Evidence for post-transcriptional regulation of clustered microRNAs in Drosophila

BMC Genomics

Volumn 12, Issue , 2011, Pages

  Ryazansky, Sergei S ^a   Gvozdev, Vladimir A ^a   Berezikov, Eugene ^b,c  

^a INSTITUTE OF MOLECULAR GENETICS   (Russian Federation)

^b UNIVERSITY MEDICAL CENTER UTRECHT   (Netherlands)

^c INSTITUTE OF CYTOLOGY AND GENETICS   (Russian Federation)

Author keywords

[No Author keywords available]

Indexed keywords

MICRORNA;

ANIMAL TISSUE; ARTICLE; CONTROLLED STUDY; DROSOPHILA MELANOGASTER; EMBRYO; FEMALE; GENE CLUSTER; GENE EXPRESSION PROFILING; GENE LIBRARY; GENE LOCATION; GENETIC REGULATION; MALE; NONHUMAN; POSTTRANSCRIPTIONAL CONTROL; PREDICTION; PROMOTER REGION; RNA PROCESSING; RNA SEQUENCE; RNA STABILITY; TRANSCRIPTION INITIATION SITE; ANIMAL; DROSOPHILA; GENETICS; METABOLISM; MULTIGENE FAMILY;

DROSOPHILA MELANOGASTER;

ANIMALS; DROSOPHILA; GENE EXPRESSION PROFILING; MICRORNAS; MULTIGENE FAMILY; PROMOTER REGIONS, GENETIC; RNA PROCESSING, POST-TRANSCRIPTIONAL; TRANSCRIPTION INITIATION SITE;

EID: 79960563030     PISSN: None     EISSN: 14712164     Source Type: Journal    
DOI: 10.1186/1471-2164-12-371     Document Type: Article

References (40)

1. Bartel DP. MicroRNAs: genomics, biogenesis, mechanism, and function. Cell 2004, 116:281-297. 10.1016/S0092-8674(04)00045-5, 14744438.
2. Filipowicz W, Bhattacharyya SN, Sonenberg N. Mechanisms of post-transcriptional regulation by microRNAs: are the answers in sight?. Nat Rev Genet 2008, 9:102-114.
3. Guo H, Ingolia NT, Weissman JS, Bartel DP. Mammalian microRNAs predominantly act to decrease target mRNA levels. Nature 2010, 466:835-840. 10.1038/nature09267, 2990499, 20703300.
4. Hendrickson DG, Hogan DJ, McCullough HL, Myers JW, Herschlag D, Ferrell JE, Brown PO. Concordant regulation of translation and mRNA abundance for hundreds of targets of a human microRNA. PLoS Biol 2009, 7:e1000238. 10.1371/journal.pbio.1000238, 2766070, 19901979.
5. Okamura K, Phillips MD, Tyler DM, Duan H, Chou YT, Lai EC. The regulatory activity of microRNA* species has substantial influence on microRNA and 3' UTR evolution. Nat Struct Mol Biol 2008, 15:354-363. 10.1038/nsmb.1409, 2698667, 18376413.
6. Ro S, Park C, Young D, Sanders KM, Yan W. Tissue-dependent paired expression of miRNAs. Nucleic Acids Res 2007, 35:5944-5953. 10.1093/nar/gkm641, 2034466, 17726050.
7. Altuvia Y, Landgraf P, Lithwick G, Elefant N, Pfeffer S, Aravin A, Brownstein MJ, Tuschl T, Margalit H. Clustering and conservation patterns of human microRNAs. Nucleic Acids Res 2005, 33:2697-2706. 10.1093/nar/gki567, 1110742, 15891114.
8. Merchan F, Boualem A, Crespi M, Frugier F. Plant polycistronic precursors containing non-homologous microRNAs target transcripts encoding functionally related proteins. Genome Biol 2009, 10:R136. 10.1186/gb-2009-10-12-r136, 2812943, 19951405.
9. Baskerville S, Bartel DP. Microarray profiling of microRNAs reveals frequent coexpression with neighboring miRNAs and host genes. RNA 2005, 11:241-247. 10.1261/rna.7240905, 1370713, 15701730.
10. Liang Y, Ridzon D, Wong L, Chen C. Characterization of microRNA expression profiles in normal human tissues. BMC Genomics 2007, 8:166. 10.1186/1471-2164-8-166, 1904203, 17565689.
11. Ruby JG, Stark A, Johnston WK, Kellis M, Bartel DP, Lai EC. Evolution, biogenesis, expression, and target predictions of a substantially expanded set of Drosophila microRNAs. Genome Res 2007, 17:1850-1864. 10.1101/gr.6597907, 2099593, 17989254.
12. Yu J, Wang F, Yang GH, Wang FL, Ma YN, Du ZW, Zhang JW. Human microRNA clusters: genomic organization and expression profile in leukemia cell lines. Biochem Biophys Res Commun 2006, 349:59-68. 10.1016/j.bbrc.2006.07.207, 16934749.
13. Kim YK, Yu J, Han TS, Park SY, Namkoong B, Kim DH, Hur K, Yoo MW, Lee HJ, Yang HK, Kim VN. Functional links between clustered microRNAs: suppression of cell-cycle inhibitors by microRNA clusters in gastric cancer. Nucleic Acids Res 2009, 37:1672-1681. 10.1093/nar/gkp002, 2655672, 19153141.
14. Xu J, Wong C. A computational screen for mouse signaling pathways targeted by microRNA clusters. RNA 2008, 14:1276-1283. 10.1261/rna.997708, 2441985, 18511500.
15. Biemar F, Zinzen R, Ronshaugen M, Sementchenko V, Manak JR, Levine MS. Spatial regulation of microRNA gene expression in the Drosophila embryo. Proc Natl Acad Sci USA 2005, 102:15907-15911. 10.1073/pnas.0507817102, 1276093, 16249329.
16. Houbaviy HB, Dennis L, Jaenisch R, Sharp PA. Characterization of a highly variable eutherian microRNA gene. RNA 2005, 11:1245-1257. 10.1261/rna.2890305, 1370808, 15987809.
17. Lee Y, Kim M, Han J, Yeom KH, Lee S, Baek SH, Kim VN. MicroRNA genes are transcribed by RNA polymerase II. EMBO J 2004, 23:4051-4060. 10.1038/sj.emboj.7600385, 524334, 15372072.
18. Heo I, Joo C, Cho J, Ha M, Han J, Kim VN. Lin28 mediates the terminal uridylation of let-7 precursor MicroRNA. Mol Cell 2008, 32:276-284. 10.1016/j.molcel.2008.09.014, 18951094.
19. Newman MA, Thomson JM, Hammond SM. Lin-28 interaction with the Let-7 precursor loop mediates regulated microRNA processing. RNA 2008, 14:1539-1549. 10.1261/rna.1155108, 2491462, 18566191.
20. Piskounova E, Viswanathan SR, Janas M, LaPierre RJ, Daley GQ, Sliz P, Gregory RI. Determinants of microRNA processing inhibition by the developmentally regulated RNA-binding protein Lin28. J Biol Chem 2008, 283:21310-21314. 10.1074/jbc.C800108200, 18550544.
21. Rybak A, Fuchs H, Smirnova L, Brandt C, Pohl EE, Nitsch R, Wulczyn FG. A feedback loop comprising lin-28 and let-7 controls pre-let-7 maturation during neural stem-cell commitment. Nat Cell Biol 2008, 10:987-993. 10.1038/ncb1759, 18604195.
22. Sokol NS, Xu P, Jan YN, Ambros V. Drosophila let-7 microRNA is required for remodeling of the neuromusculature during metamorphosis. Genes Dev 2008, 22:1591-1596. 10.1101/gad.1671708, 2428057, 18559475.
23. Graveley BR, Brooks AN, Carlson JW, Duff MO, Landolin JM, Yang L, Artieri CG, van Baren MJ, Boley N, Booth BW, Brown JB, Cherbas L, Davis CA, Dobin A, Li R, Lin W, Malone JH, Mattiuzzo NR, Miller D, Sturgill D, Tuch BB, Zaleski C, Zhang D, Blanchette M, Dudoit S, Eads B, Green RE, Hammonds A, Jiang L, Kapranov P, Langton L, Perrimon N, Sandler JE, Wan KH, Willingham A, Zhang Y, Zou Y, Andrews J, Bickel PJ, Brenner SE, Brent MR, Cherbas P, Gingeras TR, Hoskins RA, Kaufman TC, Oliver B, Celniker SE. The developmental transcriptome of Drosophila melanogaster. Nature 2010,
24. Zhou X, Ruan J, Wang G, Zhang W. Characterization and identification of microRNA core promoters in four model species. PLoS Comput Biol 2007, 3:e37. 10.1371/journal.pcbi.0030037, 1817659, 17352530.
25. FitzGerald PC, Sturgill D, Shyakhtenko A, Oliver B, Vinson C. Comparative genomics of Drosophila and human core promoters. Genome Biol 2006, 7:R53. 10.1186/gb-2006-7-7-r53, 1779564, 16827941.
26. Ohler U. Identification of core promoter modules in Drosophila and their application in accurate transcription start site prediction. Nucleic Acids Res 2006, 34:5943-5950. 10.1093/nar/gkl608, 1635271, 17068082.
27. Rach EA, Yuan HY, Majoros WH, Tomancak P, Ohler U. Motif composition, conservation and condition-specificity of single and alternative transcription start sites in the Drosophila genome. Genome Biol 2009, 10:R73. 10.1186/gb-2009-10-7-r73, 2728527, 19589141.
28. Fujita S, Iba H. Putative promoter regions of miRNA genes involved in evolutionarily conserved regulatory systems among vertebrates. Bioinformatics 2008, 24:303-308. 10.1093/bioinformatics/btm589, 18055479.
29. Saini HK, Griffiths-Jones S, Enright AJ. Genomic analysis of human microRNA transcripts. Proc Natl Acad Sci USA 2007, 104:17719-17724. 10.1073/pnas.0703890104, 2077053, 17965236.
30. Berezikov E, Robine N, Samsonova A, Westholm JO, Naqvi A, Hung JH, Okamura K, Dai Q, Bortolamiol-Becet D, Martin R, Zhao Y, Zamore PD, Hannon GJ, Marra MA, Weng Z, Perrimon N, Lai EC. Deep annotation of Drosophila melanogaster microRNAs yields insights into their processing, modification, and emergence. Genome Res 2011, 21:203-215. 10.1101/gr.116657.110, 3032924, 21177969.
31. Guil S, Caceres JF. The multifunctional RNA-binding protein hnRNP A1 is required for processing of miR-18a. Nat Struct Mol Biol 2007, 14:591-596. 10.1038/nsmb1250, 17558416.
32. Buck AH, Perot J, Chisholm MA, Kumar DS, Tuddenham L, Cognat V, Marcinowski L, Dolken L, Pfeffer S. Post-transcriptional regulation of miR-27 in murine cytomegalovirus infection. RNA 2010, 16:307-315. 10.1261/rna.1819210, 2811660, 20047990.
33. Linsen SE, de WE, Janssens G, Heater S, Chapman L, Parkin RK, Fritz B, Wyman SK, de BE, Voest EE, Kuersten S, Tewari M, Cuppen E. Limitations and possibilities of small RNA digital gene expression profiling. Nat Methods 2009, 6:474-476. 10.1038/nmeth0709-474, 19564845.
34. Pfeffer S, Sewer A, Lagos-Quintana M, Sheridan R, Sander C, Grasser FA, van Dyk LF, Ho CK, Shuman S, Chien M, Russo JJ, Ju J, Randall G, Lindenbach BD, Rice CM, Simon V, Ho DD, Zavolan M, Tuschl T. Identification of microRNAs of the herpesvirus family. Nat Methods 2005, 2:269-276. 10.1038/nmeth746, 15782219.
35. McCormick KP, Willmann MR, Meyers BC. Experimental design, preprocessing, normalization and differential expression analysis of small RNA sequencing experiments. Silence 2011, 2:2. 10.1186/1758-907X-2-2, 3055805, 21356093.
36. Munafo DB, Robb GB. Optimization of enzymatic reaction conditions for generating representative pools of cDNA from small RNA. RNA 2010, 16:2537-2552. 10.1261/rna.2242610, 2995414, 20921270.
37. Krol J, Loedige I, Filipowicz W. The widespread regulation of microRNA biogenesis, function and decay. Nat Rev Genet 2010, 11:597-610.
38. Slezak-Prochazka I, Durmus S, Kroesen BJ, van den Berg A. MicroRNAs, macrocontrol: regulation of miRNA processing. RNA 2010, 16:1087-1095. 10.1261/rna.1804410, 2874160, 20423980.
39. Karolchik D, Hinrichs AS, Furey TS, Roskin KM, Sugnet CW, Haussler D, Kent WJ. The UCSC Table Browser data retrieval tool. Nucleic Acids Res 2004, 32:D493-D496. 10.1093/nar/gkh103, 308837, 14681465.
40. Kent WJ, Sugnet CW, Furey TS, Roskin KM, Pringle TH, Zahler AM, Haussler D. The human genome browser at UCSC. Genome Res 2002, 12:996-1006. 186604, 12045153.