MiRNA-miRNA interaction implicates for potential mutual regulatory pattern

Gene

Volumn 511, Issue 2, 2012, Pages 187-194

  Guo, Li ^a   Sun, Beili ^b   Wu, Qian ^a   Yang, Sheng ^a   Chen, Feng ^a  

^a NANJING MEDICAL UNIVERSITY   (China)

^b SOUTHEAST UNIVERSITY   (China)

Author keywords

Endogenous sense antisense miRNAs; Interaction; MicroRNA (miRNA)

Indexed keywords

MICRORNA;

ANIMAL EXPERIMENT; ARTICLE; CHROMOSOME; CHROMOSOME 5; CONTROLLED STUDY; GENE CLUSTER; GENE TARGETING; HUMAN; INTERACTIONS WITH RNA; MIRNA MIRNA INTERACTION; MOUSE; NONHUMAN; PRIORITY JOURNAL; RAT; REGULATORY MECHANISM; RNA ANALYSIS; RNA SEQUENCE; RNA STRUCTURE;

ANIMALS; BASE SEQUENCE; HUMANS; MICE; MICRORNAS; MOLECULAR SEQUENCE DATA; RATS; SEQUENCE HOMOLOGY, NUCLEIC ACID;

ANIMALIA; RATTUS;

EID: 84868193851     PISSN: 03781119     EISSN: 18790038     Source Type: Journal    
DOI: 10.1016/j.gene.2012.09.066     Document Type: Article

References (49)

1. Aravin A.A., et al. The small RNA profile during Drosophila melanogaster development. Dev. Cell 2003, 5:337-350.
2. Bailey S.G., Sanchez-Elsner T., Stephanou A., Cragg M.S., Townsend P.A. Regulating the genome surveillance system: miRNAs and the p53 super family. Apoptosis 2010, 15:541-552.
3. Bartel D.P. MicroRNAs: genomics, biogenesis, mechanism, and function. Cell 2004, 116:281-297.
4. Bashirullah A., Pasquinelli A.E., Kiger A.A., Perrimon N., Ruvkun G., Thummel C.S. Coordinate regulation of small temporal RNAs at the onset of Drosophila metamorphosis. Dev. Biol. 2003, 259:1-8.
5. Burroughs A.M., et al. A comprehensive survey of 3 ' animal miRNA modification events and a possible role for 3 ' adenylation in modulating miRNA targeting effectiveness. Genome Res. 2010, 20:1398-1410.
6. Chen K., Rajewsky N. The evolution of gene regulation by transcription factors and microRNAs. Nat. Rev. Genet. 2007, 8:93-103.
7. Czech B., et al. Hierarchical rules for Argonaute loading in Drosophila. Mol. Cell 2009, 36:445-456.
8. Dykxhoorn D.M. MicroRNAs and metastasis: little RNAs go a long way. Cancer Res. 2010, 70:6401-6406.
9. Ebhardt H.A., Tsang H.H., Dai D.C., Liu Y.F., Bostan B., Fahlman R.P. Meta-analysis of small RNA-sequencing errors reveals ubiquitous post-transcriptional RNA modifications. Nucleic Acids Res. 2009, 37:2461-2470.
10. Fernandez-Valverde S.L., Taft R.J., Mattick J.S. Dynamic isomiR regulation in Drosophila development. RNA 2010, 16:1881-1888.
11. Ghildiyal M., Zamore P.D. Small silencing RNAs: an expanding universe. Nat. Rev. Genet. 2009, 10:94-108.
12. Grimson A., et al. Early origins and evolution of microRNAs and Piwi-interacting RNAs in animals. Nature 2008, 455:1193-1197.
13. Guo L., Lu Z. Global expression analysis of miRNA gene cluster and family based on isomiRs from deep sequencing data. Comput. Biol. Chem. 2010, 34:165-171.
14. Guo L., Lu Z.H. The fate of miRNA* strand through evolutionary analysis: implication for degradation as merely carrier strand or potential regulatory molecule?. PLoS One 2010, 5:e11387.
15. Guo L., Sun B.L., Sang F., Wang W., Lu Z.H. Haplotype distribution and evolutionary pattern of miR-17 and miR-124 families based on population analysis. PLoS One 2009, 4:e7944.
16. Guo L., Liang T., Gu W., Xu Y., Bai Y., Lu Z. Cross-mapping events in miRNAs reveal potential miRNA-mimics and evolutionary implications. PLoS One 2011, 6:e20517.
17. Guo L., et al. A comprehensive survey of miRNA repertoire and 3' addition events in the placentas of patients with pre-eclampsia from high-throughput sequencing. PLoS One 2011, 6:e21072.
18. Guo L., et al. Tracking miRNA precursor metabolic products and processing sites through completely analyzing high-throughput sequencing data. Mol. Biol. Rep. 2012, 39:2031-2038.
19. Hongay C.F., Grisafi P.L., Galitski T., Fink G.R. Antisense transcription controls cell fate in Saccharomyces cerevisiae. Cell 2006, 127:735-745.
20. Iorio M.V., Croce C.M. MicroRNAs in cancer: small molecules with a huge impact. J. Clin. Oncol. 2009, 27:5848-5856.
21. Jagadeeswaran G., et al. Deep sequencing of small RNA libraries reveals dynamic regulation of conserved and novel microRNAs and microRNA-stars during silkworm development. BMC Genomics 2010, 11:52.
22. Kim V.N., Nam J.W. Genomics of microRNA. Trends Genet. 2006, 22:165-173.
23. Koralov S.B., et al. Dicer ablation affects antibody diversity and cell survival in the B lymphocyte lineage. Cell 2008, 132:860-874.
24. Kuchenbauer F., et al. In-depth characterization of the microRNA transcriptome in a leukemia progression model. Genome Res. 2008, 18:1787-1797.
25. Lagos-Quintana M., Rauhut R., Lendeckel W., Tuschl T. Identification of novel genes coding for small expressed RNAs. Science 2001, 294:853-858.
26. Lagos-Quintana M., Rauhut R., Yalcin A., Meyer J., Lendeckel W., Tuschl T. Identification of tissue-specific microRNAs from mouse. Curr. Biol. 2002, 12:735-739.
27. Lagos-Quintana M., Rauhut R., Meyer J., Borkhardt A., Tuschl T. New microRNAs from mouse and human. Rna-a Publication of the Rna Society 2003, 9:175-179.
28. Lai E.C., Wiel C., Rubin G.M. Complementary miRNA pairs suggest a regulatory role for miRNA:miRNA duplexes. Rna-a Publication of the Rna Society 2004, 10:171-175.
29. Lau N.C., Lim L.P., Weinstein E.G., Bartel D.P. An abundant class of tiny RNAs with probable regulatory roles in Caenorhabditis elegans. Science 2001, 294:858-862.
30. Lee R.C., Ambros V. An extensive class of small RNAs in Caenorhabditis elegans. Science 2001, 294:862-864.
31. Lee L.W., et al. Complexity of the microRNA repertoire revealed by next generation sequencing. Rna-a Publication of the Rna Society 2010, 16:2170-2180.
32. Lewis B.P., Shih I.H., Jones-Rhoades M.W., Bartel D.P., Burge C.B. Prediction of mammalian microRNA targets. Cell 2003, 115:787-798.
33. Lim L.P., Glasner M.E., Yekta S., Burge C.B., Bartel D.P. Vertebrate MicroRNA genes. Science 2003, 299:1540-1540.
34. Lu C., et al. Genome-wide analysis for discovery of rice microRNAs reveals natural antisense microRNAs (nat-miRNAs). Proc. Natl. Acad. Sci. U. S. A. 2008, 105:4951-4956.
35. Lu S.F., Sun Y.H., Chiang V.L. Adenylation of plant miRNAs. Nucleic Acids Res. 2009, 37:1878-1885.
36. Mendell J.T. miRiad roles for the miR-17-92 cluster in development and disease. Cell 2008, 133:217-222.
37. Morin R.D., et al. Application of massively parallel sequencing to microRNA profiling and discovery in human embryonic stem cells. Genome Res. 2008, 18:610-621.
38. Morlando M., Ballarino M., Gromak N., Pagano F., Bozzoni I., Proudfoot N.J. Primary microRNA transcripts are processed co-transcriptionally. Nat. Struct. Mol. Biol. 2008, 15:902-909.
39. Okamura K., Phillips M.D., Tyler D.M., Duan H., Chou Y.T., Lai E.C. The regulatory activity of microRNA star species has substantial influence on microRNA and 3 ' UTR evolution. Nat. Struct. Mol. Biol. 2008, 15:354-363.
40. Okamura K., Liu N., Lai E.C. Distinct mechanisms for microRNA strand selection by Drosophila Argonautes. Mol. Cell 2009, 36:431-444.
41. Reid J.G., et al. Mouse let-7 miRNA populations exhibit RNA editing that is constrained in the 5'-seed/cleavage/anchor regions and stabilize predicted mmu-let-7a: mRNA duplexes. Genome Res. 2008, 18:1571-1581.
42. Ro S., Park C., Young D., Sanders K.M., Yan W. Tissue-dependent paired expression of miRNAs. Nucleic Acids Res. 2007, 35:5944-5953.
43. Ruby J.G., Stark A., Johnston W.K., Kellis M., Bartel D.P., Lai E.C. Evolution, biogenesis, expression, and target predictions of a substantially expanded set of Drosophila microRNAs. Genome Res. 2007, 17:1850-1864.
44. Shearwin K.E., Callen B.P., Egan J.B. Transcriptional interference-a crash course. Trends Genet. 2005, 21:339-345.
45. Stark A., et al. A single Hox locus in Drosophila produces functional microRNAs from opposite DNA strands. Genes Dev. 2008, 22:8-13.
46. Tanzer A., Stadler P.F. Molecular evolution of a microRNA cluster. J. Mol. Biol. 2004, 339:327-335.
47. Witten D., Tibshirani R., Gu S.G., Fire A., Lui W.O. Ultra-high throughput sequencing-based small RNA discovery and discrete statistical biomarker analysis in a collection of cervical tumours and matched controls. BMC Biol. 2010, 8:58.
48. Xu J.Z., Wong C.W. A computational screen for mouse signaling pathways targeted by microRNA clusters. Rna-a Publication of the Rna Society 2008, 14:1276-1283.
49. Yu J., et al. Human microRNA clusters: genomic organization and expression profile in leukemia cell lines. Biochem. Biophys. Res. Commun. 2006, 349:59-68.