR1genes, respectively. These expansions constitute rare fragile sites, and the article shows that R loops form at these expanded repeats, leading to accumulation of the repressive mark H3K9me2 and consequent gene silencing, which causes the disease. PubMedPubMed Central Google Scholar
Herrera-Moyano, E., Mergui, X., Garcia-Rubio, M. L., Barroso, S. & Aguilera, A. The yeast and human FACT chromatin-reorganizing complexes solve R-loop-mediated transcription-replication conflicts. Genes Dev.28, 735–748 (2014). CASPubMedPubMed Central Google Scholar
Hatchi, E. et al. BRCA1 recruitment to transcriptional pause sites is required for R-loop-driven DNA damage repair. Mol. Cell57, 636–647 (2015). This work suggests a cooperation between the human DNA repair factor BRCA1 and the RNA–DNA helicase SETX at transcription-termination regions to prevent R-loop formation, as depletion of either factor leads to increased levels of R loops. Interestingly, BRCA1 and SETX physically interact, and SETX binding to termination regions is BRCA1-dependent. BRCA1 binds genome-wide to termination regions of R-loop-accumulating genes, where BRCA1-deficient tumours show increased insertions and deletions. CASPubMedPubMed Central Google Scholar
Lin, Y., Dent, S. Y., Wilson, J. H., Wells, R. D. & Napierala, M. R loops stimulate genetic instability of CTG. CAG repeats. Proc. Natl Acad. Sci. USA107, 692–697 (2010). CASPubMed Google Scholar
Reddy, K. et al. Determinants of R-loop formation at convergent bidirectionally transcribed trinucleotide repeats. Nucleic Acids Res.39, 1749–1762 (2011). CASPubMed Google Scholar
Grabczyk, E., Mancuso, M. & Sammarco, M. C. A persistent RNA•DNA hybrid formed by transcription of the Friedreich ataxia triplet repeat in live bacteria, and by T7 RNAP in vitro. Nucleic Acids Res.35, 5351–5359 (2007). CASPubMedPubMed Central Google Scholar
Loomis, E. W., Sanz, L. A., Chedin, F. & Hagerman, P. J. Transcription-associated R-loop formation across the human FMR1 CGG-repeat region. PLoS Genet.10, e1004294 (2014). PubMedPubMed Central Google Scholar
Colak, D. et al. Promoter-bound trinucleotide repeat mRNA drives epigenetic silencing in fragile X syndrome. Science343, 1002–1005 (2014). CASPubMedPubMed Central Google Scholar
Haeusler, A. R. et al. C9orf72 nucleotide repeat structures initiate molecular cascades of disease. Nature507, 195–200 (2014). CASPubMedPubMed Central Google Scholar
Moreira, M. C. et al. Senataxin, the ortholog of a yeast RNA helicase, is mutant in ataxia- ocular apraxia 2. Nat. Genet.36, 225–227 (2004). CASPubMed Google Scholar
Chen, Y. Z. et al. DNA/RNA helicase gene mutations in a form of juvenile amyotrophic lateral sclerosis (ALS4). Am. J. Hum. Genet.74, 1128–1135 (2004). CASPubMedPubMed Central Google Scholar
Vantaggiato, C. et al. Senataxin modulates neurite growth through fibroblast growth factor 8 signalling. Brain134, 1808–1828 (2011). PubMed Google Scholar
Yeo, A. J. et al. R-loops in proliferating cells but not in the brain: implications for AOA2 and other autosomal recessive ataxias. PLoS ONE9, e90219 (2014). PubMedPubMed Central Google Scholar
Negrini, S., Gorgoulis, V. G. & Halazonetis, T. D. Genomic instability — an evolving hallmark of cancer. Nat. Rev. Mol. Cell Biol.11, 220–228 (2010). CASPubMed Google Scholar
Gaillard, H., Garcia-Muse, T. & Aguilera, A. Replication stress and cancer. Nat. Rev. Cancer15, 276–289 (2015). CASPubMed Google Scholar
Hill, S. J. et al. Systematic screening reveals a role for BRCA1 in the response to transcription-associated DNA damage. Genes Dev.28, 1957–1975 (2014). CASPubMedPubMed Central Google Scholar
Ramiro, A. R. et al. AID is required for c-myc/IgH chromosome translocations in vivo. Cell118, 431–438 (2004). CASPubMed Google Scholar
Ruiz, J. F., Gómez-González, B. & Aguilera, A. AID induces double-strand breaks at immunoglobulin switch regions and c-MYC causing chromosomal translocations in yeast THO mutants. PLoS Genet.7, e1002009 (2011). CASPubMedPubMed Central Google Scholar
Chernikova, S. B. et al. Deficiency in mammalian histone H2B ubiquitin ligase Bre1 (Rnf20/Rnf40) leads to replication stress and chromosomal instability. Cancer Res.72, 2111–2119 (2012). CASPubMedPubMed Central Google Scholar
Fregoso, O. I., Das, S., Akerman, M. & Krainer, A. R. Splicing-factor oncoprotein SRSF1 stabilizes p53 via RPL5 and induces cellular senescence. Mol. Cell50, 56–66 (2013). CASPubMedPubMed Central Google Scholar
Jackson, B. R., Noerenberg, M. & Whitehouse, A. A novel mechanism inducing genome instability in Kaposi's sarcoma-associated herpesvirus infected cells. PLoS Pathog.10, e1004098 (2014).
Huang, F. T. et al. Sequence dependence of chromosomal R-loops at the immunoglobulin heavy-chain Smu class switch region. Mol. Cell. Biol.27, 5921–5932 (2007). CASPubMedPubMed Central Google Scholar
Huang, F. T., Yu, K., Hsieh, C. L. & Lieber, M. R. Downstream boundary of chromosomal R-loops at murine switch regions: implications for the mechanism of class switch recombination. Proc. Natl Acad. Sci. USA103, 5030–5035 (2006). CASPubMedPubMed Central Google Scholar
Kao, Y. P. et al. Detection and characterization of R-loops at the murine immunoglobulin Sα region. Mol. Immunol.54, 208–216 (2013). CASPubMed Google Scholar
Yu, K., Chedin, F., Hsieh, C. L., Wilson, T. E. & Lieber, M. R. R-loops at immunoglobulin class switch regions in the chromosomes of stimulated B cells. Nat. Immunol.4, 442–451 (2003). CASPubMed Google Scholar
Reaban, M. E. & Griffin, J. A. Induction of RNA-stabilized DNA conformers by transcription of an immunoglobulin switch region. Nature348, 342–344 (1990). CASPubMed Google Scholar
Muramatsu, M. et al. Class switch recombination and hypermutation require activation-induced cytidine deaminase (AID), a potential RNA editing enzyme. Cell102, 553–563 (2000). CASPubMed Google Scholar
Revy, P. et al. Activation-induced cytidine deaminase (AID) deficiency causes the autosomal recessive form of the Hyper-IgM syndrome (HIGM2). Cell102, 565–575 (2000). CASPubMed Google Scholar
Chaudhuri, J. et al. Transcription-targeted DNA deamination by the AID antibody diversification enzyme. Nature422, 726–730 (2003). CASPubMed Google Scholar
Zheng, S. et al. Non-coding RNA generated following lariat debranching mediates targeting of AID to DNA. Cell161, 762–773 (2015). CASPubMedPubMed Central Google Scholar
Pefanis, E. et al. Noncoding RNA transcription targets AID to divergently transcribed loci in B cells. Nature514, 389–393 (2014). CASPubMedPubMed Central Google Scholar
Zhang, Z. Z. et al. The strength of an Ig switch region is determined by its ability to drive R loop formation and its number of WGCW sites. Cell Rep.8, 557–569 (2014). CASPubMedPubMed Central Google Scholar
Boguslawski, S. J. et al. Characterization of monoclonal antibody to DNA•RNA and its application to immunodetection of hybrids. J. Immunol. Methods89, 123–130 (1986). CASPubMed Google Scholar
Zhang, Z. Z., Pannunzio, N. R., Hsieh, C. L., Yu, K. & Lieber, M. R. Complexities due to single-stranded RNA during antibody detection of genomic rna:dna hybrids. BMC Res. Notes8, 127 (2015). PubMedPubMed Central Google Scholar
Jenjaroenpun, P., Wongsurawat, T., Yenamandra, S. P. & Kuznetsov, V. A. QmRLFS-finder: a model, web server and stand-alone tool for prediction and analysis of R-loop forming sequences. Nucleic Acids Res.43, W527–W534 (2015). CASPubMedPubMed Central Google Scholar
Leela, J. K., Syeda, A. H., Anupama, K. & Gowrishankar, J. Rho-dependent transcription termination is essential to prevent excessive genome-wide R-loops in Escherichia coli. Proc. Natl Acad. Sci. USA110, 258–263 (2013). CASPubMed Google Scholar
Wahba, L., Gore, S. K. & Koshland, D. The homologous recombination machinery modulates the formation of RNA•DNA hybrids and associated chromosome instability. eLife2, e00505 (2013). PubMedPubMed Central Google Scholar