Regulatory feedback from nascent RNA to chromatin and transcription (original) (raw)
Peterlin, B. M. & Price, D. H. Controlling the elongation phase of transcription with P-TEFb. Mol. Cell23, 297–305 (2006). ArticleCASPubMed Google Scholar
Rinn, J. L. et al. Functional demarcation of active and silent chromatin domains in human HOX loci by noncoding RNAs. Cell129, 1311–1323 (2007). ArticleCASPubMedPubMed Central Google Scholar
Zhao, J., Sun, B. K., Erwin, J. A., Song, J. J. & Lee, J. T. Polycomb proteins targeted by a short repeat RNA to the mouse X chromosome. Science322, 750–756 (2008). ArticleCASPubMedPubMed Central Google Scholar
Pandey, R. R. et al. Kcnq1ot1 antisense noncoding RNA mediates lineage-specific transcriptional silencing through chromatin-level regulation. Mol. Cell32, 232–246 (2008). ArticleCASPubMed Google Scholar
Rinn, J. L. & Chang, H. Y. Genome regulation by long noncoding RNAs. Annu. Rev. Biochem.81, 145–166 (2012). CASPubMed Google Scholar
Li, W., Notani, D. & Rosenfeld, M. G. Enhancers as non-coding RNA transcription units: recent insights and future perspectives. Nat. Rev. Genet.17, 207–223 (2016). ArticleCASPubMed Google Scholar
Hendrickson, D. G., Kelley, D. R., Tenen, D., Bernstein, B. & Rinn, J. L. Widespread RNA binding by chromatin-associated proteins. Genome Biol.17, 28 (2016). ArticleCAS Google Scholar
Santos-Pereira, J. M. & Aguilera, A. R loops: new modulators of genome dynamics and function. Nat. Rev. Genet.16, 583–597 (2015). ArticleCASPubMed Google Scholar
Ji, X. et al. SR proteins collaborate with 7SK and promoter-associated nascent RNA to release paused polymerase. Cell153, 855–868 (2013). ArticleCASPubMedPubMed Central Google Scholar
Yamaguchi, Y., Inukai, N., Narita, T., Wada, T. & Handa, H. Evidence that negative elongation factor represses transcription elongation through binding to a DRB sensitivity-inducing factor/RNA polymerase II complex and RNA. Mol. Cell. Biol.22, 2918–2927 (2002). ArticleCASPubMedPubMed Central Google Scholar
Missra, A. & Gilmour, D. S. Interactions between DSIF (DRB sensitivity inducing factor), NELF (negative elongation factor), and the Drosophila RNA polymerase II transcription elongation complex. Proc. Natl Acad. Sci. USA107, 11301–11306 (2010). ArticleCASPubMedPubMed Central Google Scholar
Saldi, T., Cortazar, M. A., Sheridan, R. M. & Bentley, D. L. Coupling of RNA polymerase II transcription elongation with pre-mRNA splicing. J. Mol. Biol.428, 2623–2635 (2016). ArticleCASPubMedPubMed Central Google Scholar
Naftelberg, S., Schor, I. E., Ast, G. & Kornblihtt, A. R. Regulation of alternative splicing through coupling with transcription and chromatin structure. Annu. Rev. Biochem.84, 165–198 (2015). ArticleCASPubMed Google Scholar
Custódio, N. & Carmo-Fonseca, M. Co-transcriptional splicing and the CTD code. Crit. Rev. Biochem. Mol. Biol.51, 395–411 (2016). ArticlePubMedCAS Google Scholar
Alexander, R. D., Innocente, S. A., Barrass, J. D. & Beggs, J. D. Splicing-dependent RNA polymerase pausing in yeast. Mol. Cell40, 582–593 (2010). ArticleCASPubMedPubMed Central Google Scholar
Chathoth, K. T., Barrass, J. D., Webb, S. & Beggs, J. D. A splicing-dependent transcriptional checkpoint associated with prespliceosome formation. Mol. Cell53, 779–790 (2014). ArticleCASPubMedPubMed Central Google Scholar
Jonkers, I., Kwak, H. & Lis, J. T. Genome-wide dynamics of Pol II elongation and its interplay with promoter proximal pausing, chromatin, and exons. eLife3, e02407 (2014). ArticlePubMedPubMed CentralCAS Google Scholar
Veloso, A. et al. Rate of elongation by RNA polymerase II is associated with specific gene features and epigenetic modifications. Genome Res.24, 896–905 (2014). ArticleCASPubMedPubMed Central Google Scholar
Mayer, A. et al. Native elongating transcript sequencing reveals human transcriptional activity at nucleotide resolution. Cell161, 541–554 (2015). ArticleCASPubMedPubMed Central Google Scholar
Kwak, H., Fuda, N. J., Core, L. J. & Lis, J. T. Precise maps of RNA polymerase reveal how promoters direct initiation and pausing. Science339, 950–953 (2013). ArticleCASPubMedPubMed Central Google Scholar
de Almeida, S. F. et al. Splicing enhances recruitment of methyltransferase HYPB/Setd2 and methylation of histone H3 Lys36. Nat. Struct. Mol. Biol.18, 977–983 (2011). ArticlePubMedCAS Google Scholar
Kim, S., Kim, H., Fong, N., Erickson, B. & Bentley, D. L. Pre-mRNA splicing is a determinant of histone H3K36 methylation. Proc. Natl Acad. Sci. USA108, 13564–13569 (2011). ArticleCASPubMedPubMed Central Google Scholar
Convertini, P. et al. Sudemycin E influences alternative splicing and changes chromatin modifications. Nucleic Acids Res.42, 4947–4961 (2014). ArticleCASPubMedPubMed Central Google Scholar
Yuan, W. et al. Heterogeneous nuclear ribonucleoprotein L Is a subunit of human KMT3a/Set2 complex required for H3 Lys-36 trimethylation activity in vivo. J. Biol. Chem.284, 15701–15707 (2009). ArticleCASPubMedPubMed Central Google Scholar
Davidovich, C., Zheng, L., Goodrich, K. J. & Cech, T. R. Promiscuous RNA binding by Polycomb repressive complex 2. Nat. Struct. Mol. Biol.20, 1250–1257 (2013). ArticleCASPubMedPubMed Central Google Scholar
Kaneko, S., Son, J., Shen, S. S., Reinberg, D. & Bonasio, R. PRC2 binds active promoters and contacts nascent RNAs in embryonic stem cells. Nat. Struct. Mol. Biol.20, 1258–1264 (2013). ArticleCASPubMedPubMed Central Google Scholar
Kaneko, S., Son, J., Bonasio, R., Shen, S. S. & Reinberg, D. Nascent RNA interaction keeps PRC2 activity poised and in check. Genes Dev.28, 1983–1988 (2014). ArticleCASPubMedPubMed Central Google Scholar
Riising, E. M. et al. Gene silencing triggers polycomb repressive complex 2 recruitment to CpG islands genome wide. Mol. Cell55, 347–360 (2014). ArticleCASPubMed Google Scholar
Jermann, P., Hoerner, L., Burger, L. & Schubeler, D. Short sequences can efficiently recruit histone H3 lysine 27 trimethylation in the absence of enhancer activity and DNA methylation. Proc. Natl Acad. Sci. USA111, 3415–3421 (2014). ArticleCAS Google Scholar
Cifuentes-Rojas, C., Hernandez, A. J., Sarma, K. & Lee, J. T. Regulatory interactions between RNA and polycomb repressive complex 2. Mol. Cell55, 171–185 (2014). ArticleCASPubMedPubMed Central Google Scholar
Herzog, V. A. et al. A strand-specific switch in noncoding transcription switches the function of a Polycomb/Trithorax response element. Nat. Genet.46, 973–981 (2014). ArticleCASPubMedPubMed Central Google Scholar
Chen, P. B., Chen, H. V., Acharya, D., Rando, O. J. & Fazzio, T. G. R loops regulate promoter-proximal chromatin architecture and cellular differentiation. Nat. Struct. Mol. Biol.22, 999–1007 (2015). ArticleCASPubMedPubMed Central Google Scholar
Wei, C. et al. RBFox2 binds nascent RNA to globally regulate Polycomb complex 2 targeting in mammalian genomes. Mol. Cell62, 875–889 (2016). ArticleCASPubMedPubMed Central Google Scholar
Tilgner, H. et al. Deep sequencing of subcellular RNA fractions shows splicing to be predominantly co-transcriptional in the human genome but inefficient for lncRNAs. Genome Res.22, 1616–1625 (2012). ArticleCASPubMedPubMed Central Google Scholar
Lai, F. et al. Activating RNAs associate with mediator to enhance chromatin architecture and transcription. Nature494, 497–501 (2013). ArticleCASPubMedPubMed Central Google Scholar
Yang, Y. W. et al. Essential role of lncRNA binding for WDR5 maintenance of active chromatin and embryonic stem cell pluripotency. eLife3, e02046 (2014). ArticlePubMedPubMed CentralCAS Google Scholar
Engreitz, J. M. et al. Local regulation of gene expression by lncRNA promoters, transcription and splicing. Nature539, 452–455 (2016). ArticleCASPubMedPubMed Central Google Scholar
Nickerson, J. A., Krochmalnic, G., Wan, K. M. & Penman, S. Chromatin architecture and nuclear RNA. Proc. Natl Acad. Sci. USA86, 177–181 (1989). ArticleCASPubMedPubMed Central Google Scholar
Hall, L. L. et al. Stable CoT-1 repeat RNA is abundant and associated with euchromatic interphase chromosomes. Cell156, 907–919 (2014). ArticleCASPubMedPubMed Central Google Scholar
Cerase, A., Pintacuda, G., Tattermusch, A. & Avner, P. Xist localization and function: new insights from multiple levels. Genome Biol.16, 166 (2015). ArticlePubMedPubMed CentralCAS Google Scholar
Phillips-Cremins, J. E. et al. Architectural protein subclasses shape 3D organization of genomes during lineage commitment. Cell153, 1281–1295 (2013). ArticleCASPubMedPubMed Central Google Scholar
Saldaña-Meyer, R. et al. CTCF regulates the human p53 gene through direct interaction with its natural antisense transcript, Wrap53. Genes Dev.28, 723–734 (2014). ArticlePubMedPubMed CentralCAS Google Scholar
Shevtsov, S. P. & Dundr, M. Nucleation of nuclear bodies by RNA. Nat. Cell Biol.13, 167–173 (2011). ArticleCASPubMed Google Scholar
Ulveling, D., Francastel, C. & Hubé, F. When one is better than two: RNA with dual functions. Biochimie93, 633–644 (2011). ArticleCASPubMed Google Scholar
Kole, R., Krainer, A. R. & Altman, S. RNA therapeutics: beyond RNA interference and antisense oligonucleotides. Nat. Rev. Drug Discov.11, 125–140 (2012). ArticleCASPubMedPubMed Central Google Scholar
Shechner, D. M., Hacisuleyman, E., Younger, S. T. & Rinn, J. L. Multiplexable, locus-specific targeting of long RNAs with CRISPR-Display. Nat. Methods12, 664–670 (2015). ArticleCASPubMedPubMed Central Google Scholar
Frye, M., Jaffrey, S. R., Pan, T., Rechavi, G. & Suzuki, T. RNA modifications: what have we learned and where are we headed? Nat. Rev. Genet.17, 365–372 (2016). ArticleCASPubMed 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). ArticleCASPubMedPubMed Central Google Scholar
Ginno, P. A., Lim, Y. W., Lott, P. L., Korf, I. & Chédin, 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). ArticleCASPubMedPubMed 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). ArticleCASPubMedPubMed 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). ArticleCASPubMed Google Scholar
Ginno, P. A., Lott, P. L., Christensen, H. C., Korf, I. & Chédin, F. R-Loop formation is a distinctive characteristic of unmethylated human CpG island promoters. Mol. Cell45, 814–825 (2012). ArticleCASPubMedPubMed 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). ArticleCASPubMedPubMed Central Google Scholar
Sanz, L. et al. Prevalent, dynamic, and conserved R-loop structures associate with specific epigenomic signatures in mammals. Mol. Cell63, 167–178 (2016). ArticleCASPubMedPubMed Central Google Scholar
Zhao, D. Y. et al. SMN and symmetric arginine dimethylation of RNA polymerase II C-terminal domain control termination. Nature529, 48–53 (2016). ArticlePubMedCAS 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). ArticleCASPubMedPubMed Central Google Scholar