Multiple products from microRNA transcripts

Biochemical Society Transactions

Volumn 41, Issue 4, 2013, Pages 850-854

  Marco, Antonio ^a   Ninova, Maria ^a   Griffiths Jones, Sam ^a  

^a UNIVERSITY OF MANCHESTER   (United Kingdom)

Author keywords

Arm switching; Genomics; Intronic microRNA (intronic miRNA); Linkage; Mirtron; Polycistronic transcript

Indexed keywords

MESSENGER RNA PRECURSOR; MICRORNA;

ARTICLE; CISTRON; GENE EXPRESSION REGULATION; GENE FUNCTION; GENE PRODUCT; GENETIC TRANSCRIPTION; INTRON; MOLECULAR EVOLUTION; NONHUMAN; OPEN READING FRAME; OPERON; PRIORITY JOURNAL; PROTEIN EXPRESSION; RNA SEQUENCE; RNA STRUCTURE; RNA SYNTHESIS;

ANIMALS; HUMANS; INTRONS; MICRORNAS; RNA, MESSENGER;

EID: 84880564138     PISSN: 03005127     EISSN: 14708752     Source Type: Journal    
DOI: 10.1042/BST20130035     Document Type: Article

References (57)

1. Chen, M. and Manley, J.L. (2009) Mechanisms of alternative splicing regulation: insights from molecular and genomics approaches. Nat. Rev. Mol. Cell Biol. 10, 741-754
2. Lawrence, J. (1999) Selfish operons: the evolutionary impact of gene clustering in prokaryotes and eukaryotes. Curr. Opin. Genet. Dev. 9, 642-648
3. Blumenthal, T. (2004) Operons in eukaryotes. Briefings Funct. Genomics Proteomics 3, 199-211
4. Kiss, T. (2002) Small nucleolar RNAs: an abundant group of noncoding RNAs with diverse cellular functions. Cell 109, 145-148
5. Bartel, D.P. (2004) MicroRNAs: genomics, biogenesis, mechanism, and function. Cell 116, 281-297
6. Axtell, M.J., Westholm, J.O. and Lai, E.C. (2011) Vive la différence: biogenesis and evolution of microRNAs in plants and animals. Genome Biol. 12, 221
7. Okamura, K., Phillips, M.D., Tyler, D.M., Duan, H., Chou, Y. and Lai, E.C. (2008) The regulatory activity of microRNA* species has substantial influence on microRNA and 3-UTR evolution. Nat. Struct. Mol. Biol. 15, 354-363
8. Czech, B., Zhou, R., Erlich, Y., Brennecke, J., Binari, R., Villalta, C., Gordon, A., Perrimon, N. and Hannon, G.J. (2009) Hierarchical rules for Argonaute loading in Drosophila. Mol. Cell 36, 445-456
9. Yang, J.-S., Phillips, M.D., Betel, D., Mu, P., Ventura, A., Siepel, A.C., Chen, K.C. and Lai, E.C. (2011) Widespread regulatory activity of vertebrate microRNA* species. RNA 17, 312-326
10. Glazov, E.A., Cottee, P.A., Barris, W.C., Moore, R.J., Dalrymple, B.P. and Tizard, M.L. (2008) A microRNA catalog of the developing chicken embryo identified by a deep sequencing approach. Genome Res. 18, 957-964
11. Chiang, H.R., Schoenfeld, L.W., Ruby, J.G., Auyeung, V.C., Spies, N., Baek, D., Johnston, W.K., Russ, C., Luo, S., Babiarz, J.E. et al. (2010) Mammalian microRNAs: experimental evaluation of novel and previously annotated genes. Genes Dev. 24, 992-1009
12. Ruby, J.G., Stark, A., Johnston, W.K., Kellis, M., Bartel, D.P. and Lai, E.C. (2007) Evolution, biogenesis, expression, and target predictions of a substantially expanded set of Drosophila microRNAs. Genome Res. 17, 1850-1864
13. De Wit, E., Linsen, S.E.V., Cuppen, E. and Berezikov, E. (2009) Repertoire and evolution of miRNA genes in four divergent nematode species. Genome Res. 19, 2064-2074
14. Marco, A., Hui, J.H.L., Ronshaugen, M. and Griffiths-Jones, S. (2010) Functional shifts in insect microRNA evolution. Genome Biol. Evol. 2, 686-696
15. Griffiths-Jones, S., Hui, J.H.L., Marco, A. and Ronshaugen, M. (2011) MicroRNA evolution by arm switching. EMBO Rep. 12, 172-177
16. Marco, A., MacPherson, J.I., Ronshaugen, M. and Griffiths-Jones, S. (2012) MicroRNAs from the same precursor have different targeting properties. Silence 3, 8
17. Neilsen, C.T., Goodall, G.J. and Bracken, C.P. (2012) IsomiRs: the overlooked repertoire in the dynamic microRNAome. Trends Genet. 28, 544-549
18. Han, B.W., Hung, J.-H., Weng, Z., Zamore, P.D. and Ameres, S.L. (2011) The 3-to-5-exoribonuclease nibbler shapes the 3-ends of microRNAs bound to Drosophila Argonaute1. Curr. Biol. 21, 1878-1887
19. Liu, N., Abe, M., Sabin, L.R., Hendriks, G.-J., Naqvi, A.S., Yu, Z., Cherry, S. and Bonini, N.M. (2011) The exoribonuclease nibbler controls 3-end processing of microRNAs in Drosophila. Curr. Biol. 21, 1888-1893
20. Bartel, D.P. (2009) MicroRNAs: target recognition and regulatory functions. Cell 136, 215-233
21. Wheeler, B.M., Heimberg, A.M., Moy, V.N., Sperling, E.A., Holstein, T.W., Heber, S. and Peterson, K.J. (2009) The deep evolution of metazoan microRNAs. Evol. Dev. 11, 50-68
22. Cloonan, N., Wani, S., Xu, Q., Gu, J., Lea, K., Heater, S., Barbacioru, C., Steptoe, AL., Martin, H.C., Nourbakhsh, E. et al. (2011) MicroRNAs and their isomiRs function cooperatively to target common biological pathways. Genome Biol. 12, R126
23. Lagos-Quintana, M., Rauhut, R., Lendeckel, W. and Tuschl, T. (2001) Identification of novel genes coding for small expressed RNAs. Science 294, 853-858
24. Lau, N.C., Lim, L.P., Weinstein, E.G. and Bartel, D.P. (2001) An abundant class of tiny RNAs with probable regulatory roles in Caenorhabditis elegans. Science 294, 858-862
25. Reinhart, B.J., Weinstein, E.G., Rhoades, M.W., Bartel, B. and Bartel, D.P. (2002) MicroRNAs in plants. Genes Dev. 16, 1616-1626
26. Kozomara, A. and Griffiths-Jones, S. (2011) miRBase: integrating microRNA annotation and deep-sequencing data. Nucleic Acids Res. 39, D152-D157
27. Altuvia, Y., Landgraf, P., Lithwick, G., Elefant, N., Pfeffer, S., Aravin, A., Brownstein, M.J., Tuschl, T. and Margalit, H. (2005) Clustering and conservation patterns of human microRNAs. Nucleic Acids Res. 33, 2697-2706
28. Lee, Y., Jeon, K., Lee, J.-T., Kim, S. and Kim, V.N. (2002) MicroRNA maturation: stepwise processing and subcellular localization. EMBO J. 21, 4663-4670
29. Baskerville, S. and Bartel, D.P. (2005) Microarray profiling of microRNAs reveals frequent coexpression with neighboring miRNAs and host genes. RNA 11, 241-247
30. Maher, C., Stein, L. and Ware, D. (2006) Evolution of Arabidopsis microRNA families through duplication events. Genome Res. 16, 510-519
31. Saini, H.K., Griffiths-Jones, S. and Enright, A.J. (2007) Genomic analysis of human microRNA transcripts. Proc. Natl. Acad. Sci. U.S.A. 104, 17719-17724
32. Saini, H.K., Enright, A.J. and Griffiths-Jones, S. (2008) Annotation of mammalian primary microRNAs. BMC Genomics 9, 564
33. Ryazansky, S.S., Gvozdev, V.A. and Berezikov, E. (2011) Evidence for post-transcriptional regulation of clustered microRNAs in Drosophila. BMC Genomics 12, 371
34. Aravin, A.A., Lagos-Quintana, M., Yalcin, A., Zavolan, M., Marks, D., Snyder, B., Gaasterland, T., Meyer, J. and Tuschl, T. (2003) The small RNA profile during Drosophila melanogaster development. Dev. Cell 5, 337-350
35. Lee, H.K., Hsu, A.K., Sajdak, J., Qin, J. and Pavlidis, P. (2004) Coexpression analysis of human genes across many microarray data sets. Genome Res. 14, 1085-1094
36. Hertel, J., Lindemeyer, M., Missal, K., Fried, C., Tanzer, A., Flamm, C., Hofacker, I.L. and Stadler, P.F. (2006) The expansion of the metazoan microRNA repertoire. BMC Genomics 7, 25
37. Hertel, J., Bartschat, S., Wintsche, A., Otto, C. and Stadler, P.F. (2012) Evolution of the let-7 microRNA family. RNA Biol. 9, 231-241
38. Sokol, N.S., Xu, P., Jan, Y.-N. and Ambros, V. (2008) Drosophila let-7 microRNA is required for remodeling of the neuromusculature during metamorphosis. Genes Dev. 22, 1591-1596
39. Marco, A., Hooks, K. and Griffiths-Jones, S. (2012) Evolution and function of the extended miR-2 microRNA family. RNA Biol. 9, 242-248
40. Kim, V.N. and Nam, J.-W. (2006) Genomics of microRNA. Trends Genet. 22, 165-173
41. Marco, A., Ninova, M., Ronshaugen, M. and Griffiths-Jones, S. (2013) Clusters of microRNAs emerge by new hairpins in existing transcripts. Nucleic Acids Res., doi:10.1093/nar/gkt534
42. Kim, Y.-K. and Kim, V.N. (2007) Processing of intronic microRNAs. EMBO J. 26, 775-783
43. Tang, G.-Q. and Maxwell, E.S. (2008) Xenopus microRNA genes are predominantly located within introns and are differentially expressed in adult frog tissues via post-transcriptional regulation. Genome Res. 18, 104-112
44. Hoeppner, M.P., White, S., Jeffares, D.C. and Poole, A.M. (2009) Evolutionarily stable association of intronic snoRNAs and microRNAs with their host genes. Genome Biol. Evol. 1, 420-428
45. Campo-Paysaa, F., Sémon, M., Cameron, R.A., Peterson, K.J. and Schubert, M. (2011) microRNA complements in deuterostomes: origin and evolution of microRNAs. Evol. Dev. 13, 15-27
46. Berezikov, E. (2011) Evolution of microRNA diversity and regulation in animals. Nat. Rev. Genet. 12, 846-860
47. Morlando, M., Ballarino, M., Gromak, N., Pagano, F., Bozzoni, I. and Proudfoot, N.J. (2008) Primary microRNA transcripts are processed co-transcriptionally. Nat. Struct. Mol. Biol. 15, 902-909
48. Ruby, J.G., Jan, C.H. and Bartel, D.P. (2007) Intronic microRNA precursors that bypass Drosha processing. Nature 448, 83-86
49. Westholm, J.O. and Lai, E.C. (2011) Mirtrons: microRNA biogenesis via splicing. Biochimie 93, 1897-1904
50. Rodriguez, A., Griffiths-Jones, S., Ashurst, J.L. and Bradley, A. (2004) Identification of mammalian microRNA host genes and transcription units. Genome Res. 14, 1902-1910
51. Aboobaker, A.A., Tomancak, P., Patel, N., Rubin, G.M. and Lai, E.C. (2005) Drosophila microRNAs exhibit diverse spatial expression patterns during embryonic development. Proc. Natl. Acad. Sci. U.S.A. 102, 18017-18022
52. Keniry, A., Oxley, D., Monnier, P., Kyba, M., Dandolo, L., Smits, G. and Reik, W. (2012) The H19 lincRNA is a developmental reservoir of miR-675 that suppresses growth and Igf1r. Nat. Cell Biol. 14, 659-665
53. Cumberledge, S., Zaratzian, A. and Sakonju, S. (1990) Characterization of two RNAs transcribed from the cis-regulatory region of the abd-A domain within the Drosophila bithorax complex. Proc. Natl. Acad. Sci. U.S.A. 87, 3259-3263
54. Lynch, M. (2007) The Origins of Genome Architecture, Sinauer Associates, Sunderland, MA, U.S.A.
55. Wagner, A. (2011) The Origins of Evolutionary Innovations: a Theory of Transformative Change in Living Systems, Oxford University Press, Oxford
56. Guerzoni, D. and McLysaght, A. (2011) De novo origins of human genes. PLoS Genet. 7, e1002381
57. Stark, A., Lin, M.F., Kheradpour, P., Pedersen, J.S., Parts, L., Carlson, J.W., Crosby, M.A., Rasmussen, M.D., Roy, S., Deoras, A.N. et al. (2007) Discovery of functional elements in 12 Drosophila genomes using evolutionary signatures. Nature 450, 219-232