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Substoichiometric action of long noncoding RNAs

Abstract

Low expression levels and stoichiometric imbalances of long noncoding RNAs (lncRNAs) are often used as evidence for their probable lack of function or for limiting the scope of their potential influence. Recent advances in our understanding of the substoichiometric functions of lncRNAs challenge these notions and suggest routes through which unabundant lncRNAs can affect cellular functions and gene regulatory networks.

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Fig. 1: The lncRNAs NORAD and Xist induce phase transitions with distinct regulatory functions.
Fig. 2: ncRNAs are essential for the formation and function of nuclear concentration gradients.
Fig. 3: The lncRNAs Cyrano and SLERT are recycled to modify a supra-stoichiometric number of targets.

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References

  1. Wu, M., Yang, L.-Z. & Chen, L.-L. Long noncoding RNA and protein abundance in lncRNPs. RNA 27, 1427–1440 (2021).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  2. Travers, A. Transcriptional switches: the role of mass action. Phys. Life Rev. 1, 57–69 (2004).

    Article  Google Scholar 

  3. Chong, S. et al. Imaging dynamic and selective low-complexity domain interactions that control gene transcription. Science 361, eaar2555 (2018).

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  4. Reisser, M. et al. Single-molecule imaging correlates decreasing nuclear volume with increasing TF–chromatin associations during zebrafish development. Nat. Commun. 9, 5218 (2018).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  5. Statello, L., Guo, C.-J., Chen, L.-L. & Huarte, M. Gene regulation by long non-coding RNAs and its biological functions. Nat. Rev. Mol. Cell Biol. 22, 96–118 (2021).

    Article  CAS  PubMed  Google Scholar 

  6. Henninger, J. E. et al. RNA-mediated feedback control of transcriptional condensates. Cell 184, 207–225.e24 (2021).

    Article  CAS  PubMed  Google Scholar 

  7. Roden, C. & Gladfelter, A. S. RNA contributions to the form and function of biomolecular condensates. Nat. Rev. Mol. Cell Biol. 22, 183–195 (2021).

    Article  CAS  PubMed  Google Scholar 

  8. Lyon, A. S., Peeples, W. B. & Rosen, M. K. A framework for understanding the functions of biomolecular condensates across scales. Nat. Rev. Mol. Cell Biol. 22, 215–235 (2021).

    Article  CAS  PubMed  Google Scholar 

  9. Bhat, P., Honson, D. & Guttman, M. Nuclear compartmentalization as a mechanism of quantitative control of gene expression. Nat. Rev. Mol. Cell Biol. 22, 653–670 (2021).

    Article  CAS  PubMed  Google Scholar 

  10. Brangwynne, C. P. et al. Germline P granules are liquid droplets that localize by controlled dissolution/condensation. Science 324, 1729–1732 (2009).

    Article  CAS  PubMed  Google Scholar 

  11. Banani, S. F., Lee, H. O., Hyman, A. A. & Rosen, M. K. Biomolecular condensates: organizers of cellular biochemistry. Nat. Rev. Mol. Cell Biol. 18, 285–298 (2017).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  12. Garcia-Jove Navarro, M. et al. RNA is a critical element for the sizing and the composition of phase-separated RNA–protein condensates. Nat. Commun. 10, 3230 (2019).

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  13. Wang, M. et al. Stress-induced low complexity RNA activates physiological amyloidogenesis. Cell Rep. 24, 1713–1721.e4 (2018).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  14. Hur, W. et al. CDK-regulated phase separation seeded by histone genes ensures precise growth and function of histone locus bodies. Dev. Cell 54, 379–394.e6 (2020).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  15. Guillén-Boixet, J. et al. RNA-induced conformational switching and clustering of G3BP drive stress granule assembly by condensation. Cell 181, 346–361.e17 (2020).

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  16. Yang, P. et al. G3BP1 is a tunable switch that triggers phase separation to assemble stress granules. Cell 181, 325–345.e28 (2020).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  17. Aillaud, M. & Schulte, L. N. Emerging roles of long noncoding RNAs in the cytoplasmic milieu. Noncoding RNA 6, 44 (2020).

    CAS  PubMed Central  Google Scholar 

  18. Yamazaki, T. et al. Functional domains of NEAT1 architectural lncRNA induce paraspeckle assembly through phase separation. Mol. Cell 70, 1038–1053.e7 (2018).

    Article  CAS  PubMed  Google Scholar 

  19. Fox, A. H., Nakagawa, S., Hirose, T. & Bond, C. S. Paraspeckles: where long noncoding RNA meets phase separation. Trends Biochem. Sci. 43, 124–135 (2018).

    Article  CAS  PubMed  Google Scholar 

  20. Pessina, F. et al. Functional transcription promoters at DNA double-strand breaks mediate RNA-driven phase separation of damage-response factors. Nat. Cell Biol. 21, 1286–1299 (2019).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  21. Li, R.-H. et al. A phosphatidic acid-binding lncRNA SNHG9 facilitates LATS1 liquid–liquid phase separation to promote oncogenic YAP signaling. Cell Res. 31, 1088–1105 (2021).

    Article  CAS  PubMed  Google Scholar 

  22. Daneshvar, K. et al. lncRNA DIGIT and BRD3 protein form phase-separated condensates to regulate endoderm differentiation. Nat. Cell Biol. 22, 1211–1222 (2020).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  23. Huo, X. et al. The nuclear matrix protein SAFB cooperates with major satellite RNAs to stabilize heterochromatin architecture partially through phase separation. Mol. Cell 77, 368–383.e7 (2020).

    Article  CAS  PubMed  Google Scholar 

  24. McSwiggen, D. T., Mir, M., Darzacq, X. & Tjian, R. Evaluating phase separation in live cells: diagnosis, caveats, and functional consequences. Genes Dev. 33, 1619–1634 (2019).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

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

    Article  CAS  PubMed  Google Scholar 

  26. Elguindy, M. M. & Mendell, J. T. NORAD-induced Pumilio phase separation is required for genome stability. Nature 595, 303–308 (2021).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

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

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  28. Simon, M. D. et al. High-resolution Xist binding maps reveal two-step spreading during X-chromosome inactivation. Nature 504, 465–469 (2013).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  29. Sunwoo, H., Wu, J. Y. & Lee, J. T. The Xist RNA–PRC2 complex at 20-nm resolution reveals a low Xist stoichiometry and suggests a hit-and-run mechanism in mouse cells. Proc. Natl Acad. Sci. USA 112, E4216–E4225 (2015).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  30. Pacini, G. et al. Integrated analysis of Xist upregulation and X-chromosome inactivation with single-cell and single-allele resolution. Nat. Commun. 12, 3638 (2021).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

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

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  32. Markaki, Y. et al. Xist nucleates local protein gradients to propagate silencing across the X chromosome. Cell 184, 6174–6192.e32 (2021).

    Article  CAS  PubMed  Google Scholar 

  33. Monfort, A. et al. Identification of spen as a crucial factor for xist function through forward genetic screening in haploid embryonic stem cells. Cell Rep. 12, 554–561 (2015).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  34. Lu, Z. et al. RNA duplex map in living cells reveals higher-order transcriptome structure. Cell 165, 1267–1279 (2016).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  35. Jachowicz, J. W. et al. Xist spatially amplifies SHARP/SPEN recruitment to balance chromosome-wide silencing and specificity to the X chromosome. Nat. Struct. Mol. Biol. 29, 239–249 (2022).

    Article  CAS  PubMed  Google Scholar 

  36. Pandya-Jones, A. et al. A protein assembly mediates Xist localization and gene silencing. Nature 587, 145–151 (2020).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  37. Wutz, A. & Jaenisch, R. A shift from reversible to irreversible X inactivation is triggered during ES cell differentiation. Mol. Cell 5, 695–705 (2000).

    Article  CAS  PubMed  Google Scholar 

  38. Brockdorff, N., Bowness, J. S. & Wei, G. Progress toward understanding chromosome silencing by Xist RNA. Genes Dev. 34, 733–744 (2020).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  39. Wang, C.-Y., Colognori, D., Sunwoo, H., Wang, D. & Lee, J. T. PRC1 collaborates with SMCHD1 to fold the X-chromosome and spread Xist RNA between chromosome compartments. Nat. Commun. 10, 2950 (2019).

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  40. Colognori, D., Sunwoo, H., Wang, D., Wang, C.-Y. & Lee, J. T. Xist repeats A and B account for two distinct phases of X inactivation establishment. Dev. Cell 54, 21–32.e5 (2020).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  41. Weidmann, C. A., Mustoe, A. M., Jariwala, P. B., Calabrese, J. M. & Weeks, K. M. Analysis of RNA–protein networks with RNP-MaP defines functional hubs on RNA. Nat. Biotechnol. 39, 347–356 (2021).

    Article  CAS  PubMed  Google Scholar 

  42. Frank, L. & Rippe, K. Repetitive RNAs as regulators of chromatin-associated subcompartment formation by phase separation. J. Mol. Biol. 432, 4270–4286 (2020).

    Article  CAS  PubMed  Google Scholar 

  43. Ziv, O. et al. Structural features within the NORAD long noncoding RNA underlie efficient repression of Pumilio activity. Preprint at bioRxiv https://doi.org/10.1101/2021.11.19.469243 (2021).

  44. Wutz, A., Rasmussen, T. P. & Jaenisch, R. Chromosomal silencing and localization are mediated by different domains of Xist RNA. Nat. Genet. 30, 167–174 (2002).

    Article  CAS  PubMed  Google Scholar 

  45. Lu, Z. et al. Structural modularity of the XIST ribonucleoprotein complex. Nat. Commun. 11, 6163 (2020).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

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

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  47. Quinodoz, S. A. et al. RNA promotes the formation of spatial compartments in the nucleus. Cell 184, 5775–5790.e30 (2021).

    Article  CAS  PubMed  Google Scholar 

  48. Hyman, A. A., Weber, C. A. & Jülicher, F. Liquid–liquid phase separation in biology. Annu. Rev. Cell Dev. Biol. 30, 39–58 (2014).

    Article  CAS  PubMed  Google Scholar 

  49. 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).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

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

    Article  CAS  PubMed  Google Scholar 

  51. Pintacuda, G. et al. hnRNPK Recruits PCGF3/5-PRC1 to the Xist RNA B-repeat to establish polycomb-mediated chromosomal silencing. Mol. Cell 68, 955–969 (2017).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  52. Isono, K. et al. SAM domain polymerization links subnuclear clustering of PRC1 to gene silencing. Dev. Cell 26, 565–577 (2013).

    Article  CAS  PubMed  Google Scholar 

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

    Article  CAS  PubMed  PubMed Central  Google Scholar 

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

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  55. Reichholf, B. et al. Time-resolved small RNA sequencing unravels the molecular principles of microRNA homeostasis. Mol. Cell 75, 756–768.e7 (2019).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  56. Kingston, E. R. & Bartel, D. P. Global analyses of the dynamics of mammalian microRNA metabolism. Genome Res. 29, 1777–1790 (2019).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  57. Gebert, L. F. R. & MacRae, I. J. Regulation of microRNA function in animals. Nat. Rev. Mol. Cell Biol. 20, 21–37 (2019).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  58. Shi, C. Y. et al. The ZSWIM8 ubiquitin ligase mediates target-directed microRNA degradation. Science 370, eabc9359 (2020).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  59. Han, J. et al. A ubiquitin ligase mediates target-directed microRNA decay independently of tailing and trimming. Science 370, eabc9546 (2020).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  60. Kleaveland, B., Shi, C. Y., Stefano, J. & Bartel, D. P. A network of noncoding regulatory RNAs acts in the mammalian brain. Cell 174, 350–362.e17 (2018).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  61. 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).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  62. Cazalla, D., Yario, T. & Steitz, J. A. Down-regulation of a host microRNA by a herpesvirus saimiri noncoding RNA. Science 328, 1563–1566 (2010).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  63. Ghini, F. et al. Endogenous transcripts control miRNA levels and activity in mammalian cells by target-directed miRNA degradation. Nat. Commun. 9, 3119 (2018).

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  64. Bitetti, A. et al. MicroRNA degradation by a conserved target RNA regulates animal behavior. Nat. Struct. Mol. Biol. 25, 244–251 (2018).

    Article  CAS  PubMed  Google Scholar 

  65. Denzler, R. et al. Impact of microRNA levels, target-site complementarity, and cooperativity on competing endogenous RNA-regulated gene expression. Mol. Cell 64, 565–579 (2016).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  66. Piwecka, M. et al. Loss of a mammalian circular RNA locus causes miRNA deregulation and affects brain function. Science 357, eaam8526 (2017).

    Article  PubMed  CAS  Google Scholar 

  67. Li, L. et al. Widespread microRNA degradation elements in target mRNAs can assist the encoded proteins. Genes Dev. 35, 1595–1609 (2021).

    Article  CAS  PubMed  Google Scholar 

  68. Calo, E. et al. RNA helicase DDX21 coordinates transcription and ribosomal RNA processing. Nature 518, 249–253 (2015).

    Article  CAS  PubMed  Google Scholar 

  69. Wu, M. et al. lncRNA SLERT controls phase separation of FC/DFCs to facilitate Pol I transcription. Science 373, 547–555 (2021).

    Article  CAS  PubMed  Google Scholar 

  70. Xing, Y.-H. et al. SLERT regulates DDX21 rings associated with Pol I transcription. Cell 169, 664–678.e16 (2017).

    Article  CAS  PubMed  Google Scholar 

  71. Wang, X. et al. Induced ncRNAs allosterically modify RNA-binding proteins in cis to inhibit transcription. Nature 454, 126–130 (2008).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  72. Liu, Z. et al. Hsp27 chaperones FUS phase separation under the modulation of stress-induced phosphorylation. Nat. Struct. Mol. Biol. 27, 363–372 (2020).

    Article  CAS  PubMed  Google Scholar 

  73. Jia, C. et al. Different heat shock proteins bind α-synuclein with distinct mechanisms and synergistically prevent its amyloid aggregation. Front. Neurosci. 13, 1124 (2019).

    Article  PubMed  PubMed Central  Google Scholar 

  74. Docter, B. E., Horowitz, S., Gray, M. J., Jakob, U. & Bardwell, J. C. A. Do nucleic acids moonlight as molecular chaperones? Nucleic Acids Res. 44, 4835–4845 (2016).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  75. Bevilacqua, P. C., Williams, A. M., Chou, H.-L. & Assmann, S. M. RNA multimerization as an organizing force for liquid–liquid phase separation. RNA 28, 16–26 (2022).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  76. Riback, J. A. et al. Composition-dependent thermodynamics of intracellular phase separation. Nature 581, 209–214 (2020).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  77. Turoverov, K. K. et al. Stochasticity of biological soft matter: emerging concepts in intrinsically disordered proteins and biological phase separation. Trends Biochem. Sci. 44, 716–728 (2019).

    Article  CAS  PubMed  Google Scholar 

  78. Feric, M. et al. Coexisting liquid phases underlie nucleolar subcompartments. Cell 165, 1686–1697 (2016).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  79. Peeples, W. & Rosen, M. K. Mechanistic dissection of increased enzymatic rate in a phase-separated compartment. Nat. Chem. Biol. 17, 693–702 (2021).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  80. Brockdorff, N. Local tandem repeat expansion in Xist RNA as a model for the functionalisation of ncRNA. Noncoding RNA 4, 28 (2018).

    CAS  PubMed Central  Google Scholar 

  81. Langdon, E. M. et al. mRNA structure determines specificity of a polyQ-driven phase separation. Science 360, 922–927 (2018).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  82. Spitale, R. C. et al. RNA SHAPE analysis in living cells. Nat. Chem. Biol. 9, 18–20 (2013).

    Article  CAS  PubMed  Google Scholar 

  83. Ares, P. et al. High resolution atomic force microscopy of double-stranded RNA. Nanoscale 8, 11818–11826 (2016).

    Article  CAS  PubMed  Google Scholar 

  84. Uroda, T. et al. Conserved pseudoknots in lncRNA MEG3 are essential for stimulation of the p53 pathway. Mol. Cell 75, 982–995.e9 (2019).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  85. Unfried, J. P. et al. Long noncoding RNA NIHCOLE promotes ligation efficiency of DNA double-strand breaks in hepatocellular carcinoma. Cancer Res. 81, 4910–4925 (2021).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  86. Geiger, F. et al. Liquid–liquid phase separation underpins the formation of replication factories in rotaviruses. EMBO J. 40, e107711 (2021).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  87. Merdanovic, M. et al. Activation by substoichiometric inhibition. Proc. Natl Acad. Sci. USA 117, 1414–1418 (2020).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  88. Golden, R. J. et al. An Argonaute phosphorylation cycle promotes microRNA-mediated silencing. Nature 542, 197–202 (2017).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  89. Bosson, A. D., Zamudio, J. R. & Sharp, P. A. Endogenous miRNA and target concentrations determine susceptibility to potential ceRNA competition. Mol. Cell 56, 347–359 (2014).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  90. Denzler, R., Agarwal, V., Stefano, J., Bartel, D. P. & Stoffel, M. Assessing the ceRNA hypothesis with quantitative measurements of miRNA and target abundance. Mol. Cell 54, 766–776 (2014).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  91. Robert-Finestra, T. et al. SPEN is required for Xist upregulation during initiation of X chromosome inactivation. Nat. Commun. 12, 7000 (2021).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  92. Rodermund, L. et al. Time-resolved structured illumination microscopy reveals key principles of Xist RNA spreading. Science 372, eabe7500 (2021).

    Article  CAS  PubMed  Google Scholar 

  93. Maharana, S. et al. RNA buffers the phase separation behavior of prion-like RNA binding proteins. Science 360, 918–921 (2018).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  94. Bracha, D. et al. Mapping local and global liquid phase behavior in living cells using photo-oligomerizable seeds. Cell 175, 1467–1480.e13 (2018).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

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Acknowledgements

J.P.U. is a recipient of the Azrieli International Postdoctoral Fellowship from the Azrieli Foundation, the Excellence Fellowship Program for International Postdoctoral Researchers from the Council for Higher Education & Israel Academy of Sciences & Humanities, and an EMBO Non-Stipendiary Postdoctoral Fellowship from the European Molecular Biology Organization.

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Unfried, J.P., Ulitsky, I. Substoichiometric action of long noncoding RNAs. Nat Cell Biol 24, 608–615 (2022). https://doi.org/10.1038/s41556-022-00911-1

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