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Non-coding RNAs: Classification, Biology and Functioning

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Non-coding RNAs in Colorectal Cancer

Part of the book series: Advances in Experimental Medicine and Biology ((AEMB,volume 937))

Abstract

One of the long-standing principles of molecular biology is that DNA acts as a template for transcription of messenger RNAs, which serve as blueprints for protein translation. A rapidly growing number of exceptions to this rule have been reported over the past decades: they include long known classes of RNAs involved in translation such as transfer RNAs and ribosomal RNAs, small nuclear RNAs involved in splicing events, and small nucleolar RNAs mainly involved in the modification of other small RNAs, such as ribosomal RNAs and transfer RNAs. More recently, several classes of short regulatory non-coding RNAs, including piwi-associated RNAs, endogenous short-interfering RNAs and microRNAs have been discovered in mammals, which act as key regulators of gene expression in many different cellular pathways and systems. Additionally, the human genome encodes several thousand long non-protein coding RNAs >200 nucleotides in length, some of which play crucial roles in a variety of biological processes such as epigenetic control of chromatin, promoter-specific gene regulation, mRNA stability, X-chromosome inactivation and imprinting. In this chapter, we will introduce several classes of short and long non-coding RNAs, describe their diverse roles in mammalian gene regulation and give examples for known modes of action.

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References

  1. Matera AG, Terns RM, Terns MP. Non-coding RNAs: lessons from the small nuclear and small nucleolar RNAs. Nat Rev Mol Cell Biol. 2007;8:209–20.

    Article  CAS  PubMed  Google Scholar 

  2. Rocheleau CE, Downs WD, Lin R, Wittmann C, Bei Y, Cha Y-H, et al. Wnt Signaling and an APC-Related Gene Specify Endoderm in Early C. elegans Embryos. Cell. 1997;90:707–16.

    Article  CAS  PubMed  Google Scholar 

  3. Fire A, Xu S, Montgomery MK, Kostas SA, Driver SE, Mello CC. Potent and specific genetic interference by double-stranded RNA in Caenorhabditis elegans. Nature. 1998;391:806–11.

    Article  CAS  PubMed  Google Scholar 

  4. Czech B, Hannon GJ. Small RNA sorting: matchmaking for Argonautes. Nat Rev Genet. 2011;12:19–31.

    Article  CAS  PubMed  Google Scholar 

  5. Meister G, Tuschl T. Mechanisms of gene silencing by double-stranded RNA. Nature. 2004;431:343–9.

    Article  CAS  PubMed  Google Scholar 

  6. Farazi TA, Juranek SA, Tuschl T. The growing catalog of small RNAs and their association with distinct Argonaute/Piwi family members. Development. 2008;135:1201–14.

    Article  CAS  PubMed  Google Scholar 

  7. Siomi H, Siomi MC. On the road to reading the RNA-interference code. Nature. 2009;457:396–404.

    Article  CAS  PubMed  Google Scholar 

  8. Bartel DP. MicroRNAs: target recognition and regulatory functions. Cell. 2009;136:215–33.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  9. Carthew RW, Sontheimer EJ. Origins and mechanisms of miRNAs and siRNAs. Cell. 2009;136:642–55.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  10. Siomi MC, Sato K, Pezic D, Aravin AA. PIWI-interacting small RNAs: the vanguard of genome defence. Nat Rev Mol Cell Biol. 2011;12:246–58.

    Article  CAS  PubMed  Google Scholar 

  11. Mendell JT, Olson EN. MicroRNAs in stress signaling and human disease. Cell. 2012;148:1172–87.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  12. Dueck A, Meister G. Assembly and function of small RNA – Argonaute protein complexes. Biol Chem. 2014;395:611–29.

    Article  CAS  PubMed  Google Scholar 

  13. Mattick JS. Non-coding RNAs: the architects of eukaryotic complexity. EMBO Rep. 2001;2:986–91.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  14. Consortium IHGS. Finishing the euchromatic sequence of the human genome. Nature. 2004;431:931–45.

    Article  CAS  Google Scholar 

  15. Djebali S, Davis CA, Merkel A, Dobin A, Lassmann T, Mortazavi A, et al. Landscape of transcription in human cells. Nature. 2012;489:101–8.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  16. Jia H, Osak M, Bogu GK, Stanton LW, Johnson R, Lipovich L. Genome-wide computational identification and manual annotation of human long noncoding RNA genes. RNA. 2010;16:1478–87.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  17. Cabili MN, Trapnell C, Goff L, Koziol M, Tazon-Vega B, Regev A, et al. Integrative annotation of human large intergenic noncoding RNAs reveals global properties and specific subclasses. Genes Dev. 2011;25:1915–27.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  18. Martianov I, Ramadass A, Serra Barros A, Chow N, Akoulitchev A. Repression of the human dihydrofolate reductase gene by a non-coding interfering transcript. Nature. 2007;445:666–70.

    Article  CAS  PubMed  Google Scholar 

  19. Feng J, Bi C, Clark B, Mady R, Shah P, Kohtz J. The Evf-2 noncoding RNA is transcribed from the Dlx-5/6 ultraconserved region and functions as a Dlx-2 transcriptional coactivator. Genes Dev. 2006;20:1470–84.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  20. Bond AM, VanGompel MJW, Sametsky EA, Clark MF, Savage JC, Disterhoft JF, et al. Balanced gene regulation by an embryonic brain ncRNA is critical for adult hippocampal GABA circuitry. Nat Neurosci. 2009;12:1020–7.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  21. Tian D, Sun S, Lee J. The long noncoding RNA, jpx, is a molecular switch for x chromosome inactivation. Cell. 2010;143:390–403.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  22. Lee J. Lessons from X-chromosome inactivation: long ncRNA as guides and tethers to the epigenome. Genes Dev. 2009;23:1831–42.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  23. Lee JT, Bartolomei MS. X-inactivation, imprinting, and long noncoding RNAs in health and disease. Cell. 2013;152:1308–23.

    Article  CAS  PubMed  Google Scholar 

  24. Bartolomei MS, Zemel S, Tilghman SM. Parental imprinting of the mouse H19 gene. Nature. 1991;351:153–5. Publ. Online 09 May 1991 Doi101038351153a0.

    Article  CAS  PubMed  Google Scholar 

  25. Lyle R, Watanabe D, te Vruchte D, Lerchner W, Smrzka OW, Wutz A, et al. The imprinted antisense RNA at the Igf2r locus overlaps but does not imprint Mas1. Nat Genet. 2000;25:19–21.

    Article  CAS  PubMed  Google Scholar 

  26. Sleutels F, Zwart R, Barlow D. The non-coding Air RNA is required for silencing autosomal imprinted genes. Nature. 2002;415:810–3.

    Article  CAS  PubMed  Google Scholar 

  27. Mancini-Dinardo D, Steele S, Levorse J, Ingram R, Tilghman S. Elongation of the Kcnq1ot1 transcript is required for genomic imprinting of neighboring genes. Genes Dev. 2006;20:1268–82.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  28. Williamson CM, Ball ST, Dawson C, Mehta S, Beechey CV, Fray M, et al. Uncoupling antisense-mediated silencing and DNA methylation in the imprinted Gnas cluster. PLoS Genet. 2011;7:e1001347.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  29. Mao Y, Sunwoo H, Zhang B, Spector D. Direct visualization of the co-transcriptional assembly of a nuclear body by noncoding RNAs. Nat Cell Biol. 2011;13:95–101.

    Article  CAS  PubMed  Google Scholar 

  30. Hacisuleyman E, Goff LA, Trapnell C, Williams A, Henao-Mejia J, Sun L, et al. Topological organization of multichromosomal regions by the long intergenic noncoding RNA Firre. Nat Struct Mol Biol. 2014;21:198–206.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  31. Yang F, Deng X, Ma W, Berletch JB, Rabaia N, Wei G, et al. The lncRNA Firre anchors the inactive X chromosome to the nucleolus by binding CTCF and maintains H3K27me3 methylation. Genome Biol. 2015. doi:10.1186/s13059-015-0618-0.

    Google Scholar 

  32. Krol J, Loedige I, Filipowicz W. The widespread regulation of microRNA biogenesis, function and decay. Nat Rev Genet. 2010;11:597–610.

    CAS  PubMed  Google Scholar 

  33. Esteller M. Non-coding RNAs in human disease. Nat Rev Genet. 2011;12:861–74.

    Article  CAS  PubMed  Google Scholar 

  34. Gutschner T, Diederichs S. The hallmarks of cancer. RNA Biol. 2012;9:703–19.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  35. Huntzinger E, Izaurralde E. Gene silencing by microRNAs: contributions of translational repression and mRNA decay. Nat Rev Genet. 2011;12:99–110.

    Article  CAS  PubMed  Google Scholar 

  36. Sayed D, Abdellatif M. MicroRNAs in development and disease. Physiol Rev. 2011;91:827–87.

    Article  CAS  PubMed  Google Scholar 

  37. Friedman RC, Farh KK-H, Burge CB, Bartel DP. Most mammalian mRNAs are conserved targets of microRNAs. Genome Res. 2009;19:92–105.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  38. Lin S, Gregory RI. MicroRNA biogenesis pathways in cancer. Nat Rev Cancer. 2015;15:321–33.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  39. Liu N, Olson EN. MicroRNA regulatory networks in cardiovascular development. Dev Cell. 2010;18:510–25.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  40. Olson EN. MicroRNAs as therapeutic targets and biomarkers of cardiovascular disease. Sci Transl Med. 2014;6:239ps3.

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  41. Issler O, Chen A. Determining the role of microRNAs in psychiatric disorders. Nat Rev Neurosci. 2015;16:201–12.

    Article  CAS  PubMed  Google Scholar 

  42. Treiber T, Treiber N, Meister G. Regulation of microRNA biogenesis and function. Thromb Haemost. 2012;107:605–10.

    Article  CAS  PubMed  Google Scholar 

  43. Jonas S, Izaurralde E. Towards a molecular understanding of microRNA-mediated gene silencing. Nat Rev Genet. 2015;16:421–33.

    Article  CAS  PubMed  Google Scholar 

  44. Du P, Wang L, Sliz P, Gregory RI. A biogenesis step upstream of microprocessor controls miR-17 ∼ 92 expression. Cell. 2015;162:885–99.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  45. Luteijn MJ, Ketting RF. PIWI-interacting RNAs: from generation to transgenerational epigenetics. Nat Rev Genet. 2013;14:523–34.

    Article  CAS  PubMed  Google Scholar 

  46. Claycomb JM. Ancient endo-siRNA pathways reveal new tricks. Curr Biol. 2014;24:R703–15.

    Article  CAS  PubMed  Google Scholar 

  47. Nayak A, Tassetto M, Kunitomi M, Andino R. RNA interference-mediated intrinsic antiviral immunity in invertebrates. In: Cullen BR, editor. Intrinsic immun. Berlin/Heidelberg: Springer; 2013. p. 183–200.

    Chapter  Google Scholar 

  48. Szittya G, Burgyán J. RNA interference-mediated intrinsic antiviral immunity in plants. In: Cullen BR, editor. Intrinsic immun. Berlin /Heidelberg: Springer; 2013. p. 153–81.

    Chapter  Google Scholar 

  49. García-Sastre A. Induction and evasion of type I interferon responses by influenza viruses. Virus Res. 2011;162:12–8.

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  50. Billy E, Brondani V, Zhang H, Müller U, Filipowicz W. Specific interference with gene expression induced by long, double-stranded RNA in mouse embryonal teratocarcinoma cell lines. Proc Natl Acad Sci. 2001;98:14428–33.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  51. Li Y, Lu J, Han Y, Fan X, Ding S-W. RNA interference functions as an antiviral immunity mechanism in mammals. Science. 2013;342:231–4.

    Article  CAS  PubMed  Google Scholar 

  52. Maillard PV, Ciaudo C, Marchais A, Li Y, Jay F, Ding SW, et al. Antiviral RNA interference in mammalian cells. Science. 2013;342:235–8.

    Article  CAS  PubMed  Google Scholar 

  53. Pare JM, Sullivan CS. Distinct antiviral responses in pluripotent versus differentiated cells. PLoS Pathog. 2014. doi:10.1371/journal.ppat.1003865.

    PubMed  PubMed Central  Google Scholar 

  54. Tam OH, Aravin AA, Stein P, Girard A, Murchison EP, Cheloufi S, et al. Pseudogene-derived small interfering RNAs regulate gene expression in mouse oocytes. Nature. 2008;453:534–8.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  55. Watanabe T, Totoki Y, Toyoda A, Kaneda M, Kuramochi-Miyagawa S, Obata Y, et al. Endogenous siRNAs from naturally formed dsRNAs regulate transcripts in mouse oocytes. Nature. 2008;453:539–43.

    Article  CAS  PubMed  Google Scholar 

  56. Ender C, Krek A, Friedländer MR, Beitzinger M, Weinmann L, Chen W, et al. A human snoRNA with microRNA-like functions. Mol Cell. 2008;32:519–28.

    Article  CAS  PubMed  Google Scholar 

  57. Brameier M, Herwig A, Reinhardt R, Walter L, Gruber J. Human box C/D snoRNAs with miRNA like functions: expanding the range of regulatory RNAs. Nucleic Acids Res. 2011;39:675–86.

    Article  CAS  PubMed  Google Scholar 

  58. Röther S, Meister G. Small RNAs derived from longer non-coding RNAs. Biochimie. 2011;93:1905–15.

    Article  PubMed  CAS  Google Scholar 

  59. Bratkovič T, Rogelj B. The many faces of small nucleolar RNAs. Biochim Biophys Acta BBA - Gene Regul Mech. 1839;2014:438–43.

    Google Scholar 

  60. Siprashvili Z, Webster DE, Johnston D, Shenoy RM, Ungewickell AJ, Bhaduri A, et al. The noncoding RNAs SNORD50A and SNORD50B bind K-Ras and are recurrently deleted in human cancer. Nat Genet. 2016;48:53–8.

    Article  CAS  PubMed  Google Scholar 

  61. Haussecker D, Huang Y, Lau A, Parameswaran P, Fire AZ, Kay MA. Human tRNA-derived small RNAs in the global regulation of RNA silencing. RNA. 2010;16:673–95.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  62. Gebetsberger J, Polacek N. Slicing tRNAs to boost functional ncRNA diversity. RNA Biol. 2013;10:1798–806.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  63. Sharma U, Conine CC, Shea JM, Boskovic A, Derr AG, Bing XY, et al. Biogenesis and function of tRNA fragments during sperm maturation and fertilization in mammals. Science. 2016;351:391–6.

    Article  CAS  PubMed  Google Scholar 

  64. Goodarzi H, Liu X, Nguyen HCB, Zhang S, Fish L, Tavazoie SF. Endogenous tRNA-derived fragments suppress breast cancer progression via YBX1 displacement. Cell. 2015;161:790–802.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  65. Kung JTY, Colognori D, Lee JT. Long noncoding RNAs: past, present, and future. Genetics. 2013;193:651–69.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  66. Bassett AR, Akhtar A, Barlow DP, Bird AP, Brockdorff N, Duboule D, et al. Considerations when investigating lncRNA function in vivo. eLife. 2014. doi:10.7554/eLife.03058.

    PubMed  PubMed Central  Google Scholar 

  67. Guttman M, Rinn J. Modular regulatory principles of large non-coding RNAs. Nature. 2012;482:339–46.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  68. Mercer TR, Mattick JS. Structure and function of long noncoding RNAs in epigenetic regulation. Nat Struct Mol Biol. 2013;20:300–7.

    Article  CAS  PubMed  Google Scholar 

  69. Batista PJ, Chang HY. Long noncoding RNAs: cellular address codes in development and disease. Cell. 2013;152:1298–307.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  70. Morris KV, Mattick JS. The rise of regulatory RNA. Nat Rev Genet. 2014;15:423–37.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  71. Wang K, Chang H. Molecular mechanisms of long noncoding RNAs. Mol Cell. 2014;43:904–14.

    Article  CAS  Google Scholar 

  72. Berghoff EG, Clark MF, Chen S, Cajigas I, Leib DE, Kohtz JD. Evf2 (Dlx6as) lncRNA regulates ultraconserved enhancer methylation and the differential transcriptional control of adjacent genes. Development. 2013;140:4407–16.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  73. Kim T-K, Hemberg M, Gray JM, Costa AM, Bear DM, Wu J, et al. Widespread transcription at neuronal activity-regulated enhancers. Nature. 2010;465:182–7.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  74. Melo CA, Drost J, Wijchers PJ, van de Werken H, de Wit E, Vrielink JAFO, et al. eRNAs are required for p53-dependent enhancer activity and gene transcription. Mol Cell. 2013;49:524–35.

    Article  CAS  PubMed  Google Scholar 

  75. Arner E, Daub CO, Vitting-Seerup K, Andersson R, Lilje B, Drabløs F, et al. Transcribed enhancers lead waves of coordinated transcription in transitioning mammalian cells. Science. 2015;347:1010–4.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  76. Léveillé N, Melo CA, Rooijers K, Díaz-Lagares A, Melo SA, Korkmaz G, et al. Genome-wide profiling of p53-regulated enhancer RNAs uncovers a subset of enhancers controlled by a lncRNA. Nat Commun. 2015;6:6520.

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  77. Sigova AA, Abraham BJ, Ji X, Molinie B, Hannett NM, Guo YE, et al. Transcription factor trapping by RNA in gene regulatory elements. Science. 2015;350:978–81.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  78. Vance KW, Sansom SN, Lee S, Chalei V, Kong L, Cooper SE, et al. The long non-coding RNA Paupar regulates the expression of both local and distal genes. EMBO J. 2014;33:296–311.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  79. Lai F, Orom UA, Cesaroni M, Beringer M, Taatjes DJ, Blobel GA, et al. Activating RNAs associate with mediator to enhance chromatin architecture and transcription. Nature. 2013;494:497–501.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  80. Khalil A, Guttman M, Huarte M, Garber M, Raj A, Rivea Morales D, et al. Many human large intergenic noncoding RNAs associate with chromatin-modifying complexes and affect gene expression. Proc Natl Acad Sci U S A. 2009;106:11667–72.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  81. Grote P, Wittler L, Hendrix D, Koch F, Währisch S, Beisaw A, et al. The tissue-specific lncRNA Fendrr is an essential regulator of heart and body wall development in the mouse. Dev Cell. 2013;24:206–14.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  82. Grote P, Herrmann BG. The long non-coding RNA Fendrr links epigenetic control mechanisms to gene regulatory networks in mammalian embryogenesis. RNA Biol. 2013;10.

    Google Scholar 

  83. Rinn J, Kertesz M, Wang J, Squazzo S, Xu X, Brugmann S, et al. Functional demarcation of active and silent chromatin domains in human HOX loci by noncoding RNAs. Cell. 2007;129:1311–23.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  84. Tsai M, Manor O, Wan Y, Mosammaparast N, Wang J, Lan F, et al. Long noncoding RNA as modular scaffold of histone modification complexes. Science. 2010;329:689–93.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  85. Gupta RA, Shah N, Wang KC, Kim J, Horlings HM, Wong DJ, et al. Long non-coding RNA HOTAIR reprograms chromatin state to promote cancer metastasis. Nature. 2010;464:1071–6.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  86. Sunwoo H, Dinger ME, Wilusz JE, Amaral PP, Mattick JS, Spector DL. MEN ε/β nuclear-retained non-coding RNAs are up-regulated upon muscle differentiation and are essential components of paraspeckles. Genome Res. 2009;19:347–59.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  87. Chen L-L, Carmichael GG. Altered nuclear retention of mRNAs containing inverted repeats in human embryonic stem cells: functional role of a nuclear noncoding RNA. Mol Cell. 2009;35:467–78.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  88. Clemson CM, Hutchinson JN, Sara SA, Ensminger AW, Fox AH, Chess A, et al. An architectural role for a nuclear noncoding RNA: NEAT1 RNA is essential for the structure of paraspeckles. Mol Cell. 2009;33:717–26.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  89. Zhao J, Sun B, Erwin J, Song J, Lee J. Polycomb proteins targeted by a short repeat RNA to the mouse X chromosome. Science. 2008;322:750–6.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  90. Yoon J-H, Abdelmohsen K, Gorospe M. Posttranscriptional gene regulation by long noncoding RNA. J Mol Biol. 2013;425:3723–30.

    Article  CAS  PubMed  Google Scholar 

  91. Gong C, Maquat L. lncRNAs transactivate STAU1-mediated mRNA decay by duplexing with 3′ UTRs via Alu elements. Nature. 2011;470:284–8.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  92. Schoenberg D, Maquat L. Regulation of cytoplasmic mRNA decay. Nat Rev Genet. 2012;1–14.

    Google Scholar 

  93. Blanpain C, Fuchs E. Epidermal homeostasis: a balancing act of stem cells in the skin. Nat Rev Mol Cell Biol. 2009;10:207–17.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  94. Kretz M, Siprashvili Z, Chu C, Webster DE, Zehnder A, Qu K, et al. Control of somatic tissue differentiation by the long non-coding RNA TINCR. Nature. 2013;493:231–5.

    Article  CAS  PubMed  Google Scholar 

  95. Hombach S, Kretz M. The non-coding skin: exploring the roles of long non-coding RNAs in epidermal homeostasis and disease. BioEssays. 2013;35:1093–100.

    Article  CAS  PubMed  Google Scholar 

  96. Lopez-Pajares V, Qu K, Zhang J, Webster DE, Barajas BC, Siprashvili Z, et al. A LncRNA-MAF:MAFB transcription factor network regulates epidermal differentiation. Dev Cell. 2015;32:693–706.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  97. Sun BK, Boxer LD, Ransohoff JD, Siprashvili Z, Qu K, Lopez-Pajares V, et al. CALML5 is a ZNF750- and TINCR-induced protein that binds stratifin to regulate epidermal differentiation. Genes Dev. 2015;29:2225–30.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  98. Yoon J-H, Abdelmohsen K, Srikantan S, Yang X, Martindale JL, De S, et al. LincRNA-p21 suppresses target mRNA translation. Mol Cell. 2012;47:648–55.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  99. Ebert M, Sharp P. Emerging roles for natural microRNA sponges. Curr Biol CB. 2010;20:R858–61.

    Article  CAS  PubMed  Google Scholar 

  100. Salmena L, Poliseno L, Tay Y, Kats L, Pandolfi P. A ceRNA hypothesis: the rosetta stone of a hidden RNA language? Cell. 2011;146:353–8.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  101. Wang Y, Xu Z, Jiang J, Xu C, Kang J, Xiao L, et al. Endogenous miRNA sponge lincRNA-RoR regulates Oct4, Nanog, and Sox2 in human embryonic stem cell self-renewal. Dev Cell. 2013;25:69–80.

    Article  CAS  PubMed  Google Scholar 

  102. Tay Y, Rinn J, Pandolfi PP. The multilayered complexity of ceRNA crosstalk and competition. Nature. 2014;505:344–52.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  103. Poliseno L, Salmena L, Zhang J, Carver B, Haveman WJ, Pandolfi PP. A coding-independent function of gene and pseudogene mRNAs regulates tumour biology. Nature. 2010;465:1033–8.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  104. Lee DY, Jeyapalan Z, Fang L, Yang J, Zhang Y, Yee AY, et al. Expression of versican 3′-untranslated region modulates endogenous microRNA functions. PLoS One. 2010;5:e13599.

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  105. Karreth FA, Tay Y, Perna D, Ala U, Tan SM, Rust AG, et al. In vivo identification of tumor- suppressive PTEN ceRNAs in an oncogenic BRAF-induced mouse model of melanoma. Cell. 2011;147:382–95.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  106. Tay Y, Kats L, Salmena L, Weiss D, Tan SM, Ala U, et al. Coding-independent regulation of the tumor suppressor PTEN by competing endogenous mRNAs. Cell. 2011;147:344–57.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  107. Poliseno L, Pandolfi PP. PTEN ceRNA networks in human cancer. Methods. 2015;77–78:41–50.

    Article  PubMed  CAS  Google Scholar 

  108. Cesana M, Cacchiarelli D, Legnini I, Santini T, Sthandier O, Chinappi M, et al. A long noncoding RNA controls muscle differentiation by functioning as a competing endogenous RNA. Cell. 2011;147:358–69.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  109. Legnini I, Morlando M, Mangiavacchi A, Fatica A, Bozzoni I. A feedforward regulatory loop between HuR and the long noncoding RNA linc-MD1 controls early phases of myogenesis. Mol Cell. 2014;53:506–14.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  110. Kallen AN, Zhou X-B, Xu J, Qiao C, Ma J, Yan L, et al. The imprinted H19 LncRNA antagonizes Let-7 MicroRNAs. Mol Cell. 2013;52:101–12.

    Article  CAS  PubMed  Google Scholar 

  111. Jeck WR, Sharpless NE. Detecting and characterizing circular RNAs. Nat Biotechnol. 2014;32:453–61.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  112. Hansen TB, Jensen TI, Clausen BH, Bramsen JB, Finsen B, Damgaard CK, et al. Natural RNA circles function as efficient microRNA sponges. Nature. 2013;495:384–8.

    Article  CAS  PubMed  Google Scholar 

  113. Memczak S, Jens M, Elefsinioti A, Torti F, Krueger J, Rybak A, et al. Circular RNAs are a large class of animal RNAs with regulatory potency. Nature. 2013;495:333–8.

    Article  CAS  PubMed  Google Scholar 

  114. Carninci P, Kasukawa T, Katayama S, Gough J, Frith M, Maeda N, et al. The transcriptional landscape of the mammalian genome. Science. 2005;309:1559–63.

    Article  CAS  PubMed  Google Scholar 

  115. Consortium RGERG and GSG (Genome NPCG and the Katayama S, Tomaru Y, Kasukawa T, Waki K, Nakanishi M, et al. Antisense transcription in the mammalian transcriptome. Science. 2005;309:1564–6.

    Google Scholar 

  116. Kawaji H, Severin J, Lizio M, Waterhouse A, Katayama S, Irvine K, et al. The FANTOM web resource: from mammalian transcriptional landscape to its dynamic regulation. Genome Biol. 2009;10:R40.

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  117. Kondo T, Plaza S, Zanet J, Benrabah E, Valenti P, Hashimoto Y, et al. Small peptides switch the transcriptional activity of Shavenbaby during Drosophila embryogenesis. Science. 2010;329:336–9.

    Article  CAS  PubMed  Google Scholar 

  118. Anderson DM, Anderson KM, Chang C-L, Makarewich CA, Nelson BR, McAnally JR, et al. A micropeptide encoded by a putative long noncoding RNA regulates muscle performance. Cell. 2015;160:595–606.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  119. Li M, Gou H, Tripathi BK, Huang J, Jiang S, Dubois W, et al. An Apela RNA-containing negative feedback loop regulates p53-mediated apoptosis in embryonic stem cells. Cell Stem Cell. 2015;16:669–83.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  120. Chu C, Qu K, Zhong FL, Artandi SE, Chang HY. Genomic maps of long noncoding RNA occupancy reveal principles of RNA-chromatin interactions. Mol Cell. 2011;44:667–78.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  121. Simon MD, Wang CI, Kharchenko PV, West JA, Chapman BA, Alekseyenko AA, et al. The genomic binding sites of a noncoding RNA. Proc Natl Acad Sci. 2011;108:20497–502.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  122. Engreitz JM, Pandya-Jones A, McDonel P, Shishkin A, Sirokman K, Surka C, et al. The Xist lncRNA exploits three-dimensional genome architecture to spread across the X chromosome. Science. 2013;341:1237973.

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  123. Chu C, Spitale RC, Chang HY. Technologies to probe functions and mechanisms of long noncoding RNAs. Nat Struct Mol Biol. 2015;22:29–35.

    Article  CAS  PubMed  Google Scholar 

  124. Chu C, Zhang QC, da Rocha ST, Flynn RA, Bharadwaj M, Calabrese JM, et al. Systematic discovery of Xist RNA binding proteins. Cell. 2015;161:404–16.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  125. McHugh CA, Chen C-K, Chow A, Surka CF, Tran C, McDonel P, et al. The Xist lncRNA interacts directly with SHARP to silence transcription through HDAC3. Nature. 2015;521:232–6.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  126. Minajigi A, Froberg JE, Wei C, Sunwoo H, Kesner B, Colognori D, et al. A comprehensive Xist interactome reveals cohesin repulsion and an RNA-directed chromosome conformation. Science. 2015;349:aab2276.

    Google Scholar 

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Authors and Affiliations

  1. Institute of Biochemistry, Genetics and Microbiology, University of Regensburg, Regensburg, Germany

    Sonja Hombach & Markus Kretz

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  1. Sonja Hombach
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  2. Markus Kretz
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Correspondence to Sonja Hombach .

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Editors and Affiliations

  1. Central European Institute of Technology, Masaryk University, Brno, Czech Republic

    Ondrej Slaby

  2. Department of Experimental Therapeutics Division of Cancer Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, USA

    George A. Calin

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Hombach, S., Kretz, M. (2016). Non-coding RNAs: Classification, Biology and Functioning. In: Slaby, O., Calin, G. (eds) Non-coding RNAs in Colorectal Cancer. Advances in Experimental Medicine and Biology, vol 937. Springer, Cham. https://doi.org/10.1007/978-3-319-42059-2_1

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