Computational analysis of microRNA function in heart development

Acta Biochimica et Biophysica Sinica

Volumn 42, Issue 9, 2010, Pages 662-670

  Liu, Ganqiang ^a,b   Ding, Min ^b   Chen, Jiajia ^a,c   Huang, Jinyan ^b   Wang, Haiyun ^b   Jing, Qing ^d   Shen, Bairong ^a  

^a SOOCHOW UNIVERSITY   (China)

^b TONGJI UNIVERSITY   (China)

^c SUZHOU UNIVERSITY OF SCIENCE AND TECHNOLOGY   (China)

^d Chinese Academy of Sciences   (China)

Author keywords

database; enrichment analysis; heart development; microRNA

Indexed keywords

MICRORNA;

ALGORITHM; ANIMAL; ARTICLE; BIOLOGY; GENE EXPRESSION PROFILING; GENE EXPRESSION REGULATION; GENETIC DATABASE; GENETICS; GROWTH, DEVELOPMENT AND AGING; HEART; HEART MUSCLE; INTERNET; METABOLISM; METHODOLOGY; MOUSE; PHYSIOLOGY; PRENATAL DEVELOPMENT; SIGNAL TRANSDUCTION;

ALGORITHMS; ANIMALS; COMPUTATIONAL BIOLOGY; DATABASES, GENETIC; GENE EXPRESSION PROFILING; GENE EXPRESSION REGULATION, DEVELOPMENTAL; HEART; INTERNET; MICE; MICRORNAS; MYOCARDIUM; SIGNAL TRANSDUCTION;

EID: 77956293290     PISSN: 16729145     EISSN: 17457270     Source Type: Journal    
DOI: 10.1093/abbs/gmq072     Document Type: Article

References (43)

1. Bartel DP. MicroRNAs: genomics, biogenesis, mechanism, and function. Cell 2004, 116: 281-297.
2. Farh KK, Grimson A, Jan C, Lewis BP, Johnston WK, Lim LP and Burge CB, et al. The widespread impact of mammalian MicroRNAs on mRNA repression and evolution. Science 2005, 310: 1817-1821.
3. Wang Y, Stricker HM, Gou D and Liu L. MicroRNA: past and present. Front Biosci 2007, 12: 2316-2329.
4. Warkman AS and Krieg PA. Xenopus as a model system for vertebrate heart development. Semin Cell Dev Biol 2007, 18: 46-53.
5. Griffiths-Jones S, Saini HK, van Dongen S and Enright AJ. miRBase: tools for microRNA genomics. Nucleic Acids Res 2008, 36: D154-D158.
6. Megraw M, Sethupathy P, Corda B and Hatzigeorgiou AG. miRGen: a database for the study of animal microRNA genomic organization and function. Nucleic Acids Res 2007, 35: D149-D155.
7. Nam S, Kim B, Shin S and Lee S. miRGator: an integrated system for functional annotation of microRNAs. Nucleic Acids Res 2008, 36: D159-D164.
8. Sprague J, Bayraktaroglu L, Clements D, Conlin T, Fashena D, Frazer K and Haendel M, et al. The Zebrafish Information Network: the zebrafish model organism database. Nucleic Acids Res 2006, 34: D581-D585.
9. Darnell DK, Kaur S, Stanislaw S, Davey S, Konieczka JH, Yatskievych TA and Antin PB. GEISHA: an in situ hybridization gene expression resource for the chicken embryo. Cytogenet Genome Res 2007, 117: 30-35.
10. Smith CM, Finger JH, Hayamizu TF, McCright IJ, Eppig JT, Kadin JA and Richardson JE, et al. The mouse Gene Expression Database (GXD): 2007 update. Nucleic Acids Res 2007, 35: D618-D623.
11. Bruneau BG. Developmental biology: tiny brakes for a growing heart. Nature 2005, 436: 181-182.
12. Thum T, Catalucci D and Bauersachs J. MicroRNAs: novel regulators in cardiac development and disease. Cardiovasc Res 2008, 79: 562-570.
13. Callis TE and Wang DZ. Taking microRNAs to heart. Trends Mol Med 2008, 14: 254-260.
14. Cordes KR and Srivastava D. MicroRNA regulation of cardiovascular development. Circ Res 2009, 104: 724-732.
15. Zhao Y, Samal E and Srivastava D. Serum response factor regulates a muscle-specific microRNA that targets Hand2 during cardiogenesis. Nature 2005, 436: 214-220.
16. Zhao Y, Ransom JF, Li A, Vedantham V, von Drehle M, Muth AN and Tsuchihashi T, et al. Dysregulation of cardiogenesis, cardiac conduction, and cell cycle in mice lacking miRNA-1-2. Cell 2007, 129: 303-317.
17. Chen JF, Mandel EM, Thomson JM, Wu Q, Callis TE, Hammond SM and Conlon FL, et al. The role of microRNA-1 and microRNA-133 in skeletal muscle proliferation and differentiation. Nat Genet 2006, 38: 228-233.
18. Liu N, Bezprozvannaya S, Williams AH, Qi X, Richardson JA, Bassel-Duby R and Olson EN. microRNA-133a regulates cardiomyocyte proliferation and suppresses smooth muscle gene expression in the heart. Genes Dev 2008, 22: 3242-3254.
19. Morton SU, Scherz PJ, Cordes KR, Ivey KN, Stainier DY and Srivastava D. microRNA-138 modulates cardiac patterning during embryonic development. Proc Natl Acad Sci USA 2008, 105: 17830-17835.
20. Cordes KR, Sheehy NT, White MP, Berry EC, Morton SU, Muth AN and Lee TH, et al. miR-145 and miR-143 regulate smooth muscle cell fate and plasticity. Nature 2009, 460: 705-710.
21. Ivey KN, Muth A, Arnold J, King FW, Yeh RF, Fish JE and Hsiao EC, et al. MicroRNA regulation of cell lineages in mouse and human embryonic stem cells. Cell Stem Cell 2008, 2: 219-229.
22. Papadopoulos GL, Reczko M, Simossis VA, Sethupathy P and Hatzigeorgiou AG. The database of experimentally supported targets: a functional update of TarBase. Nucleic Acids Res 2009, 37: D155-D158.
23. Xiao F, Zuo Z, Cai G, Kang S, Gao X and Li T. miRecords: an integrated resource for microRNA-target interactions. Nucleic Acids Res 2009, 37: D105-D110.
24. Gusev Y. Computational methods for analysis of cellular functions and pathways collectively targeted by differentially expressed microRNA. Methods 2008, 44: 61-72.
25. Betel D, Wilson M, Gabow A, Marks DS and Sander C. The microRNA.org resource: targets and expression. Nucleic Acids Res 2008, 36: D149-D153.
26. Lewis BP, Burge CB and Bartel DP. Conserved seed pairing, often flanked by adenosines, indicates that thousands of human genes are microRNA targets. Cell 2005, 120: 15-20.
27. Wang X. miRDB: a microRNA target prediction and functional annotation database with a wiki interface. RNA 2008, 14: 1012-1017.
28. Wang X and El Naqa IM. Prediction of both conserved and nonconserved microRNA targets in animals. Bioinformatics 2008, 24: 325-332.
29. Kertesz M, Iovino N, Unnerstall U, Gaul U and Segal E. The role of site accessibility in microRNA target recognition. Nat Genet 2007, 39: 1278-1284.
30. Rehmsmeier M, Steffen P, Hochsmann M and Giegerich R. Fast and effective prediction of microRNA/target duplexes. RNA 2004, 10: 1507-1517.
31. Sethupathy P, Megraw M and Hatzigeorgiou AG. A guide through present computational approaches for the identification of mammalian microRNA targets. Nat Methods 2006, 3: 881-886.
32. Ashburner M, Ball CA, Blake JA, Botstein D, Butler H, Cherry JM and Davis AP, et al. Gene ontology: tool for the unification of biology. The Gene Ontology Consortium. Nat Genet 2000, 25: 25-29.
33. Kanehisa M and Goto S. KEGG: kyoto encyclopedia of genes and genomes. Nucleic Acids Res 2000, 28: 27-30.
34. Tanoue T and Nishida E. Docking interactions in the mitogen-activated protein kinase cascades. Pharmacol Ther 2002, 93: 193-202.
35. Brade T, Manner J and Kuhl M. The role of Wnt signalling in cardiac development and tissue remodelling in the mature heart. Cardiovasc Res 2006, 72: 198-209.
36. Eisenberg LM and Eisenberg CA. Evaluating the role of Wnt signal transduction in promoting the development of the heart. Sci World J 2007, 7: 161-176.
37. Cohen ED, Tian Y and Morrisey EE. Wnt signaling: an essential regulator of cardiovascular differentiation, morphogenesis and progenitor selfrenewal. Development 2008, 135: 789-798.
38. Liu G, Ding M, Wang H, Huang J, Jing Q and Shen B. Pathway analysis of microRNAs in mouse heart development. Int J Bioinform Res Appl 2010, 6: 12-20.
39. Iwamoto R and Mekada E. ErbB and HB-EGF signaling in heart development and function. Cell Struct Funct 2006, 31: 1-14.
40. Ikeda S, He A, Kong SW, Lu J, Bejar R, Bodyak N and Lee KH, et al. MicroRNA-1 negatively regulates expression of the hypertrophyassociated calmodulin and Mef2a genes. Mol Cell Biol 2009, 29: 2193-2204.
41. Zhang L, Ding L, Cheung TH, Dong MQ, Chen J, Sewell AK and Liu X, et al. Systematic identification of C. elegans miRISC proteins, miRNAs, and mRNA targets by their interactions with GW182 proteins AIN-1 and AIN-2. Mol Cell 2007, 28: 598-613.
42. Easow G, Teleman AA and Cohen SM. Isolation of microRNA targets by miRNP immunopurification. RNA 2007, 13: 1198-1204.
43. Beitzinger M, Peters L, Zhu JY, Kremmer E and Meister G. Identification of human microRNA targets from isolated argonaute protein complexes. RNA Biol 2007, 4: 76-84.