MiRT: A Database of Validated Transcription Start Sites of Human MicroRNAs

Genomics, Proteomics and Bioinformatics

Volumn 10, Issue 5, 2012, Pages 310-316

  Bhattacharyya, Malay ^a   Das, Manali ^b   Bandyopadhyay, Sanghamitra ^a  

^a INDIAN STATISTICAL INSTITUTE   (India)

^b MAULANA ABUL KALAM AZAD UNIVERSITY OF TECHNOLOGY   (India)

Author keywords

Database; MicroRNA; Primary transcript; Transcription start site; Transcriptional regulation

Indexed keywords

ENDONUCLEASE; MICRORNA;

ARTICLE; DATA BASE; DNA TRANSCRIPTION; GENE LOCUS; GENETIC VARIABILITY; PROMOTER REGION; RNA SEQUENCE; TRANSCRIPTION INITIATION SITE; TRANSCRIPTION REGULATION;

3' UNTRANSLATED REGIONS; DATABASES, NUCLEIC ACID; GENOME, HUMAN; HUMANS; MICRORNAS; RNA, MESSENGER; TRANSCRIPTION INITIATION SITE;

EID: 84870330917     PISSN: 16720229     EISSN: 22103244     Source Type: Journal    
DOI: 10.1016/j.gpb.2012.08.005     Document Type: Article

References (32)

1. Li M., Marin-Muller C., Bharadwaj U., Chow K.H., Yao Q., Chen C. MicroRNAs: control and loss of control in human physiology and disease. World J Surg 2009, 33:667-684.
2. Bartel D.P. MicroRNAs: target recognition and regulatory functions. Cell 2009, 136:215-233.
3. Saini H.K., Griffiths-Jones S., Enright A.J. Genomic analysis of human microRNA transcripts. Proc Natl Acad Sci U S A 2007, 104:17719-17724.
4. 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.
5. Chen D., Farwell M.A., Zhang B. MicroRNA as a new player in the cell cycle. J Cell Physiol 2010, 225:296-301.
6. Lee Y., Ahn C., Han J., Choi H., Kim J., Yim J., et al. The nuclear RNase III drosha initiates microRNA processing. Nature 2003, 425:415-419.
7. Griffiths-Jones S., Saini H.K., van Dongen S., Enright A.J. miRBase: tools for microRNA genomics. Nucleic Acids Res 2008, 36:D154-D158.
8. Lee Y., Jeon K., Lee J., Kim S., Kim V.N. MicroRNA maturation: stepwise processing and subcellular localization. EMBO J 2002, 21:4663-4670.
9. Zeng Y., Cullen B.R. Sequence requirements for microRNA processing and function in human cells. RNA 2003, 9:112-123.
10. Krol J., Sobczak K., Wilczynska U., Drath M., Jasinska A., Kaczynska D., et al. Structural features of microRNA (miRNA) precursors and their relevance to miRNA biogenesis and small interfering RNA/short hairpin RNA design. J Biol Chem 2004, 279:42230-42239.
11. Lund E., Güttinger S., Calado A., Dahlberg J.E., Kutay U. Nuclear export of microRNA precursors. Science 2004, 303:95-98.
12. Yi R., Qin Y., Macara I.G., Cullen B.R. Exportin-5 mediates the nuclear export of pre-microRNAs and short hairpin RNAs. Genes Dev 2003, 17:3011-3016.
13. Khvorova A., Reynolds A., Jayasena S.D. Functional siRNAs and miRNAs exhibit strand bias. Cell 2003, 115:209-216.
14. Schwarz D.S., Hutvágner G., Du T., Xu Z., Aronin N., Zamore P.D. Asymmetry in the assembly of the RNAi enzyme complex. Cell 2003, 115:199-208.
15. Hammond S.M., Bernstein E., Beach D., Hannon G.J. An RNA-directed nuclease mediates posttranscriptional gene silencing in Drosophila cells. Nature 2000, 404:293-296.
16. Martinez J., Patkaniowska A., Urlaub H., Lührmann R., Tuschl T. Single-stranded antisense siRNAs guide target RNA cleavage in RNAi. Cell 2002, 110:563-574.
17. Schwarz D.S., Hutvágner G., Haley B., Zamore P.D. Evidence that siRNAs function as guides, not primers, in the Drosophila and human RNAi pathways. Mol Cell 2002, 10:537-548.
18. Bhattacharyya M., Feuerbach L., Bhadra T., Lengauer T., Bandyopadhyay S. MicroRNA transcription start site prediction with multi-objective feature selection. Stat Appl Genet Mol Biol 2012, 11:6.
19. Corcoran D.L., Pandit K.V., Gordon B., Bhattacharjee A., Kaminski N., Benos P.V. Features of mammalian microRNA promoters emerge from polymerase II chromatin immunoprecipitation data. PLoS ONE 2009, 4:e5279.
20. Cai X., Hagedorn C.H., Cullen B.R. Human microRNAs are processed from capped, polyadenylated transcripts that can also function as mRNAs. RNA 2004, 10:1957-1966.
21. Kim Y.K., Kim V.N. Processing of intronic microRNAs. EMBO J 2007, 26:775-783.
22. Lee Y., Kim M., Han J., Yeom K., Lee S., Baek S.H., et al. MicroRNA genes are transcribed by RNA polymerase II. EMBO J 2004, 23:4051-4060.
23. Taganov K.D., Boldin M.P., Chang K.J., Baltimore D. NF-kappaB-dependent induction of microRNA miR-146, an inhibitor targeted to signaling proteins of innate immune responses. Proc Natl Acad Sci U S A 2006, 103:12481-12486.
24. Landgraf P., Rusu M., Sheridan R., Sewer A., Iovino N., Aravin A., et al. A mammalian microRNA expression atlas based on small RNA library sequencing. Cell 2007, 129:1401-1414.
25. Ozsolak F., Poling L.L., Wang Z., Liu H., Liu X.S., Roeder R.G., et al. Chromatin structure analyses identify miRNA promoters. Genes Dev 2008, 22:3172-3183.
26. Fujita S., Iba H. Putative promoter regions of miRNA genes involved in evolutionary conserved regulatory systems among vertebrates. Bioinformatics 2008, 24:303-308.
27. Marson A., Levine S.S., Cole M.F., Frampton G.M., Brambrink T., Johnstone S., et al. Connecting microRNA genes to the core transcriptional regulatory circuitry of embryonic stem cells. Cell 2008, 134:521-533.
28. Mahony S., Auron P.E., Benos P.V. DNA familial binding profiles made easy: comparison of various motif alignment and clustering strategies. PLoS Comput Biol 2007, 3:e61.
29. Chien C., Sun Y., Chang W., Chiang-Hsieh P., Lee T., Tsai W., et al. Identifying transcriptional start sites of human microRNAs based on high-throughput sequencing data. Nucleic Acids Res 2011, 39:9345-9356.
30. Alexiou P., Vergoulis T., Gleditzsch M., Prekas G., Dalamagas T., Megraw M., et al. MiRGen 2.0: a database of microRNA genomic information and regulation. Nucleic Acids Res 2010, 38:D137-D141.
31. Blankenberg D., Kuster G.V., Coraor N., Ananda G., Lazarus R., Mangan M., et al. Galaxy: a web based genome analysis tool for experimentalists. Curr Protoc Mol Biol 2010, 19:1-21.
32. Stählera C.F., Kellera A., Leidingerb P., Backesb C., Chandranc A., Wischhusenc J., et al. Whole miRNome wide differential co-expression of microRNAs. Genomics Proteomics Bioinformatics 2012, 10:285-294.