Genome-wide annotation of microRNA primary transcript structures reveals novel regulatory mechanisms

Genome Research

Volumn 25, Issue 9, 2015, Pages 1401-1409

  Chang, Tsung Cheng ^a   Pertea, Mihaela ^b   Lee, Sungyul ^a   Salzberg, Steven L ^b,c   Mendell, Joshua T ^a,d,e  

^a UNIVERSITY OF TEXAS SOUTHWESTERN MEDICAL CENTER   (United States)

^b Johns Hopkins University   (United States)

^c JOHNS HOPKINS UNIVERSITY   (United States)

^d Department of Molecular Biology Hamon Center for Regenerative Science and Medicine UT Southwestern   (United States)

^e UNIVERSITY OF TEXAS SOUTHWESTERN MEDICAL CENTER   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

MICRORNA; NUCLEAR RNA; TRANSCRIPTOME; DROSHA PROTEIN, HUMAN; RIBONUCLEASE III; UNTRANSLATED RNA;

ALTERNATIVE RNA SPLICING; AMPLICON; ANIMAL CELL; ARTICLE; CHROMATIN IMMUNOPRECIPITATION; CPG ISLAND; EXPRESSED SEQUENCE TAG; FIBROBLAST; GENE EXPRESSION; GENE STRUCTURE; GENETIC ASSOCIATION; HISTONE MODIFICATION; HUMAN; HUMAN CELL; NONHUMAN; PRIORITY JOURNAL; PROMOTER REGION; REGULATORY MECHANISM; RNA SEQUENCE; RNA STRUCTURE; STEADY STATE; TRANSCRIPTION INITIATION SITE; CHEMISTRY; CONFORMATION; GENE EXPRESSION REGULATION; GENETIC TRANSCRIPTION; GENETICS; GENOME-WIDE ASSOCIATION STUDY; HIGH THROUGHPUT SEQUENCING; METABOLISM; MOLECULAR EVOLUTION; MOLECULAR GENETICS; MULTIGENE FAMILY; OPEN READING FRAME; PROCEDURES; SEQUENCE ANALYSIS;

ALTERNATIVE SPLICING; EVOLUTION, MOLECULAR; GENE EXPRESSION REGULATION; GENOME-WIDE ASSOCIATION STUDY; HIGH-THROUGHPUT NUCLEOTIDE SEQUENCING; HUMANS; MICRORNAS; MOLECULAR SEQUENCE ANNOTATION; MULTIGENE FAMILY; NUCLEIC ACID CONFORMATION; OPEN READING FRAMES; PROMOTER REGIONS, GENETIC; RIBONUCLEASE III; RNA, UNTRANSLATED; SEQUENCE ANALYSIS, RNA; TRANSCRIPTION, GENETIC;

EID: 84940983900     PISSN: 10889051     EISSN: 15495469     Source Type: Journal    
DOI: 10.1101/gr.193607.115     Document Type: Article

References (41)

1. Bartel DP. 2009. MicroRNAs: Target recognition and regulatory functions. Cell 136: 215-233.
2. Baskerville S, Bartel DP. 2005. Microarray profiling of microRNAs reveals frequent coexpression with neighboring miRNAs and host genes. RNA 11: 241-247.
3. Cai X, Hagedorn CH, Cullen BR. 2004. Human microRNAs are processed from capped, polyadenylated transcripts that can also function as mRNAs. RNA 10: 1957-1966.
4. Chang TC, Wentzel EA, Kent OA, Ramachandran K, Mullendore M, Lee KH, Feldmann G, Yamakuchi M, Ferlito M, Lowenstein CJ, et al. 2007. Transactivation of miR-34a by p53 broadly influences gene expression and promotes apoptosis. Mol Cell 26: 745-752.
5. Chiang HR, Schoenfeld LW, Ruby JG, Auyeung VC, Spies N, Baek D, Johnston WK, Russ C, Luo S, Babiarz JE, et al. 2010. Mammalian microRNAs: Experimental evaluation of novel and previously annotated genes. Genes Dev 24: 992-1009.
6. Chien CH, Sun YM, Chang WC, Chiang-Hsieh PY, Lee TY, Tsai WC, Horng JT, Tsou AP, Huang HD. 2011. Identifying transcriptional start sites of human microRNAs based on high-throughput sequencing data. Nucleic Acids Res 39: 9345-9356.
7. Di-Leva G, Garofalo M, Croce CM. 2014. MicroRNAs in cancer. Annu Rev Pathol 9: 287-314.
8. Ernst J, Kheradpour P, Mikkelsen TS, Shoresh N, Ward LD, Epstein CB, Zhang X, Wang L, Issner R, Coyne M, et al. 2011. Mapping and analysis of chromatin state dynamics in nine human cell types. Nature 473: 43-49.
9. Georgakilas G, Vlachos IS, Paraskevopoulou MD, Yang P, Zhang Y, Economides AN, Hatzigeorgiou AG. 2014. microTSS: Accurate microRNA transcription start site identification reveals a significant number of divergent pri-miRNAs. Nat Commun 5: 5700.
10. Gurtan AM, Sharp PA. 2013. The role of miRNAs in regulating gene expression networks. J Mol Biol 425: 3582-3600.
11. Guttman M, Garber M, Levin JZ, Donaghey J, Robinson J, Adiconis X, Fan L, Koziol MJ, Gnirke A, Nusbaum C, et al. 2010. Ab initio reconstruction of cell type-specific transcriptomes in mouse reveals the conserved multiexonic structure of lincRNAs. Nat Biotechnol 28: 503-510.
12. Ha M, Kim VN. 2014. Regulation of microRNA biogenesis. Nat Rev Mol Cell Biol 15: 509-524.
13. Heo I, Joo C, Cho J, Ha M, Han J, Kim VN. 2008. Lin28 mediates the terminal uridylation of let-7 precursor microRNA. Mol Cell 32: 276-284.
14. Kim D, Pertea G, Trapnell C, Pimentel H, Kelley R, Salzberg SL. 2013. TopHat2: Accurate alignment of transcriptomes in the presence of insertions, deletions and gene fusions. Genome Biol 14: R36.
15. Kozomara A, Griffiths-Jones S. 2014. miRBase: Annotating high confidence microRNAs using deep sequencing data. Nucleic Acids Res 42: D68-D73.
16. Landgraf P, Rusu M, Sheridan R, Sewer A, Iovino N, Aravin A, Pfeffer S, Rice A, Kamphorst AO, Landthaler M, et al. 2007. A mammalian microRNA expression atlas based on small RNA library sequencing. Cell 129: 1401-1414.
17. Landthaler M, Yalcin A, Tuschl T. 2004. The human DiGeorge syndrome critical region gene 8 and its D. melanogaster homolog are required for miRNA biogenesis. Curr Biol 14: 2162-2167.
18. Lee Y, Kim M, Han J, Yeom KH, Lee S, Baek SH, Kim VN. 2004. MicroRNA genes are transcribed by RNA polymerase II. EMBO J 23: 4051-4060.
19. Li W, Feng J, Jiang T. 2011. IsoLasso: A LASSO regression approach to RNASeq based transcriptome assembly. J Comput Biol 18: 1693-1707.
20. Liang Y, Ridzon D, Wong L, Chen C. 2007. Characterization of microRNA expression profiles in normal human tissues. BMC Genomics 8: 166.
21. Lotterman CD, Kent OA, Mendell JT. 2008. Functional integration of microRNAs into oncogenic and tumor suppressor pathways. Cell Cycle 7: 2493-2499.
22. Marsico A, Huska MR, Lasserre J, Hu H, Vucicevic D, Musahl A, Orom U, Vingron M. 2013. PROmiRNA: A new miRNA promoter recognition method uncovers the complex regulation of intronic miRNAs. Genome Biol 14: R84.
23. Marson A, Levine SS, Cole MF, Frampton GM, Brambrink T, Johnstone S, Guenther MG, Johnston WK, Wernig M, Newman J, et al. 2008. Connecting microRNA genes to the core transcriptional regulatory circuitry of embryonic stem cells. Cell 134: 521-533.
24. Martin JA, Wang Z. 2011. Next-generation transcriptome assembly. Nat Rev Genet 12: 671-682.
25. McGettigan PA. 2013. Transcriptomics in the RNA-seq era. Curr Opin Chem Biol 17: 4-11.
26. Megraw M, Pereira F, Jensen ST, Ohler U, Hatzigeorgiou AG. 2009. A transcription factor affinity-based code for mammalian transcription initiation. Genome Res 19: 644-656.
27. Melamed Z, Levy A, Ashwal-Fluss R, Lev-Maor G, Mekahel K, Atias N, Gilad S, Sharan R, Levy C, Kadener S, et al. 2013. Alternative splicing regulates biogenesis of miRNAs located across exon-intron junctions. Mol Cell 50: 869-881.
28. Mikkelsen TS, Ku M, Jaffe DB, Issac B, Lieberman E, Giannoukos G, Alvarez P, Brockman W, Kim TK, Koche RP, et al. 2007. Genome-wide maps of chromatin state in pluripotent and lineage-committed cells. Nature 448: 553-560.
29. Olive V, Minella AC, He L. 2015. Outside the coding genome, mammalian microRNAs confer structural and functional complexity. Sci Signal 8: Re2.
30. Olson EN. 2014. MicroRNAs as therapeutic targets and biomarkers of cardiovascular disease. Sci Transl Med 6: 239ps3.
31. Ozsolak F, Poling LL, Wang Z, Liu H, Liu XS, Roeder RG, Zhang X, Song JS, Fisher DE. 2008. Chromatin structure analyses identify miRNA promoters. Genes Dev 22: 3172-3183.
32. Pasquinelli AE. 2012. MicroRNAs and their targets: Recognition, regulation and an emerging reciprocal relationship. Nat Rev Genet 13: 271-282.
33. Pertea M, Pertea GM, Antonescu CM, Chang TC, Mendell JT, Salzberg SL. 2015. StringTie enables improved reconstruction of a transcriptome from RNA-seq reads. Nat Biotechnol 33: 290-295.
34. Rakheja D, Chen KS, Liu Y, Shukla AA, Schmid V, Chang TC, Khokhar S, Wickiser JE, Karandikar NJ, Malter JS, et al. 2014. Somatic mutations in DROSHA and DICER1 impair microRNA biogenesis through distinct mechanisms in Wilms tumours. Nat Commun 2: 4802.
35. Rodriguez A, Griffiths-Jones S, Ashurst JL, Bradley A. 2004. Identification of mammalian microRNA host genes and transcription units. Genome Res 14: 1902-1910.
36. Roush S, Slack FJ. 2008. The let-7 family of microRNAs. Trends Cell Biol 18: 505-516.
37. Schanen BC, Li X. 2011. Transcriptional regulation of mammalian miRNA genes. Genomics 97: 1-6.
38. Trapnell C, Williams BA, Pertea G, Mortazavi A, Kwan G, van Baren MJ, Salzberg SL, Wold BJ, Pachter L. 2010. Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation. Nat Biotechnol 28: 511-515.
39. Vidigal JA, Ventura A. 2015. The biological functions of miRNAs: lessons from in vivo studies. Trends Cell Biol 25: 137-147.
40. Winter J, Jung S, Keller S, Gregory RI, Diederichs S. 2009. Many roads to maturity: microRNA biogenesis pathways and their regulation. Nat Cell Biol 11: 228-234.
41. Xiao Y, Liu T, Zhao H, Li X, Guan J, Xu C, Ping Y, Fan H, Wang L, Zhao T, et al. 2014. Integrating epigenetic marks for identification of transcriptionally active miRNAs. Genomics 104: 70-78.