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RNA motifs and combinatorial prediction of interactions, stability and localization of noncoding RNAs

Abstract

Although the number of documented noncoding RNAs (ncRNAs) is rapidly increasing, knowledge of their molecular function is lagging behind. The identification of specific RNA motifs that mediate transcript stability, interactions and localization may aid in the prediction of these features in new transcripts and may have potential implications for ncRNA function. Here, we review RNA motifs, focusing on four recent studies identifying nuclear-retention motifs, and discuss the limited specificity of short-RNA motifs and the resulting challenge for effective functional prediction. Future approaches may succeed by integrating combinatorial and cooperative effects of additional partially sequence-based properties.

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References

  1. 1.

    Ulitsky, I. & Bartel, D. P. lincRNAs: genomics, evolution, and mechanisms. Cell 154, 26–46 (2013).

  2. 2.

    Gutschner, T. & Diederichs, S. The hallmarks of cancer: a long non-coding RNA point of view. RNA Biol. 9, 703–719 (2012).

  3. 3.

    Zhang, J., Lau, M. W. & Ferré-D’Amaré, A. R. Ribozymes and riboswitches: modulation of RNA function by small molecules. Biochemistry 49, 9123–9131 (2010).

  4. 4.

    Narberhaus, F., Waldminghaus, T. & Chowdhury, S. RNA thermometers. FEMS Microbiol. Rev. 30, 3–16 (2006).

  5. 5.

    Salehi-Ashtiani, K., Lupták, A., Litovchick, A. & Szostak, J. W. A genomewide search for ribozymes reveals an HDV-like sequence in the human CPEB3 gene. Science 313, 1788–1792 (2006).

  6. 6.

    Teixeira, A. et al. Autocatalytic RNA cleavage in the human β-globin pre-mRNA promotes transcription termination. Nature 432, 526–530 (2004).

  7. 7.

    Ray, D. et al. A compendium of RNA-binding motifs for decoding gene regulation. Nature 499, 172–177 (2013). This study constitutes a systematic analysis of RNA-binding proteins with 205 unique genes in 24 different eukaryotes. The identified motifs display evolutionary conservation and binding specificity, and correlate with in vivo data.

  8. 8.

    Dreyfus, M. & Régnier, P. The poly(A) tail of mRNAs: bodyguard in eukaryotes, scavenger in bacteria. Cell 111, 611–613 (2002).

  9. 9.

    Clerici, M., Faini, M., Muckenfuss, L. M., Aebersold, R. & Jinek, M. Structural basis of AAUAAA polyadenylation signal recognition by the human CPSF complex. Nat. Struct. Mol. Biol. 25, 135–138 (2018).

  10. 10.

    Elkon, R., Ugalde, A. P. & Agami, R. Alternative cleavage and polyadenylation: extent, regulation and function. Nat. Rev. Genet. 14, 496–506 (2013).

  11. 11.

    Marzluff, W. F. & Koreski, K. P. Birth and death of histone mRNAs. Trends Genet. 33, 745–759 (2017).

  12. 12.

    Stoecklin, G., Stoeckle, P., Lu, M., Muehlemann, O. & Moroni, C. Cellular mutants define a common mRNA degradation pathway targeting cytokine AU-rich elements. RNA 7, 1578–1588 (2001).

  13. 13.

    Roy, N., Laflamme, G. & Raymond, V. 5′ untranslated sequences modulate rapid mRNA degradation mediated by 3′ AU-rich element in v-/c-fos recombinants. Nucleic Acids Res. 20, 5753–5762 (1992).

  14. 14.

    Espel, E. The role of the AU-rich elements of mRNAs in controlling translation. Semin. Cell Dev. Biol. 16, 59–67 (2005).

  15. 15.

    Leppek, K. et al. Roquin promotes constitutive mRNA decay via a conserved class of stem-loop recognition motifs. Cell 153, 869–881 (2013).

  16. 16.

    Meister, G. et al. Human Argonaute2 mediates RNA cleavage targeted by miRNAs and siRNAs. Mol. Cell 15, 185–197 (2004).

  17. 17.

    Yang, L., Duff, M. O., Graveley, B. R., Carmichael, G. G. & Chen, L. L. Genomewide characterization of non-polyadenylated RNAs. Genome Biol. 12, R16 (2011).

  18. 18.

    Beaulieu, Y. B., Kleinman, C. L., Landry-Voyer, A. M., Majewski, J. & Bachand, F. Polyadenylation-dependent control of long noncoding RNA expression by the poly(A)-binding protein nuclear 1. PLoS Genet. 8, e1003078 (2012).

  19. 19.

    Booy, E. P. et al. RNA helicase associated with AU-rich element (RHAU/DHX36) interacts with the 3′-tail of the long non-coding RNA BC200 (BCYRN1). J. Biol. Chem. 291, 5355–5372 (2016).

  20. 20.

    Yoon, J. H., Abdelmohsen, K. & Gorospe, M. Functional interactions among microRNAs and long noncoding RNAs. Semin. Cell Dev. Biol. 34, 9–14 (2014).

  21. 21.

    Ji, P. et al. MALAT-1, a novel noncoding RNA, and thymosin beta4 predict metastasis and survival in early-stage non-small cell lung cancer. Oncogene 22, 8031–8041 (2003).

  22. 22.

    Gutschner, T. et al. The noncoding RNA MALAT1 is a critical regulator of the metastasis phenotype of lung cancer cells. Cancer Res. 73, 1180–1189 (2013).

  23. 23.

    Hutchinson, J. N. et al. A screen for nuclear transcripts identifies two linked noncoding RNAs associated with SC35 splicing domains. BMC Genomics 8, 39 (2007).

  24. 24.

    Chen, L. L. & Carmichael, G. G. Altered nuclear retention of mRNAs containing inverted repeats in human embryonic stem cells: functional role of a nuclear noncoding RNA. Mol. Cell 35, 467–478 (2009).

  25. 25.

    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).

  26. 26.

    Wilusz, J. E. et al. A triple helix stabilizes the 3′ ends of long noncoding RNAs that lack poly(A) tails. Genes Dev. 26, 2392–2407 (2012). This study shows that despite the lack of poly(A) tails, the 3′ ends of lncRNAs such as MALAT1 and MENβ are protected from cleavage by 3′–5′ exonucleases through a conserved triple-helical structure.

  27. 27.

    Brown, J. A. et al. Structural insights into the stabilization of MALAT1 noncoding RNA by a bipartite triple helix. Nat. Struct. Mol. Biol. 21, 633–640 (2014).

  28. 28.

    Yin, Q. F. et al. Long noncoding RNAs with snoRNA ends. Mol. Cell 48, 219–230 (2012).

  29. 29.

    Memczak, S. et al. Circular RNAs are a large class of animal RNAs with regulatory potency. Nature 495, 333–338 (2013).

  30. 30.

    Hansen, T. B. et al. Natural RNA circles function as efficient microRNA sponges. Nature 495, 384–388 (2013).

  31. 31.

    Arora, R. et al. RNaseH1 regulates TERRA-telomeric DNA hybrids and telomere maintenance in ALT tumour cells. Nat. Commun. 5, 5220 (2014).

  32. 32.

    Graf, M. et al. Telomere length determines TERRA and R-loop regulation through the cell cycle. Cell 170, 72–85.e14 (2017).

  33. 33.

    Postepska-Igielska, A. et al. LncRNA Khps1 regulates expression of the proto-oncogene SPHK1 via triplex-mediated changes in chromatin structure. Mol. Cell 60, 626–636 (2015). This study reports the activation of SPHK1 by the antisense regulatory lncRNA KHPS1, which directly associates with the promoter via a DNA–RNA triplex structure to which chromatin-modifying enzymes are recruited and promote SPHK1 transcription.

  34. 34.

    Clemson, C. M., McNeil, J. A., Willard, H. F. & Lawrence, J. B. XIST RNA paints the inactive X chromosome at interphase: evidence for a novel RNA involved in nuclear/chromosome structure. J. Cell Biol. 132, 259–275 (1996).

  35. 35.

    Poliseno, L. et al. A coding-independent function of gene and pseudogene mRNAs regulates tumour biology. Nature 465, 1033–1038 (2010).

  36. 36.

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

  37. 37.

    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).

  38. 38.

    Schoeftner, S. et al. Recruitment of PRC1 function at the initiation of X inactivation independent of PRC2 and silencing. EMBO J. 25, 3110–3122 (2006).

  39. 39.

    Tripathi, V. et al. The nuclear-retained noncoding RNA MALAT1 regulates alternative splicing by modulating SR splicing factor phosphorylation. Mol. Cell 39, 925–938 (2010).

  40. 40.

    Klingenberg, M. et al. The lncRNA CASC9 and RNA binding protein HNRNPL form a complex and co-regulate genes linked to AKT signaling. Hepatology 68, 1817–1832 (2018).

  41. 41.

    Hämmerle, M. et al. Posttranscriptional destabilization of the liver-specific long noncoding RNA HULC by the IGF2 mRNA-binding protein 1 (IGF2BP1). Hepatology 58, 1703–1712 (2013).

  42. 42.

    Roth, A. & Diederichs, S. Molecular biology: Rap and chirp about X inactivation. Nature 521, 170–171 (2015).

  43. 43.

    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).

  44. 44.

    Lerner, M. R. & Steitz, J. A. Antibodies to small nuclear RNAs complexed with proteins are produced by patients with systemic lupus erythematosus. Proc. Natl. Acad. Sci. USA 76, 5495–5499 (1979).

  45. 45.

    Ule, J. et al. CLIP identifies Nova-regulated RNA networks in the brain. Science 302, 1212–1215 (2003).

  46. 46.

    Hafner, M. et al. Transcriptome-wide identification of RNA-binding protein and microRNA target sites by PAR-CLIP. Cell 141, 129–141 (2010). This study presents a cell-based cross-linking method called PAR–CLIP to map sites for RNA-binding proteins transcriptome wide. Binding sites for PUM2, QKI, IGF2BP1–3, AGO/EIF2C1–4 and TNRC6A–C were determined.

  47. 47.

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

  48. 48.

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

  49. 49.

    Aw, J. G. et al. In vivo mapping of eukaryotic RNA interactomes reveals principles of higher-order organization and regulation. Mol. Cell 62, 603–617 (2016).

  50. 50.

    Nguyen, T. C. et al. Mapping RNA–RNA interactome and RNA structure in vivo by MARIO. Nat. Commun. 7, 12023 (2016).

  51. 51.

    Sharma, E., Sterne-Weiler, T., O’Hanlon, D. & Blencowe, B. J. Global mapping of human RNA-RNA interactions. Mol. Cell 62, 618–626 (2016).

  52. 52.

    Chen, L. L. Linking long noncoding RNA localization and function. Trends Biochem. Sci. 41, 761–772 (2016).

  53. 53.

    Braidotti, G. et al. The Air noncoding RNA: an imprinted cis-silencing transcript. Cold Spring Harb. Symp. Quant. Biol. 69, 55–66 (2004).

  54. 54.

    Holdt, L. M. et al. Alu elements in ANRIL non-coding RNA at chromosome 9p21 modulate atherogenic cell functions through trans-regulation of gene networks. PLoS Genet. 9, e1003588 (2013).

  55. 55.

    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.e10 (2017).

  56. 56.

    Yang, L. et al. ncRNA- and Pc2 methylation-dependent gene relocation between nuclear structures mediates gene activation programs. Cell 147, 773–788 (2011).

  57. 57.

    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).

  58. 58.

    Tsai, M. C. et al. Long noncoding RNA as modular scaffold of histone modification complexes. Science 329, 689–693 (2010).

  59. 59.

    Marín-Béjar, O. et al. Pint lincRNA connects the p53 pathway with epigenetic silencing by the Polycomb repressive complex 2. Genome Biol. 14, R104 (2013).

  60. 60.

    Gonzalez, I. et al. A lncRNA regulates alternative splicing via establishment of a splicing-specific chromatin signature. Nat. Struct. Mol. Biol. 22, 370–376 (2015).

  61. 61.

    Sasaki, Y. T., Ideue, T., Sano, M., Mituyama, T. & Hirose, T. MENepsilon/beta noncoding RNAs are essential for structural integrity of nuclear paraspeckles. Proc. Natl Acad. Sci. USA 106, 2525–2530 (2009).

  62. 62.

    Mao, Y. S., Sunwoo, H., Zhang, B. & Spector, D. L. Direct visualization of the co-transcriptional assembly of a nuclear body by noncoding RNAs. Nat. Cell Biol. 13, 95–101 (2011). By developing a live-cell imaging system for detecting transcription and visualizing an RNA transcript, this study shows that the transcription of the lncRNA MENε/β drives the de novo assembly of paraspeckles by recruiting paraspeckle proteins.

  63. 63.

    Mas-Ponte, D. et al. LncATLAS database for subcellular localization of long noncoding RNAs. RNA 23, 1080–1087 (2017).

  64. 64.

    Soares, R. J. et al. Evaluation of fluorescence in situ hybridization techniques to study long non-coding RNA expression in cultured cells. Nucleic Acids Res. 46, e4 (2018).

  65. 65.

    Martin, K. C. & Ephrussi, A. mRNA localization: gene expression in the spatial dimension. Cell 136, 719–730 (2009).

  66. 66.

    Giulietti, M., Milantoni, S. A., Armeni, T., Principato, G. & Piva, F. ExportAid: database of RNA elements regulating nuclear RNA export in mammals. Bioinformatics 31, 246–251 (2015).

  67. 67.

    Borensztein, M. et al. Xist-dependent imprinted X inactivation and the early developmental consequences of its failure. Nat. Struct. Mol. Biol. 24, 226–233 (2017).

  68. 68.

    Lee, J. T. & Jaenisch, R. Long-range cis effects of ectopic X-inactivation centres on a mouse autosome. Nature 386, 275–279 (1997).

  69. 69.

    Cohen, H. R. & Panning, B. XIST RNA exhibits nuclear retention and exhibits reduced association with the export factor TAP/NXF1. Chromosoma 116, 373–383 (2007).

  70. 70.

    Prasanth, K. V. et al. Regulating gene expression through RNA nuclear retention. Cell 123, 249–263 (2005).

  71. 71.

    Chen, L. L., DeCerbo, J. N. & Carmichael, G. G. Alu element-mediated gene silencing. EMBO J. 27, 1694–1705 (2008).

  72. 72.

    Hacisuleyman, E., Shukla, C. J., Weiner, C. L. & Rinn, J. L. Function and evolution of local repeats in the Firre locus. Nat. Commun. 7, 11021 (2016).

  73. 73.

    Miyagawa, R. et al. Identification of cis- and trans-acting factors involved in the localization of MALAT-1 noncoding RNA to nuclear speckles. RNA 18, 738–751 (2012). This study identified that large fragments of regions E and M of MALAT1 are required for the localization of MALAT1 to nuclear speckles.

  74. 74.

    Zhang, B. et al. A novel RNA motif mediates the strict nuclear localization of a long noncoding RNA. Mol. Cell. Biol. 34, 2318–2329 (2014).

  75. 75.

    Hwang, H. W., Wentzel, E. A. & Mendell, J. T. A hexanucleotide element directs microRNA nuclear import. Science 315, 97–100 (2007).

  76. 76.

    Lange, T. S., Borovjagin, A., Maxwell, E. S. & Gerbi, S. A. Conserved boxes C and D are essential nucleolar localization elements of U14 and U8 snoRNAs. EMBO J. 17, 3176–3187 (1998).

  77. 77.

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

  78. 78.

    Shukla, C. J. et al. High-throughput identification of RNA nuclear enrichment sequences. EMBO J. 37, e98452 (2018).

  79. 79.

    Yin, Y. et al. U1 snRNP reglates chromatin retention of noncoding RNAs. Preprint at https://www.biorxiv.org/content/early/2018/04/29/310433 (2018).

  80. 80.

    Carlevaro-Fita, J., Polidori, T., Das, M., Navarro, C. & Johnson, R. Ancient exapted transposable elements drive nuclear localisation of lncRNAs. Preprint at https://www.biorxiv.org/content/early/2017/10/23/189753 (2017).

  81. 81.

    Brown, C. J. et al. The human XIST gene: analysis of a 17 kb inactive X-specific RNA that contains conserved repeats and is highly localized within the nucleus. Cell 71, 527–542 (1992).

  82. 82.

    Sunwoo, H., Colognori, D., Froberg, J. E., Jeon, Y. & Lee, J. T. Repeat E anchors Xist RNA to the inactive X chromosomal compartment through CDKN1A-interacting protein (CIZ1). Proc. Natl Acad. Sci. USA 114, 10654–10659 (2017).

  83. 83.

    Ridings-Figueroa, R. et al. The nuclear matrix protein CIZ1 facilitates localization of Xist RNA to the inactive X-chromosome territory. Genes Dev. 31, 876–888 (2017).

  84. 84.

    Johnson, R. & Guigó, R. The RIDL hypothesis: transposable elements as functional domains of long noncoding RNAs. RNA 20, 959–976 (2014).

  85. 85.

    Guttman, M. & Rinn, J. L. Modular regulatory principles of large non-coding RNAs. Nature 482, 339–346 (2012).

  86. 86.

    Feschotte, C. Transposable elements and the evolution of regulatory networks. Nat. Rev. Genet. 9, 397–405 (2008).

  87. 87.

    Carrieri, C. et al. Long non-coding antisense RNA controls Uchl1 translation through an embedded SINEB2 repeat. Nature 491, 454–457 (2012).

  88. 88.

    Chillón, I. & Pyle, A. M. Inverted repeat Alu elements in the human lincRNA-p21 adopt a conserved secondary structure that regulates RNA function. Nucleic Acids Res. 44, 9462–9471 (2016). This study identified an inverted Alu repeat in the exonic sequence of the p53-regulated lncRNA hLincRNA-p21 relevant for its nuclear localization.

  89. 89.

    Elisaphenko, E. A. et al. A dual origin of the Xist gene from a protein-coding gene and a set of transposable elements. PLoS One 3, e2521 (2008).

  90. 90.

    Paz, I., Kosti, I., Ares, M. Jr., Cline, M. & Mandel-Gutfreund, Y. RBPmap: a web server for mapping binding sites of RNA-binding proteins. Nucleic Acids Res. 42, W361–W367 (2014).

  91. 91.

    Allis, C. D. & Jenuwein, T. The molecular hallmarks of epigenetic control. Nat. Rev. Genet. 17, 487–500 (2016).

  92. 92.

    Rando, O. J. Combinatorial complexity in chromatin structure and function: revisiting the histone code. Curr. Opin. Genet. Dev. 22, 148–155 (2012).

  93. 93.

    Slattery, M. et al. Absence of a simple code: how transcription factors read the genome. Trends Biochem. Sci. 39, 381–399 (2014).

  94. 94.

    Chang, T. H. et al. An enhanced computational platform for investigating the roles of regulatory RNA and for identifying functional RNA motifs. BMC Bioinformatics 14(Suppl. 2), S4 (2013).

  95. 95.

    Alam, T. et al. FARNA: knowledgebase of inferred functions of non-coding RNA transcripts. Nucleic Acids Res. 45, 2838–2848 (2017).

  96. 96.

    Li, J. H., Liu, S., Zhou, H., Qu, L. H. & Yang, J. H. starBase v2.0: decoding miRNA-ceRNA, miRNA-ncRNA and protein-RNA interaction networks from large-scale CLIP-Seq data. Nucleic Acids Res. 42, D92–D97 (2014).

  97. 97.

    Cao, H., Wahlestedt, C. & Kapranov, P. Strategies to annotate and characterize long noncoding RNAs: advantages and pitfalls. Trends Genet. 34, 704–721 (2018).

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Acknowledgements

S.D. is supported by the Deutsche Forschungsgemeinschaft (German Research Foundation), Di1421/7-1.

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Correspondence to Sven Diederichs.

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Unrelated to this work, S.D. is a co-owner of siTOOLs Biotech GmbH, Martinsried, Germany.

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Fig. 1: Screening for RNA localization motifs.
Fig. 2: Combinatorial determinants of RNA-motif function.