Regulation of gene expression by cis-acting long non-coding RNAs

Article metrics

Abstract

Long non-coding RNAs (lncRNAs) are diverse transcription products emanating from thousands of loci in mammalian genomes. Cis-acting lncRNAs, which constitute a substantial fraction of lncRNAs with an attributed function, regulate gene expression in a manner dependent on the location of their own sites of transcription, at varying distances from their targets in the linear genome. Through various mechanisms, cis-acting lncRNAs have been demonstrated to activate, repress or otherwise modulate the expression of target genes. We discuss the activities that have been ascribed to cis-acting lncRNAs, the evidence and hypotheses regarding their modes of action, and the methodological advances that enable their identification and characterization. The emerging principles highlight lncRNAs as transcriptional units highly adept at contributing to gene regulatory networks and to the generation of fine-tuned spatial and temporal gene expression programmes.

Access options

Rent or Buy article

Get time limited or full article access on ReadCube.

from$8.99

All prices are NET prices.

Fig. 1: Genomic locations and prevalence of cis-acting long non-coding RNAs.
Fig. 2: Mechanisms of action of activating cis-acting long non-coding RNAs.
Fig. 3: Functions of repressive cis-acting long non-coding RNAs.
Fig. 4: Plausible functions of cis-acting long non-coding RNAs.
Fig. 5: Methods for mapping functional features in cis-acting long non-coding RNAs.

References

  1. 1.

    Guttman, M. et al. Chromatin signature reveals over a thousand highly conserved large non-coding RNAs in mammals. Nature 458, 223–227 (2009).

  2. 2.

    Mercer, T. R. et al. Targeted RNA sequencing reveals the deep complexity of the human transcriptome. Nat. Biotechnol. 30, 99–104 (2011).

  3. 3.

    Carninci, P. et al. The transcriptional landscape of the mammalian genome. Science 309, 1559–1563 (2005).

  4. 4.

    Samata, M. & Akhtar, A. Dosage compensation of the X chromosome: a complex epigenetic assignment involving chromatin regulators and long noncoding RNAs. Annu. Rev. Biochem. 87, 323–350 (2018).

  5. 5.

    Sherstyuk, V. V., Medvedev, S. P. & Zakian, S. M. Noncoding RNAs in the regulation of pluripotency and reprogramming. Stem Cell Rev. 14, 58–70 (2018).

  6. 6.

    Quinodoz, S. & Guttman, M. Long noncoding RNAs: an emerging link between gene regulation and nuclear organization. Trends Cell Biol. 24, 651–663 (2014).

  7. 7.

    Lin, C. & Yang, L. Long noncoding RNA in cancer: wiring signaling circuitry. Trends Cell Biol. 28, 287–301 (2018).

  8. 8.

    Scheuermann, J. C. & Boyer, L. A. Getting to the heart of the matter: long non-coding RNAs in cardiac development and disease. EMBO J. 32, 1805–1816 (2013).

  9. 9.

    Guo, J., Liu, Z. & Gong, R. Long noncoding RNA: an emerging player in diabetes and diabetic kidney disease. Clin. Sci. 133, 1321–1339 (2019).

  10. 10.

    Zuckerman, B. & Ulitsky, I. Predictive models of subcellular localization of long RNAs. RNA 25, 557–572 (2019).

  11. 11.

    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).

  12. 12.

    Melé, M. et al. Chromatin environment, transcriptional regulation, and splicing distinguish lincRNAs and mRNAs. Genome Res. 27, 27–37 (2017).

  13. 13.

    Hezroni, H. et al. Principles of long noncoding RNA evolution derived from direct comparison of transcriptomes in 17 species. Cell Rep. 11, 1110–1122 (2015).

  14. 14.

    Tichon, A. et al. A conserved abundant cytoplasmic long noncoding RNA modulates repression by Pumilio proteins in human cells. Nat. Commun. 7, 12209 (2016).

  15. 15.

    Lee, S. et al. Noncoding RNA NORAD regulates genomic stability by sequestering PUMILIO proteins. Cell 164, 69–80 (2016).

  16. 16.

    Musgrove, C., Jansson, L. I. & Stone, M. D. New perspectives on telomerase RNA structure and function. WIREs RNA9, e1456 (2018).

  17. 17.

    Vendramin, R. et al. SAMMSON fosters cancer cell fitness by concertedly enhancing mitochondrial and cytosolic translation. Nat. Struct. Mol. Biol. 25, 1035–1046 (2018).

  18. 18.

    Grote, P. et al. The tissue-specific lncRNA Fendrr is an essential regulator of heart and body wall development in the mouse. Dev. Cell 24, 206–214 (2013).

  19. 19.

    Huarte, M. et al. A large intergenic noncoding RNA induced by p53 mediates global gene repression in the p53 response. Cell 142, 409–419 (2010).

  20. 20.

    Andersen, R. E. et al. The long noncoding RNA Pnky is a trans-acting regulator of cortical development in vivo. Dev. Cell 49, 632–642.e7 (2019).

  21. 21.

    Werner, M. S. & Ruthenburg, A. J. Nuclear fractionation reveals thousands of chromatin-tethered noncoding RNAs adjacent to active genes. Cell Rep. 12, 1089–1098 (2015). This study uses nuclear fractionations to show that the majority of lncRNAs, including many previously unannotated intergenic transcripts, are enriched in the chromatin fraction. These chromatin-enriched lncRNAs are dependent on Pol II elongation for their association with chromatin.

  22. 22.

    Derrien, T. et al. The GENCODE v7 catalog of human long noncoding RNAs: analysis of their gene structure, evolution, and expression. Genome Res. 22, 1775–1789 (2012).

  23. 23.

    Pauli, A. et al. Systematic identification of long noncoding RNAs expressed during zebrafish embryogenesis. Genome Res. 22, 577–591 (2012).

  24. 24.

    Ulitsky, I. Evolution to the rescue: using comparative genomics to understand long non-coding RNAs. Nat. Rev. Genet. 17, 601–614 (2016).

  25. 25.

    Hacisuleyman, E. et al. Topological organization of multichromosomal regions by the long intergenic noncoding RNA Firre. Nat. Struct. Mol. Biol. 21, 198–206 (2014).

  26. 26.

    Lewandowski, J. P. et al. The Firre locus produces a trans-acting RNA molecule that functions in hematopoiesis. Preprint at bioRxiv https://doi.org/10.1101/648279 (2019).

  27. 27.

    Clemson, C. M. et al. An architectural role for a nuclear noncoding RNA: NEAT1 RNA is essential for the structure of paraspeckles. Mol. Cell 33, 717–726 (2009).

  28. 28.

    Naganuma, T. et al. Alternative 3′-end processing of long noncoding RNA initiates construction of nuclear paraspeckles. EMBO J. 31, 4020–4034 (2012).

  29. 29.

    Rom, A. et al. Regulation of CHD2 expression by the Chaserr long noncoding RNA is essential for viability. Nat. Commun. 10, 5092 (2019).

  30. 30.

    Isoda, T. et al. Non-coding transcription instructs chromatin folding and compartmentalization to dictate enhancer–promoter communication and T cell fate. Cell 171, 103–119.e18 (2017). This study characterizes the enhancer-transcribed ThymoD lncRNA, whose transcription promotes the activity of the underlying enhancer through repositioning it away from the nuclear periphery, demonstrating the interdependence between (lncRNA) transcription, nuclear positioning and enhancer activity.

  31. 31.

    Perry, R. B., Hezroni, H., Goldrich, M. J. & Ulitsky, I. Regulation of neuroregeneration by long noncoding RNAs. Mol. Cell 72, 553–567 (2018).

  32. 32.

    Kotzin, J. J. et al. The long non-coding RNA Morrbid regulates Bim and short-lived myeloid cell lifespan. Nature 537, 239–243 (2016).

  33. 33.

    Engreitz, J. M. et al. Local regulation of gene expression by lncRNA promoters, transcription and splicing. Nature 539, 452–455 (2016). This study demonstrates that promoters of some lncRNAs, but also of some mRNAs, affect the expression of neighbouring genes, emphasizing that studies of the functions of cis-acting lncRNAs are also applicable to other transcriptional units.

  34. 34.

    VučiĆeviĆ, D., Corradin, O., Ntini, E., Scacheri, P. C. & Ørom, U. A. Long ncRNA expression associates with tissue-specific enhancers. Cell Cycle 14, 253–260 (2015).

  35. 35.

    De Santa, F. et al. A large fraction of extragenic RNA pol II transcription sites overlap enhancers. PLOS Biol. 8, e1000384 (2010).

  36. 36.

    Marques, A. C. et al. Chromatin signatures at transcriptional start sites separate two equally populated yet distinct classes of intergenic long noncoding RNAs. Genome Biol. 14, R131 (2013). Through analysis of chromatin modifications at regions of transcription initiation, this study notes two distinct classes of intergenic lncRNAs, one with characteristics of enhancers and one with characteristics of promoters.

  37. 37.

    Ernst, J. & Kellis, M. Chromatin-state discovery and genome annotation with ChromHMM. Nat. Protoc. 12, 2478–2492 (2017).

  38. 38.

    Gil, N. & Ulitsky, I. Production of spliced long noncoding RNAs specifies regions with increased enhancer activity. Cell Syst. 7, 537–547.e3 (2018).

  39. 39.

    Ulitsky, I., Shkumatava, A., Jan, C. H., Sive, H. & Bartel, D. P. Conserved function of lincRNAs in vertebrate embryonic development despite rapid sequence evolution. Cell 147, 1537–1550 (2011).

  40. 40.

    Wamstad, J. A. et al. Dynamic and coordinated epigenetic regulation of developmental transitions in the cardiac lineage. Cell 151, 206–220 (2012).

  41. 41.

    Ponjavic, J., Oliver, P. L., Lunter, G. & Ponting, C. P. Genomic and transcriptional co-localization of protein-coding and long non-coding RNA pairs in the developing brain. PLOS Genet. 5, e1000617 (2009).

  42. 42.

    Schwanhausser, B. et al. Global quantification of mammalian gene expression control. Nature 473, 337–342 (2011).

  43. 43.

    Kutter, C. et al. Rapid turnover of long noncoding RNAs and the evolution of gene expression. PLOS Genet. 8, e1002841 (2012).

  44. 44.

    Werner, M. S. et al. Chromatin-enriched lncRNAs can act as cell-type specific activators of proximal gene transcription. Nat. Struct. Mol. Biol. 24, 596–603 (2017).

  45. 45.

    Engreitz, J. M. et al. The Xist lncRNA exploits three-dimensional genome architecture to spread across the X chromosome. Science 341, 1237973 (2013).

  46. 46.

    Schertzer, M. D. et al. lncRNA-induced spread of polycomb controlled by genome architecture, RNA abundance, and CpG island DNA. Mol. Cell 75, 523–537.e10 (2019).

  47. 47.

    Ballarino, M. et al. Deficiency in the nuclear long noncoding RNA causes myogenic defects and heart remodeling in mice. EMBO J. 37, e99697 (2018).

  48. 48.

    Groff, A. F., Barutcu, A. R., Lewandowski, J. P. & Rinn, J. L. Enhancers in the Peril lincRNA locus regulate distant but not local genes. Genome Biol. 19, 219 (2018).

  49. 49.

    Amaral, P. P. et al. Genomic positional conservation identifies topological anchor point RNAs linked to developmental loci. Genome Biol. 19, 32 (2018).

  50. 50.

    Tan, J. Y. et al. Cis-acting complex-trait-associated lincRNA expression correlates with modulation of chromosomal architecture. Cell Rep. 18, 2280–2288 (2017).

  51. 51.

    Rinn, J. L. & Chang, H. Y. Genome regulation by long noncoding RNAs. Annu. Rev. Biochem. 81, 145–166 (2012).

  52. 52.

    Ma, L., Bajic, V. B. & Zhang, Z. On the classification of long non-coding RNAs. RNA Biol. 10, 925–933 (2013).

  53. 53.

    Fanucchi, S. et al. Immune genes are primed for robust transcription by proximal long noncoding RNAs located in nuclear compartments. Nat. Genet. 51, 138–150 (2019). This article presents a well-studied example of a lncRNA that activates expression of its target gene through recruitment of activating factors — in this case, the WDR5–MLL complex — to the target promoter, utilizing pre-existing spatial proximity.

  54. 54.

    Xiang, J.-F. et al. Human colorectal cancer-specific CCAT1-L lncRNA regulates long-range chromatin interactions at the MYC locus. Cell Res. 24, 513–531 (2014). This work is one of the first examples of an enhancer-transcribed lncRNA that affects the expression of its target gene through promoting the formation of enhancer–promoter chromatin loops, in this case through recruitment of CTCF.

  55. 55.

    Sleutels, F., Zwart, R. & Barlow, D. P. The non-coding Air RNA is required for silencing autosomal imprinted genes. Nature 415, 810–813 (2002).

  56. 56.

    Kherdjemil, Y. et al. Evolution of Hoxa11 regulation in vertebrates is linked to the pentadactyl state. Nature 539, 89–92 (2016).

  57. 57.

    Pandey, R. R. et al. Kcnq1ot1 antisense noncoding RNA mediates lineage-specific transcriptional silencing through chromatin-level regulation. Mol. Cell 32, 232–246 (2008).

  58. 58.

    Tahira, A. C. et al. Long noncoding intronic RNAs are differentially expressed in primary and metastatic pancreatic cancer. Mol. Cancer 10, 141 (2011).

  59. 59.

    Anderson, K. M. et al. Transcription of the non-coding RNA upperhand controls Hand2 expression and heart development. Nature 539, 433–436 (2016).

  60. 60.

    Frank, S. et al. yylncT defines a class of divergently transcribed lncRNAs and safeguards the T-mediated mesodermal commitment of human PSCs. Cell Stem Cell 24, 318–327.e8 (2019).

  61. 61.

    Martens, J. A., Laprade, L. & Winston, F. Intergenic transcription is required to repress the Saccharomyces cerevisiae SER3 gene. Nature 429, 571–574 (2004).

  62. 62.

    Bergmann, J. H. et al. Regulation of the ESC transcriptome by nuclear long noncoding RNAs. Genome Res. 25, 1336–1346 (2015).

  63. 63.

    Heintzman, N. D. et al. Histone modifications at human enhancers reflect global cell-type-specific gene expression. Nature 459, 108–112 (2009).

  64. 64.

    Xi, H. et al. Identification and characterization of cell type-specific and ubiquitous chromatin regulatory structures in the human genome. PLOS Genet. 3, e136 (2007).

  65. 65.

    Chen, H., Du, G., Song, X. & Li, L. Non-coding transcripts from enhancers: new insights into enhancer activity and gene expression regulation. Genomics Proteomics Bioinformatics 15, 201–207 (2017).

  66. 66.

    Ding, M. et al. Enhancer RNAs (eRNAs): new insights into gene transcription and disease treatment. J. Cancer 9, 2334–2340 (2018).

  67. 67.

    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).

  68. 68.

    Koch, F. et al. Transcription initiation platforms and GTF recruitment at tissue-specific enhancers and promoters. Nat. Struct. Mol. Biol. 18, 956–963 (2011).

  69. 69.

    Lai, F. et al. Activating RNAs associate with mediator to enhance chromatin architecture and transcription. Nature 494, 497–501 (2013).

  70. 70.

    Nozawa, R.-S. et al. SAF-A regulates interphase chromosome structure through oligomerization with chromatin-associated RNAs. Cell 169, 1214–1227.e18 (2017).

  71. 71.

    Xiao, R. et al. Nuclear matrix factor hnRNP U/SAF-A exerts a global control of alternative splicing by regulating U2 snRNP maturation. Mol. Cell 45, 656–668 (2012).

  72. 72.

    Elling, R. et al. Genetic models reveal cis and trans immune-regulatory activities for lincRNA-Cox2. Cell Rep. 25, 1511–1524.e6 (2018).

  73. 73.

    Han, X. et al. The lncRNA Hand2os1/Uph locus orchestrates heart development through regulation of precise expression of Hand2. Development 146, dev176198 (2019).

  74. 74.

    Ntini, E. et al. Long ncRNA A-ROD activates its target gene DKK1 at its release from chromatin. Nat. Commun. 9, 1636 (2018).

  75. 75.

    Krawczyk, M. & Emerson, B. M. p50-associated COX-2 extragenic RNA (PACER) activates COX-2 gene expression by occluding repressive NF-κB complexes. eLife 3, e01776 (2014).

  76. 76.

    Wang, K. C. et al. A long noncoding RNA maintains active chromatin to coordinate homeotic gene expression. Nature 472, 120–124 (2011).

  77. 77.

    Tan, J. Y., Biasini, A., Young, R. S. & Marques, A. An unexpected contribution of lincRNA splicing to enhancer function. Preprint at bioRxiv https://doi.org/10.1101/287706 (2018).

  78. 78.

    Haerty, W. & Ponting, C. P. Unexpected selection to retain high GC content and splicing enhancers within exons of multiexonic lncRNA loci. RNA 21, 333–346 (2015).

  79. 79.

    Schüler, A., Ghanbarian, A. T. & Hurst, L. D. Purifying selection on splice-related motifs, not expression level nor RNA folding, explains nearly all constraint on human lincRNAs. Mol. Biol. Evol. 31, 3164–3183 (2014).

  80. 80.

    Lamond, A. I. & Spector, D. L. Nuclear speckles: a model for nuclear organelles. Nat. Rev. Mol. Cell Biol. 4, 605–612 (2003).

  81. 81.

    Kim, J., Khanna, N. & Belmont, A. S. Transcription amplification by nuclear speckle association. Preprint at bioRxiv https://doi.org/10.1101/604298 (2019).

  82. 82.

    Ding, F. & Elowitz, M. B. Constitutive splicing and economies of scale in gene expression. Nat. Struct. Mol. Biol. 26, 424–432 (2019).

  83. 83.

    Fong, Y. W. & Zhou, Q. Stimulatory effect of splicing factors on transcriptional elongation. Nature 414, 929–933 (2001).

  84. 84.

    Sahakyan, A., Yang, Y. & Plath, K. The role of xist in X-chromosome dosage compensation. Trends Cell Biol. 28, 999–1013 (2018).

  85. 85.

    Robert Finestra, T. & Gribnau, J. X chromosome inactivation: silencing, topology and reactivation. Curr. Opin. Cell Biol. 46, 54–61 (2017).

  86. 86.

    da Rocha, S. T. & Heard, E. Novel players in X inactivation: insights into Xist-mediated gene silencing and chromosome conformation. Nat. Struct. Mol. Biol. 24, 197–204 (2017).

  87. 87.

    Swiezewski, S., Liu, F., Magusin, A. & Dean, C. Cold-induced silencing by long antisense transcripts of an arabidopsis polycomb target. Nature 462, 799–802 (2009).

  88. 88.

    Rosa, S., Duncan, S. & Dean, C. Mutually exclusive sense–antisense transcription at FLC facilitates environmentally induced gene repression. Nat. Commun. 7, 13031 (2016).

  89. 89.

    Whittaker, C. & Dean, C. The FLC locus: a platform for discoveries in epigenetics and adaptation. Annu. Rev. Cell Dev. Biol. 33, 555–575 (2017).

  90. 90.

    Beckedorff, F. C. et al. The intronic long noncoding RNA ANRASSF1 recruits PRC2 to the RASSF1A promoter, reducing the expression of RASSF1A and increasing cell proliferation. PLOS Genet. 9, e1003705 (2013).

  91. 91.

    Cho, S. W. et al. Promoter of lncRNA gene PVT1 is a tumor-suppressor DNA boundary element. Cell 173, 1398–1412.e22 (2018). This article presents an example of a lncRNA gene that represses its target through enhancer competition: the PVT1 promoter competes with the MYC promoter on association with and activation by proximally situated enhancers.

  92. 92.

    Wang, F. et al. Oncofetal long noncoding RNA PVT1 promotes proliferation and stem cell-like property of hepatocellular carcinoma cells by stabilizing NOP2. Hepatology 60, 1278–1290 (2014).

  93. 93.

    Tseng, Y. Y. et al. PVT1 dependence in cancer with MYC copy-number increase. Nature 512, 82–86 (2014).

  94. 94.

    Xiao, M., Feng, Y., Liu, C. & Zhang, Z. Prognostic values of long noncoding RNA PVT1 in various carcinomas: an updated systematic review and meta-analysis. Cell Prolif. 51, e12519 (2018).

  95. 95.

    Latos, P. A. et al. Airn transcriptional overlap, but not its lncRNA products, induces imprinted Igf2r silencing. Science 338, 1469–1472 (2012). This study is a compelling demonstration that transcription through specific regions of a lncRNA gene can be functionally significant, and thus demonstrates the importance of careful selection of integration sites for sequences that interfere with transcription.

  96. 96.

    Hongay, C. F., Grisafi, P. L., Galitski, T. & Fink, G. R. Antisense transcription controls cell fate in Saccharomyces cerevisiae. Cell 127, 735–745 (2006).

  97. 97.

    van Werven, F. J. et al. Transcription of two long noncoding RNAs mediates mating-type control of gametogenesis in budding yeast. Cell 150, 1170–1181 (2012).

  98. 98.

    Bumgarner, S. L., Dowell, R. D., Grisafi, P., Gifford, D. K. & Fink, G. R. Toggle involving cis-interfering noncoding RNAs controls variegated gene expression in yeast. Proc. Natl Acad. Sci. USA 106, 18321–18326 (2009).

  99. 99.

    Thebault, P. et al. Transcription regulation by the noncoding RNA SRG1 requires Spt2-dependent chromatin deposition in the wake of RNA polymerase II. Mol. Cell. Biol. 31, 1288–1300 (2011).

  100. 100.

    Canzio, D. et al. Antisense lncRNA transcription mediates DNA demethylation to drive stochastic protocadherin α promoter choice. Cell 177, 639–653.e15 (2019).

  101. 101.

    Bumgarner, S. L. et al. Single-cell analysis reveals that noncoding RNAs contribute to clonal heterogeneity by modulating transcription factor recruitment. Mol. Cell 45, 470–482 (2012).

  102. 102.

    Ritter, N. et al. The lncRNA locus Handsdown regulates cardiac gene programs and is essential for early mouse development. Dev. Cell 50, 644–657.e8 (2019).

  103. 103.

    Richard, J. L. C. & Ogawa, Y. Understanding the complex circuitry of lncRNAs at the X-inactivation center and its implications in disease conditions. Curr. Top. Microbiol. Immunol. 394, 1–27 (2016).

  104. 104.

    Tajul-Arifin, K. et al. Identification and analysis of chromodomain-containing proteins encoded in the mouse transcriptome. Genome Res. 13, 1416–1429 (2003).

  105. 105.

    Paralkar, V. R. et al. Unlinking an lncRNA from its associated cis element. Mol. Cell 62, 104–110 (2016).

  106. 106.

    Alexanian, M. et al. A transcribed enhancer dictates mesendoderm specification in pluripotency. Nat. Commun. 8, 1806 (2017).

  107. 107.

    Carmona, S., Lin, B., Chou, T., Arroyo, K. & Sun, S. lncRNA Jpx induces xist expression in mice using both trans and cis mechanisms. PLOS Genet. 14, e1007378 (2018).

  108. 108.

    Nagano, T. et al. The Air noncoding RNA epigenetically silences transcription by targeting G9a to chromatin. Science 322, 1717–1720 (2008).

  109. 109.

    Sigova, A. A. et al. Transcription factor trapping by RNA in gene regulatory elements. Science 350, 978–981 (2015).

  110. 110.

    Khalil, A. M. et al. Many human large intergenic noncoding RNAs associate with chromatin-modifying complexes and affect gene expression. Proc. Natl Acad. Sci. USA 106, 11667–11672 (2009).

  111. 111.

    Zhao, J. et al. Genome-wide identification of polycomb-associated RNAs by RIP-seq. Mol. Cell 40, 939–953 (2010).

  112. 112.

    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). This study finds that PRC2 binds RNA with high affinity but low specificity both in vitro and in vivo, with its promiscuous binding patterns correlating with RNA lengths or expression levels, and with no apparent specificity for biologically significant interactions. This casts doubt on the proposed role of many lncRNAs in recruiting PRC2 to their transcription sites.

  113. 113.

    Cifuentes-Rojas, C., Hernandez, A. J., Sarma, K. & Lee, J. T. Regulatory interactions between RNA and polycomb repressive complex 2. Mol. Cell 55, 171–185 (2014). This study notes that whereas the EZH2 subunit of PRC2 displays high-affinity RNA binding but with low specificity, other subunits – mostly EED – increase the selectivity of the complex’s RNA interactions.

  114. 114.

    Wang, X. et al. Targeting of polycomb repressive complex 2 to RNA by short repeats of consecutive guanines. Mol. Cell 65, 1056–1067.e5 (2017).

  115. 115.

    Colognori, D., Sunwoo, H., Kriz, A. J., Wang, C.-Y. & Lee, J. T. Xist deletional analysis reveals an interdependency between Xist RNA and polycomb complexes for spreading along the inactive X. Mol. Cell 74, 101–117.e10 (2019).

  116. 116.

    Baltz, A. G. et al. The mRNA-bound proteome and its global occupancy profile on protein-coding transcripts. Mol. Cell 46, 674–690 (2012).

  117. 117.

    Perez-Perri, J. I. et al. Discovery of RNA-binding proteins and characterization of their dynamic responses by enhanced RNA interactome capture. Nat. Commun. 9, 4408 (2018).

  118. 118.

    He, C. et al. High-resolution mapping of RNA-binding regions in the nuclear proteome of embryonic stem cells. Mol. Cell 64, 416–430 (2016).

  119. 119.

    Castello, A. et al. Comprehensive identification of RNA-binding domains in human cells. Mol. Cell 63, 696–710 (2016). In this study, the authors develop RBDmap, a strategy for identifying RNA-binding regions in proteins through ultraviolet crosslinking, oligo(dT) capture and identification of crosslinked peptides using mass spectrometry. This and similar methods detailed in Baltz et al., Perez-Perri et al and He et al. unravelled a myriad of known and novel RNA-binding proteins and domains.

  120. 120.

    Hansen, A. S. et al. Distinct classes of chromatin loops revealed by deletion of an RNA-binding region in CTCF. Mol. Cell 76, 395–411.e13 (2019).

  121. 121.

    Sun, S. et al. Jpx RNA activates Xist by evicting CTCF. Cell 153, 1537–1551 (2013).

  122. 122.

    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).

  123. 123.

    Beltran, M. et al. The interaction of PRC2 with RNA or chromatin is mutually antagonistic. Genome Res. 26, 896–907 (2016).

  124. 124.

    Hosogane, M., Funayama, R., Shirota, M. & Nakayama, K. Lack of transcription triggers H3K27me3 accumulation in the gene body. Cell Rep. 16, 696–706 (2016).

  125. 125.

    Beltran, M. et al. G-tract RNA removes polycomb repressive complex 2 from genes. Nat. Struct. Mol. Biol. 26, 899–900 (2019).

  126. 126.

    Sims, R. J. Elongation by RNA polymerase II: the short and long of it. Genes Dev. 18, 2437–2468 (2004).

  127. 127.

    Brandão, H. B. et al. RNA polymerases as moving barriers to condensin loop extrusion. Proc. Natl Acad. Sci. USA 116, 20489–20499 (2019).

  128. 128.

    Hsieh, T.-H. S. et al. Resolving the 3D landscape of transcription-linked mammalian chromatin folding. Preprint at bioRxiv https://doi.org/10.1101/638775 (2019).

  129. 129.

    Heinz, S. et al. Transcription elongation can affect genome 3D structure. Cell 174, 1522–1536.e22 (2018).

  130. 130.

    Gu, B. et al. Transcription-coupled changes in nuclear mobility of mammalian cis-regulatory elements. Science 359, 1050–1055 (2018).

  131. 131.

    Nagashima, R. et al. Single nucleosome imaging reveals loose genome chromatin networks via active RNA polymerase II. J. Cell Biol. 218, 1511–1530 (2019).

  132. 132.

    Kopp, F. & Mendell, J. T. Functional classification and experimental dissection of long noncoding RNAs. Cell 172, 393–407 (2018).

  133. 133.

    Sander, J. D. & Joung, J. K. CRISPR–Cas systems for editing, regulating and targeting genomes. Nat. Biotechnol. 32, 347–355 (2014).

  134. 134.

    Dominguez, A. A., Lim, W. A. & Qi, L. S. Beyond editing: repurposing CRISPR–Cas9 for precision genome regulation and interrogation. Nat. Rev. Mol. Cell Biol. 17, 5–15 (2016).

  135. 135.

    Lavalou, P. et al. Strategies for genetic inactivation of long noncoding RNAs in zebrafish. RNA 25, 897–904 (2019).

  136. 136.

    Fulco, C. P. et al. Systematic mapping of functional enhancer–promoter connections with CRISPR interference. Science 354, 769–773 (2016).

  137. 137.

    Simeonov, D. R. et al. Discovery of stimulation-responsive immune enhancers with CRISPR activation. Nature 549, 111–115 (2017).

  138. 138.

    Abudayyeh, O. O. et al. RNA targeting with CRISPR–Cas13. Nature 550, 280–284 (2017).

  139. 139.

    Cox, D. B. T. et al. RNA editing with CRISPR–Cas13. Science 358, 1019–1027 (2017).

  140. 140.

    Shechner, D. M., Hacisuleyman, E., Younger, S. T. & Rinn, J. L. Multiplexable, locus-specific targeting of long RNAs with CRISPR–Display. Nat. Methods 12, 664–670 (2015).

  141. 141.

    Carullo, N. V. N. et al. Enhancer RNAs are necessary and sufficient for activity-dependent neuronal gene transcription. Preprint at bioRxiv https://doi.org/10.1101/270967 (2018).

  142. 142.

    Tuck, A. C. et al. Distinctive features of lincRNA gene expression suggest widespread RNA-independent functions. Life Sci. Alliance 1, e201800124 (2018).

  143. 143.

    Nomura, Y., Zhou, L., Miu, A. & Yokobayashi, Y. Controlling mammalian gene expression by allosteric hepatitis delta virus ribozymes. ACS Synth. Biol. 2, 684–689 (2013).

  144. 144.

    Nojima, T. et al. Mammalian NET-seq reveals genome-wide nascent transcription coupled to RNA processing. Cell 161, 526–540 (2015).

  145. 145.

    Sarshad, A. A. et al. Argonaute–miRNA complexes silence target mRNAs in the nucleus of mammalian stem cells. Mol. Cell 71, 1040–1050.e8 (2018).

  146. 146.

    Wee, K. B. et al. Dynamics of co-transcriptional pre-mRNA folding influences the induction of dystrophin exon skipping by antisense oligonucleotides. PLOS ONE 3, e1844 (2008).

  147. 147.

    Sioud, M. Promises and challenges in developing RNAi as a research tool and therapy. Methods Mol. Biol. 703, 173–187 (2011).

  148. 148.

    Stojic, L. et al. Specificity of RNAi, LNA and CRISPRi as loss-of-function methods in transcriptional analysis. Nucleic Acids Res. 46, 5950–5966 (2018).

  149. 149.

    Engreitz, J., Lander, E. S. & Guttman, M. RNA antisense purification (RAP) for mapping RNA interactions with chromatin. Methods Mol. Biol. 1262, 183–197 (2015).

  150. 150.

    Li, X. & Fu, X.-D. Chromatin-associated RNAs as facilitators of functional genomic interactions. Nat. Rev. Genet. 20, 503–519 (2019). This work is an excellent recent review, particularly useful for those looking for detailed information about techniques used to identify chromatin binding sites of lncRNAs.

  151. 151.

    Li, X. et al. GRID-seq reveals the global RNA–chromatin interactome. Nat. Biotechnol. 35, 940–950 (2017).

  152. 152.

    Bell, J. C. et al. Chromatin-associated RNA sequencing (ChAR-seq) maps genome-wide RNA-to-DNA contacts. eLife 7, e27024 (2018).

  153. 153.

    Sridhar, B. et al. Systematic mapping of RNA–chromatin interactions in vivo. Curr. Biol. 27, 610–612 (2017).

  154. 154.

    Bonetti, A. et al. RADICL-seq identifies general and cell type-specific principles of genome-wide RNA–chromatin interactions. Preprint at bioRxiv https://doi.org/10.1101/681924 (2019).

  155. 155.

    Shao, W. et al. U1 snRNP regulates chromatin retention of noncoding RNAs. Preprint at bioRxiv https://doi.org/10.1101/310433 (2018).

  156. 156.

    Lubelsky, Y. & Ulitsky, I. Sequences enriched in Alu repeats drive nuclear localization of long RNAs in human cells. Nature 555, 107–111 (2018).

  157. 157.

    Shukla, C. J. et al. High-throughput identification of RNA nuclear enrichment sequences. EMBO J. 37, e9845 (2018).

  158. 158.

    Matsui, M. & Corey, D. R. Non-coding RNAs as drug targets. Nat. Rev. Drug Discov. 16, 167–179 (2017).

  159. 159.

    Dao, L. T. M. et al. Genome-wide characterization of mammalian promoters with distal enhancer functions. Nat. Genet. 49, 1073–1081 (2017).

  160. 160.

    Carelli, F. N., Liechti, A., Halbert, J., Warnefors, M. & Kaessmann, H. Repurposing of promoters and enhancers during mammalian evolution. Nat. Commun. 9, 4066 (2018). This study identifies prevalent repurposing of enhancers to promoters (or vice versa) during evolution, demonstrating the large potential that enhancers serve in creating novel transcriptional units, including lncRNAs.

  161. 161.

    Marques, A. C. et al. Evidence for conserved post-transcriptional roles of unitary pseudogenes and for frequent bifunctionality of mRNAs. Genome Biol. 13, R102 (2012).

  162. 162.

    Hezroni, H. et al. A subset of conserved mammalian long non-coding RNAs are fossils of ancestral protein-coding genes. Genome Biol. 18, 162 (2017).

  163. 163.

    Cabili, M. N. et al. Localization and abundance analysis of human lncRNAs at single-cell and single-molecule resolution. Genome Biol. 16, 20 (2015).

  164. 164.

    Carlevaro-Fita, J. & Johnson, R. Global positioning system: understanding long noncoding RNAs through subcellular localization. Mol. Cell 73, 869–883 (2019).

  165. 165.

    Ernst, J. & Kellis, M. ChromHMM: automating chromatin-state discovery and characterization. Nat. Methods 9, 215–216 (2012).

  166. 166.

    Roadmap Epigenomics Consortium. et al. Integrative analysis of 111 reference human epigenomes. Nature 518, 317–330 (2015).

  167. 167.

    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. Science 322, 750–756 (2008).

  168. 168.

    Minajigi, A. et al. Chromosomes. A comprehensive Xist interactome reveals cohesin repulsion and an RNA-directed chromosome conformation. Science https://doi.org/10.1126/science.aab2276 (2015).

  169. 169.

    Sarma, K. et al. ATRX directs binding of PRC2 to Xist RNA and polycomb targets. Cell 159, 869–883 (2014).

  170. 170.

    Chu, C. et al. Systematic discovery of Xist RNA binding proteins. Cell 161, 404–416 (2015).

  171. 171.

    McHugh, C. A. et al. The Xist lncRNA interacts directly with SHARP to silence transcription through HDAC3. Nature 521, 232–236 (2015).

  172. 172.

    Hasegawa, Y. et al. The matrix protein hnRNP U is required for chromosomal localization of Xist RNA. Dev. Cell 19, 469–476 (2010).

  173. 173.

    Dinger, M. E. et al. Long noncoding RNAs in mouse embryonic stem cell pluripotency and differentiation. Genome Res. 18, 1433–1445 (2008).

  174. 174.

    Luo, S. et al. Divergent lncRNAs regulate gene expression and lineage differentiation in pluripotent cells. Cell Stem Cell 18, 637–652 (2016).

  175. 175.

    Knauss, J. L. et al. Long noncoding RNA Sox2ot and transcription factor YY1 co-regulate the differentiation of cortical neural progenitors by repressing Sox2. Cell Death Dis. 9, 799 (2018).

  176. 176.

    Jeon, Y. & Lee, J. T. YY1 tethers Xist RNA to the inactive X nucleation center. Cell 146, 119–133 (2011).

Download references

Acknowledgements

The authors would like to thank A. Shkumatava, S. Nakagawa, L. Chen, C. Ross, H. Hezroni, M. Goldrich and members of the Ulitsky laboratory for helpful discussions and comments on the manuscript.

Author information

The authors contributed equally to all aspects of the article.

Correspondence to Igor Ulitsky.

Ethics declarations

Competing interests

The authors declare no competing interests.

Additional information

Peer review information

Nature Reviews Genetics thanks C. Ponting and the other, anonymous, reviewer(s) for their contribution to the peer review of this work.

Publisher’s note

Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.

Glossary

Enhancers

DNA regulatory elements that activate gene transcription. Enhancers can operate from nearby or within their targets, or across large genomic distances.

Transcription factors

(TFs). Proteins that bind to specific DNA sequence motifs found within regulatory DNA elements — either promoters or enhancers — to modulate gene expression.

Chromatin remodellers

Proteins that regulate gene expression by altering chromatin structure. Two main groups exist: those that mediate post-translational modifications of histones; and ATP-dependent chromatin remodellers, which regulate the association with and location of nucleosomes along the DNA.

Super-enhancer

A particularly active and cell type-specific enhancer. Demarcated by high levels of chromatin modifications such as histone 3 lysine 27 acetylation (H3K27ac) and long sequence stretches bound by transcription factors and coactivators such as Mediator.

Topologically associating domain

(TAD). A genomic region with an average size of ~1 Mb characterized by high-density chromatin interactions. Sequences within TADs tend to form interactions with one another but less so with sequences in other TADs.

Enhancer RNAs

(eRNAs). A species of bidirectional, unstable non-coding RNAs produced at enhancers. Considered a hallmark of active enhancers and sometimes used for enhancer annotation.

CTCF

A transcription factor that acts primarily in chromatin 3D architecture regulation, through anchoring long-range chromatin loops and demarcating topologically associating domain boundaries.

Polycomb repressive complex 2

(PRC2). A histone methyltransferase protein complex that induces trimethylation of histone 3 lysine 27 (H3K27), a histone modification associated with long-term epigenetic silencing.

Vernalization

The process of induction of plant flowering, brought on by exposure to prolonged cold temperatures.

Enhancer competition

Two (or more) transcriptional units that can be activated by the same enhancer, and which compete over direct binding to and activation by that enhancer.

Transcriptional interference

A process whereby transcription through one genomic region interferes with transcription of a nearby (often overlapping) locus, for example, by curbing the recruitment of trans factors such as transcription factors or chromatin remodellers, or through deposition of chromatin modifications incompatible with transcription initiation.

Auto-regulatory feedback loops

A type of transcriptional regulation network in which a gene product regulates its own levels, for example, a transcription factor which binds its own locus and activates (or represses) transcription.

Disordered regions

Proteins or regions within proteins that do not adopt an ordered or well-defined 3D structure. These regions can serve as linkers between structured regions, or be functional themselves.

CRISPR–Cas9

A bacterial immune mechanism whereby a Cas9 protein uses short guide RNA (gRNA) sequences to target and cleave foreign DNA. CRISPR–Cas9 can be used for gene editing, by ectopic expression of both Cas9 and a gRNA that targets the gene of interest.

CRISPR display

Utilization of CRISPR–Cas9 for the recruitment of non-protein components. For example, long non-coding RNA sequences can be fused to the guide RNA and be brought to the target locus via ‘dead’ Cas9.

Self-cleaving ribozyme sequences

RNA sequences that can catalyse a reaction that would cut their own RNA.

RNA interference

(RNAi). Short non-coding RNA molecules — either microRNAs or short interfering RNAs — bind to complementary sequences in the target genes, leading to translation inhibition or target RNA degradation.

Rights and permissions

Reprints and Permissions

About this article

Verify currency and authenticity via CrossMark

Cite this article

Gil, N., Ulitsky, I. Regulation of gene expression by cis-acting long non-coding RNAs. Nat Rev Genet (2019) doi:10.1038/s41576-019-0184-5

Download citation