Abstract
The revolution of miRNA discovery, in the early 2000s, shed a new light in the exciting field of small non-coding RNAs. Since then, and owing to outstanding breakthroughs in RNomic techniques, novel small non-coding RNA families have been regularly discovered, e.g., piRNAs, tiRNAs, and many others.
In this review, we provide a very succinct historical and functional overview on most prominent small non-coding RNA families.
Access this chapter
Tax calculation will be finalised at checkout
Purchases are for personal use only
Similar content being viewed by others
References
Holley RW, Apgar J, Doctor BP (1960) Separation of amino acid-specific “soluble”-fraction ribonucleic acids. Ann N Y Acad Sci 88:745–751
Holley RW, Apgar J, Everett GA, Madison JT, Marquisee M, Merrill SH, Penswick JR, Zamir A (1965) Structure of a ribonucleic acid. Science 147(3664):1462–1465
Eddy SR (2001) Non-coding RNA genes and the modern RNA world. Nat Rev Genet 2(12):919–929. doi:10.1038/35103511, 35103511 [pii]
Busch H, Reddy R, Rothblum L, Choi YC (1982) SnRNAs, SnRNPs, and RNA processing. Annu Rev Biochem 51:617–654. doi:10.1146/annurev.bi.51.070182.003153
Weinberg RA, Penman S (1968) Small molecular weight monodisperse nuclear RNA. J Mol Biol 38(3):289–304, doi:0022-2836(68)90387-2 [pii]
Lerner MR, Steitz JA (1979) Antibodies to small nuclear RNAs complexed with proteins are produced by patients with systemic lupus erythematosus. Proc Natl Acad Sci U S A 76(11):5495–5499
Lerner MR, Boyle JA, Mount SM, Wolin SL, Steitz JA (1980) Are snRNPs involved in splicing? Nature 283(5743):220–224
Matera AG, Terns RM, Terns MP (2007) Non-coding RNAs: lessons from the small nuclear and small nucleolar RNAs. Nat Rev Mol Cell Biol 8(3):209–220. doi:10.1038/nrm2124, nrm2124 [pii]
Marmier-Gourrier N, Clery A, Schlotter F, Senty-Segault V, Branlant C (2011) A second base pair interaction between U3 small nucleolar RNA and the 5′-ETS region is required for early cleavage of the yeast pre-ribosomal RNA. Nucleic Acids Res 39(22):9731–9745. doi:10.1093/nar/gkr675, gkr675 [pii]
Huttenhofer A, Kiefmann M, Meier-Ewert S, O′Brien J, Lehrach H, Bachellerie JP, Brosius J (2001) RNomics: an experimental approach that identifies 201 candidates for novel, small, non-messenger RNAs in mouse. EMBO J 20(11):2943–2953. doi:10.1093/emboj/20.11.2943
Wightman B, Burglin TR, Gatto J, Arasu P, Ruvkun G (1991) Negative regulatory sequences in the lin-14 3′-untranslated region are necessary to generate a temporal switch during Caenorhabditis elegans development. Genes Dev 5(10):1813–1824
Lee RC, Feinbaum RL, Ambros V (1993) The C. elegans heterochronic gene lin-4 encodes small RNAs with antisense complementarity to lin-14. Cell 75(5):843–854, doi: 0092-8674(93)90529-Y [pii]
Wightman B, Ha I, Ruvkun G (1993) Posttranscriptional regulation of the heterochronic gene lin-14 by lin-4 mediates temporal pattern formation in C. elegans. Cell 75(5):855–862, doi: 0092-8674(93)90530-4 [pii]
Pasquinelli AE, Reinhart BJ, Slack F, Martindale MQ, Kuroda MI, Maller B, Hayward DC, Ball EE, Degnan B, Muller P, Spring J, Srinivasan A, Fishman M, Finnerty J, Corbo J, Levine M, Leahy P, Davidson E, Ruvkun G (2000) Conservation of the sequence and temporal expression of let-7 heterochronic regulatory RNA. Nature 408(6808):86–89. doi:10.1038/35040556
Lagos-Quintana M, Rauhut R, Lendeckel W, Tuschl T (2001) Identification of novel genes coding for small expressed RNAs. Science 294(5543):853–858. doi:10.1126/science.1064921, 294/5543/853 [pii]
Lau NC, Lim LP, Weinstein EG, Bartel DP (2001) An abundant class of tiny RNAs with probable regulatory roles in Caenorhabditis elegans. Science 294(5543):858–862. doi:10.1126/science.1065062, 294/5543/858 [pii]
Lee RC, Ambros V (2001) An extensive class of small RNAs in Caenorhabditis elegans. Science 294(5543):862–864. doi:10.1126/science.1065329, 294/5543/862 [pii]
Nathans R, Chu CY, Serquina AK, Lu CC, Cao H, Rana TM (2009) Cellular microRNA and P bodies modulate host-HIV-1 interactions. Mol Cell 34(6):696–709. doi:10.1016/j.molcel.2009.06.003, S1097-2765(09)00394-3 [pii]
Pfeffer S, Zavolan M, Grasser FA, Chien M, Russo JJ, Ju J, John B, Enright AJ, Marks D, Sander C, Tuschl T (2004) Identification of virus-encoded microRNAs. Science 304(5671):734–736. doi:10.1126/science.1096781, 304/5671/734 [pii]
Fire A, Xu S, Montgomery MK, Kostas SA, Driver SE, Mello CC (1998) Potent and specific genetic interference by double-stranded RNA in Caenorhabditis elegans. Nature 391(6669):806–811. doi:10.1038/35888
Hutvagner G, McLachlan J, Pasquinelli AE, Balint E, Tuschl T, Zamore PD (2001) A cellular function for the RNA-interference enzyme Dicer in the maturation of the let-7 small temporal RNA. Science 293(5531):834–838. doi:10.1126/science.1062961, 1062961 [pii]
Napoli C, Lemieux C, Jorgensen R (1990) Introduction of a chimeric chalcone synthase gene into petunia results in reversible co-suppression of homologous genes in trans. Plant Cell 2(4):279–289. doi:10.1105/tpc.2.4.279, 2/4/279 [pii]
Bartel DP (2004) MicroRNAs: genomics, biogenesis, mechanism, and function. Cell 116(2):281–297, doi: S0092867404000455 [pii]
Ender C, Krek A, Friedlander MR, Beitzinger M, Weinmann L, Chen W, Pfeffer S, Rajewsky N, Meister G (2008) A human snoRNA with microRNA-like functions. Mol Cell 32(4):519–528. doi:10.1016/j.molcel.2008.10.017, S1097-2765(08)00733-8 [pii]
Rother S, Meister G (2011) Small RNAs derived from longer non-coding RNAs. Biochimie 93(11):1905–1915. doi:10.1016/j.biochi.2011.07.032, S0300-9084(11)00290-2 [pii]
Tuschl T, Zamore PD, Lehmann R, Bartel DP, Sharp PA (1999) Targeted mRNA degradation by double-stranded RNA in vitro. Genes Dev 13(24):3191–3197
Zamore PD, Tuschl T, Sharp PA, Bartel DP (2000) RNAi: double-stranded RNA directs the ATP-dependent cleavage of mRNA at 21 to 23 nucleotide intervals. Cell 101(1):25–33. doi:10.1016/S0092-8674(00)80620-0, S0092-8674(00)80620-0 [pii]
Braun JE, Huntzinger E, Izaurralde E (2013) The role of GW182 proteins in miRNA-mediated gene silencing. Adv Exp Med Biol 768:147–163. doi:10.1007/978-1-4614-5107-5_9
Eulalio A, Tritschler F, Izaurralde E (2009) The GW182 protein family in animal cells: new insights into domains required for miRNA-mediated gene silencing. RNA 15(8):1433–1442. doi:10.1261/rna.1703809, rna.1703809 [pii]
Verdel A, Jia S, Gerber S, Sugiyama T, Gygi S, Grewal SI, Moazed D (2004) RNAi-mediated targeting of heterochromatin by the RITS complex. Science 303(5658):672–676. doi:10.1126/science.1093686, 1093686 [pii]
Aravin A, Gaidatzis D, Pfeffer S, Lagos-Quintana M, Landgraf P, Iovino N, Morris P, Brownstein MJ, Kuramochi-Miyagawa S, Nakano T, Chien M, Russo JJ, Ju J, Sheridan R, Sander C, Zavolan M, Tuschl T (2006) A novel class of small RNAs bind to MILI protein in mouse testes. Nature 442(7099):203–207. doi:10.1038/nature04916, nature04916 [pii]
Chuma S, Pillai RS (2009) Retrotransposon silencing by piRNAs: **-pong players mark their sub-cellular boundaries. PLoS Genet 5(12):e1000770. doi:10.1371/journal.pgen.1000770
Siomi MC, Sato K, Pezic D, Aravin AA (2011) PIWI-interacting small RNAs: the vanguard of genome defence. Nat Rev Mol Cell Biol 12(4):246–258. doi:10.1038/nrm3089, nrm3089 [pii]
Taft RJ, Glazov EA, Cloonan N, Simons C, Stephen S, Faulkner GJ, Lassmann T, Forrest AR, Grimmond SM, Schroder K, Irvine K, Arakawa T, Nakamura M, Kubosaki A, Hayashida K, Kawazu C, Murata M, Nishiyori H, Fukuda S, Kawai J, Daub CO, Hume DA, Suzuki H, Orlando V, Carninci P, Hayashizaki Y, Mattick JS (2009) Tiny RNAs associated with transcription start sites in animals. Nat Genet 41(5):572–578. doi:10.1038/ng.312, ng.312 [pii]
Valen E, Preker P, Andersen PR, Zhao X, Chen Y, Ender C, Dueck A, Meister G, Sandelin A, Jensen TH (2011) Biogenic mechanisms and utilization of small RNAs derived from human protein-coding genes. Nat Struct Mol Biol 18(9):1075–1082. doi:10.1038/nsmb.2091, nsmb.2091 [pii]
Jacquier A (2009) The complex eukaryotic transcriptome: unexpected pervasive transcription and novel small RNAs. Nat Rev Genet 10(12):833–844. doi:10.1038/nrg2683, nrg2683 [pii]
Seila AC, Calabrese JM, Levine SS, Yeo GW, Rahl PB, Flynn RA, Young RA, Sharp PA (2008) Divergent transcription from active promoters. Science 322(5909):1849–1851. doi:10.1126/science.1162253, 1162253 [pii]
Flynn RA, Almada AE, Zamudio JR, Sharp PA (2011) Antisense RNA polymerase II divergent transcripts are P-TEFb dependent and substrates for the RNA exosome. Proc Natl Acad Sci U S A 108(26):10460–10465. doi:10.1073/pnas.1106630108, 1106630108 [pii]
Neil H, Malabat C, d’ Aubenton-Carafa Y, Xu Z, Steinmetz LM, Jacquier A (2009) Widespread bidirectional promoters are the major source of cryptic transcripts in yeast. Nature 457(7232):1038–1042. doi:10.1038/nature07747, nature07747 [pii]
van Dijk EL, Chen CL, d’Aubenton-Carafa Y, Gourvennec S, Kwapisz M, Roche V, Bertrand C, Silvain M, Legoix-Ne P, Loeillet S, Nicolas A, Thermes C, Morillon A (2011) XUTs are a class of Xrn1-sensitive antisense regulatory non-coding RNA in yeast. Nature 475(7354):114–117. doi:10.1038/nature10118, nature10118 [pii]
Xu Z, Wei W, Gagneur J, Perocchi F, Clauder-Munster S, Camblong J, Guffanti E, Stutz F, Huber W, Steinmetz LM (2009) Bidirectional promoters generate pervasive transcription in yeast. Nature 457(7232):1033–1037. doi:10.1038/nature07728, nature07728 [pii]
Mercer TR, Dinger ME, Mattick JS (2009) Long non-coding RNAs: insights into functions. Nat Rev Genet 10(3):155–159. doi:10.1038/nrg2521, nrg2521 [pii]
Ponting CP, Oliver PL, Reik W (2009) Evolution and functions of long noncoding RNAs. Cell 136(4):629–641. doi:10.1016/j.cell.2009.02.006, S0092-8674(09)00142-1 [pii]
Yazgan O, Krebs JE (2007) Noncoding but nonexpendable: transcriptional regulation by large noncoding RNA in eukaryotes. Biochem Cell Biol 85(4):484–496. doi:10.1139/O07-061, o07-061 [pii]
Aalto AP, Pasquinelli AE (2012) Small non-coding RNAs mount a silent revolution in gene expression. Curr Opin Cell Biol 24(3):333–340. doi:10.1016/j.ceb.2012.03.006, S0955-0674(12)00037-3 [pii]
Birney E, Stamatoyannopoulos JA, Dutta A, Guigo R, Gingeras TR, Margulies EH, Weng Z, Snyder M, Dermitzakis ET, Thurman RE, Kuehn MS, Taylor CM, Neph S, Koch CM, Asthana S, Malhotra A, Adzhubei I, Greenbaum JA, Andrews RM, Flicek P, Boyle PJ, Cao H, Carter NP, Clelland GK, Davis S, Day N, Dhami P, Dillon SC, Dorschner MO, Fiegler H, Giresi PG, Goldy J, Hawrylycz M, Haydock A, Humbert R, James KD, Johnson BE, Johnson EM, Frum TT, Rosenzweig ER, Karnani N, Lee K, Lefebvre GC, Navas PA, Neri F, Parker SC, Sabo PJ, Sandstrom R, Shafer A, Vetrie D, Weaver M, Wilcox S, Yu M, Collins FS, Dekker J, Lieb JD, Tullius TD, Crawford GE, Sunyaev S, Noble WS, Dunham I, Denoeud F, Reymond A, Kapranov P, Rozowsky J, Zheng D, Castelo R, Frankish A, Harrow J, Ghosh S, Sandelin A, Hofacker IL, Baertsch R, Keefe D, Dike S, Cheng J, Hirsch HA, Sekinger EA, Lagarde J, Abril JF, Shahab A, Flamm C, Fried C, Hackermuller J, Hertel J, Lindemeyer M, Missal K, Tanzer A, Washietl S, Korbel J, Emanuelsson O, Pedersen JS, Holroyd N, Taylor R, Swarbreck D, Matthews N, Dickson MC, Thomas DJ, Weirauch MT, Gilbert J, Drenkow J, Bell I, Zhao X, Srinivasan KG, Sung WK, Ooi HS, Chiu KP, Foissac S, Alioto T, Brent M, Pachter L, Tress ML, Valencia A, Choo SW, Choo CY, Ucla C, Manzano C, Wyss C, Cheung E, Clark TG, Brown JB, Ganesh M, Patel S, Tammana H, Chrast J, Henrichsen CN, Kai C, Kawai J, Nagalakshmi U, Wu J, Lian Z, Lian J, Newburger P, Zhang X, Bickel P, Mattick JS, Carninci P, Hayashizaki Y, Weissman S, Hubbard T, Myers RM, Rogers J, Stadler PF, Lowe TM, Wei CL, Ruan Y, Struhl K, Gerstein M, Antonarakis SE, Fu Y, Green ED, Karaoz U, Siepel A, Taylor J, Liefer LA, Wetterstrand KA, Good PJ, Feingold EA, Guyer MS, Cooper GM, Asimenos G, Dewey CN, Hou M, Nikolaev S, Montoya-Burgos JI, Loytynoja A, Whelan S, Pardi F, Massingham T, Huang H, Zhang NR, Holmes I, Mullikin JC, Ureta-Vidal A, Paten B, Seringhaus M, Church D, Rosenbloom K, Kent WJ, Stone EA, Batzoglou S, Goldman N, Hardison RC, Haussler D, Miller W, Sidow A, Trinklein ND, Zhang ZD, Barrera L, Stuart R, King DC, Ameur A, Enroth S, Bieda MC, Kim J, Bhinge AA, Jiang N, Liu J, Yao F, Vega VB, Lee CW, Ng P, Yang A, Moqtaderi Z, Zhu Z, Xu X, Squazzo S, Oberley MJ, Inman D, Singer MA, Richmond TA, Munn KJ, Rada-Iglesias A, Wallerman O, Komorowski J, Fowler JC, Couttet P, Bruce AW, Dovey OM, Ellis PD, Langford CF, Nix DA, Euskirchen G, Hartman S, Urban AE, Kraus P, Van Calcar S, Heintzman N, Kim TH, Wang K, Qu C, Hon G, Luna R, Glass CK, Rosenfeld MG, Aldred SF, Cooper SJ, Halees A, Lin JM, Shulha HP, Xu M, Haidar JN, Yu Y, Iyer VR, Green RD, Wadelius C, Farnham PJ, Ren B, Harte RA, Hinrichs AS, Trumbower H, Clawson H, Hillman-Jackson J, Zweig AS, Smith K, Thakkapallayil A, Barber G, Kuhn RM, Karolchik D, Armengol L, Bird CP, de Bakker PI, Kern AD, Lopez-Bigas N, Martin JD, Stranger BE, Woodroffe A, Davydov E, Dimas A, Eyras E, Hallgrimsdottir IB, Huppert J, Zody MC, Abecasis GR, Estivill X, Bouffard GG, Guan X, Hansen NF, Idol JR, Maduro VV, Maskeri B, McDowell JC, Park M, Thomas PJ, Young AC, Blakesley RW, Muzny DM, Sodergren E, Wheeler DA, Worley KC, Jiang H, Weinstock GM, Gibbs RA, Graves T, Fulton R, Mardis ER, Wilson RK, Clamp M, Cuff J, Gnerre S, Jaffe DB, Chang JL, Lindblad-Toh K, Lander ES, Koriabine M, Nefedov M, Osoegawa K, Yoshinaga Y, Zhu B, De Jong PJ (2007) Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project. Nature 447(7146):799–816. doi:10.1038/nature05874
Clark MB, Amaral PP, Schlesinger FJ, Dinger ME, Taft RJ, Rinn JL, Ponting CP, Stadler PF, Morris KV, Morillon A, Rozowsky JS, Gerstein MB, Wahlestedt C, Hayashizaki Y, Carninci P, Gingeras TR, Mattick JS (2011) The reality of pervasive transcription. PLoS Biol 9(7):e1000625. doi:10.1371/journal.pbio.1000625, discussion e1001102, 10-PLBI-PS-8040R3 [pii]
Clark MB, Choudhary A, Smith MA, Taft RJ, Mattick JS (2013) The dark matter rises: the expanding world of regulatory RNAs. Essays Biochem 54:1–16. doi:10.1042/bse0540001, bse0540001 [pii]
Jochl C, Rederstorff M, Hertel J, Stadler PF, Hofacker IL, Schrettl M, Haas H, Huttenhofer A (2008) Small ncRNA transcriptome analysis from Aspergillus fumigatus suggests a novel mechanism for regulation of protein synthesis. Nucleic Acids Res 36(8):2677–2689. doi:10.1093/nar/gkn123, gkn123 [pii]
Metzker ML (2010) Sequencing technologies – the next generation. Nat Rev Genet 11(1):31–46. doi:10.1038/nrg2626, nrg2626 [pii]
Rederstorff M (2012) Generation of cDNA libraries from RNP-derived regulatory noncoding RNAs. Methods Mol Biol 925:211–218. doi:10.1007/978-1-62703-011-3_14
Rederstorff M, Bernhart SH, Tanzer A, Zywicki M, Perfler K, Lukasser M, Hofacker IL, Huttenhofer A (2010) RNPomics: defining the ncRNA transcriptome by cDNA library generation from ribonucleo-protein particles. Nucleic Acids Res 38(10):e113. doi:10.1093/nar/gkq057, gkq057 [pii]
Rederstorff M, Huttenhofer A (2011) cDNA library generation from ribonucleoprotein particles. Nat Protoc 6(2):166–174. doi:10.1038/nprot.2010.186, nprot.2010.186 [pii]
Shen M, Eyras E, Wu J, Khanna A, Josiah S, Rederstorff M, Zhang MQ, Stamm S (2011) Direct cloning of double-stranded RNAs from RNase protection analysis reveals processing patterns of C/D box snoRNAs and provides evidence for widespread antisense transcript expression. Nucleic Acids Res 39(22):9720–9730. doi:10.1093/nar/gkr684, gkr684 [pii]
Skreka K, Schafferer S, Nat IR, Zywicki M, Salti A, Apostolova G, Griehl M, Rederstorff M, Dechant G, Huttenhofer A (2012) Identification of differentially expressed non-coding RNAs in embryonic stem cell neural differentiation. Nucleic Acids Res 40(13):6001–6015. doi:10.1093/nar/gks311, gks311 [pii]
Acknowledgment
This work was supported by the Centre National pour la Recherche Scientifique, the Université de Lorraine, the Région Lorraine and La Ligue contre le Cancer.
Author information
Authors and Affiliations
Corresponding author
Editor information
Editors and Affiliations
Rights and permissions
Copyright information
© 2015 Springer Science+Business Media New York
About this protocol
Cite this protocol
Clerget, G., Abel, Y., Rederstorff, M. (2015). Small Non-Coding RNAs: A Quick Look in the Rearview Mirror. In: Rederstorff, M. (eds) Small Non-Coding RNAs. Methods in Molecular Biology, vol 1296. Humana Press, New York, NY. https://doi.org/10.1007/978-1-4939-2547-6_1
Download citation
DOI: https://doi.org/10.1007/978-1-4939-2547-6_1
Publisher Name: Humana Press, New York, NY
Print ISBN: 978-1-4939-2546-9
Online ISBN: 978-1-4939-2547-6
eBook Packages: Springer Protocols