In silico detection and characteristics of novel microRNA genes in the Equus caballus genome using an integrated ab initio and comparative genomic approach

Genomics

Volumn 94, Issue 2, 2009, Pages 125-131

  Zhou, Meng ^a   Wang, Qianghu ^a   Sun, Jie ^a   Li, Xia ^a   Xu, Liangde ^a   Yang, Haixiu ^a   Shi, Hongbo ^a   Ning, Shangwei ^a   Chen, Li ^a   Li, Yan ^a   He, Taotao ^a   Zheng, Yan ^a  

^a HARBIN MEDICAL UNIVERSITY   (China)

Author keywords

Comparative genomics; Horse; In silico detection; Integrated approach; microRNA

Indexed keywords

MICRORNA;

AB INITIO CALCULATION; ARTICLE; CISTRON; COMPUTER MODEL; CONTROLLED STUDY; GENE CLUSTER; GENE IDENTIFICATION; GENE SEQUENCE; GENOME ANALYSIS; HORSE; MULTIGENE FAMILY; NONHUMAN; PRIORITY JOURNAL;

ANIMALS; CHROMOSOMES, MAMMALIAN; COMPUTERS; GENOME; HORSES; MICRORNAS; TRANSCRIPTION, GENETIC;

ANIMALIA; EQUIDAE; EQUUS CABALLUS;

EID: 67649945833     PISSN: 08887543     EISSN: 10898646     Source Type: Journal    
DOI: 10.1016/j.ygeno.2009.04.006     Document Type: Article

References (47)

1. Shimoni Y., et al. Regulation of gene expression by small non-coding RNAs: a quantitative view. Mol. Syst. Biol. 3 (2007) 138
2. Rodriguez A., Griffiths-Jones S., Ashurst J.L., and Bradley A. Identification of mammalian microRNA host genes and transcription units. Genome Res. 14 (2004) 1902-1910
3. Hwang H.W., and Mendell J.T. MicroRNAs in cell proliferation, cell death, and tumorigenesis. Br. J. Cancer 94 (2006) 776-780
4. Ambros V., et al. A uniform system for microRNA annotation. RNA 9 (2003) 277-279
5. Dezulian T., Remmert M., Palatnik J.F., Weigel D., and Huson D.H. Identification of plant microRNA homologs. Bioinformatics 22 (2006) 359-360
6. Engels B.M., and Hutvagner G. Principles and effects of microRNA-mediated post-transcriptional gene regulation. Oncogene 25 (2006) 6163-6169
7. Carrington J.C., and Ambros V. Role of microRNAs in plant and animal development. Science 301 (2003) 336-338
8. Kidner C.A., and Martienssen R.A. The developmental role of microRNA in plants. Curr. Opin. Plant Biol. 8 (2005) 38-44
9. Allen E., Xie Z., Gustafson A.M., and Carrington J.C. microRNA-directed phasing during trans-acting siRNA biogenesis in plants. Cell 121 (2005) 207-221
10. Zhang B., Pan X., Cannon C.H., Cobb G.P., and Anderson T.A. Conservation and divergence of plant microRNA genes. Plant J. 46 (2006) 243-259
11. Dezulian T., Remmert M., Palatnik J.F., Weigel D., and Huson D.H. Identification of plant microRNA homologs. Bioinformatics 22 (2006) 359-360
12. Horse Genome Project, http://www.broad.mit.edu.
13. Chowdhary B.P., and Raudsepp T. The horse genome. Genome Dyn. 2 (2006) 97-110
14. Chowdhary B.P., and Raudsepp T. The horse genome derby: racing from map to whole genome sequence. Chromosom. Res. 16 (2008) 109-127
15. Paulis M., Moralli D., Bensi M., De Carli L., and Raimondi E. Isolation from the horse genome of a new DNA transposon belonging to the Tigger family. Mamm. Genome 15 (2004) 399-403
16. Raudsepp T., et al. A 4,103 marker integrated physical and comparative map of the horse genome. Cytogenet. Genome Res. 122 (2008) 28-36
17. Griffiths-Jones S., Saini H.K., van Dongen S., and Enright A.J. miRBase: tools for microRNA genomics. Nucleic Acids Res. 36 (2008) D154-158
18. Maselli V., Di Bernardo D., and Banfi S. CoGemiR: a comparative genomics microRNA database. BMC Genomics 9 (2008) 457
19. Megraw M., Sethupathy P., Corda B., and Hatzigeorgiou A.G. miRGen: a database for the study of animal microRNA genomic organization and function. Nucleic Acids Res. 35 (2007) D149-155
20. He P.A., et al. Identification and characteristics of microRNAs from Bombyx mori. BMC Genomics 9 (2008) 248
21. Lai E.C., Tomancak P., Williams R.W., and Rubin G.M. Computational identification of Drosophila microRNA genes. Genome Biol. 4 (2003) R42
22. Lim L.P., Glasner M.E., Yekta S., Burge C.B., and Bartel D.P. Vertebrate microRNA genes. Science 299 (2003) 1540
23. Sunkar R., and Jagadeeswaran G. In silico identification of conserved microRNAs in large number of diverse plant species. BMC Plant Biol. 8 (2008) 37
24. Thatcher E.J., Bond J., Paydar I., and Patton J.G. Genomic organization of zebrafish microRNAs. BMC Genomics 9 (2008) 253
25. Xie F.L., et al. Computational identification of novel microRNAs and targets in Brassica napus. FEBS Lett. 581 (2007) 1464-1474
26. Yue J., Sheng Y., and Orwig K.E. Identification of novel homologous microRNA genes in the rhesus macaque genome. BMC Genomics 9 (2008) 8
27. Zhang B., Pan X., and Stellwag E.J. Identification of soybean microRNAs and their targets. Planta 229 (2008) 161-182
28. Liu N., et al. The evolution and functional diversification of animal microRNA genes. Cell Res. 18 (2008) 985-996
29. Wang X., et al. MicroRNA identification based on sequence and structure alignment. Bioinformatics 21 (2005) 3610-3614
30. Zhang B.H., Pan X.P., Cox S.B., Cobb G.P., and Anderson T.A. Evidence that miRNAs are different from other RNAs. Cell. Mol. Life Sci. 63 (2006) 246-254
31. Nam J.W., Kim J., Kim S.K., and Zhang B.T. ProMiR II: a web server for the probabilistic prediction of clustered, nonclustered, conserved and nonconserved microRNAs. Nucleic Acids Res. 34 (2006) W455-458
32. Bender W. MicroRNAs in the Drosophila bithorax complex. Genes Dev. 22 (2008) 14-19
33. Stark A., et al. A single Hox locus in Drosophila produces functional microRNAs from opposite DNA strands. Genes Dev. 22 (2008) 8-13
34. Tyler D.M. Functionally distinct regulatory RNAs generated by bidirectional transcription and processing of microRNA loci. Genes Dev. 22 (2008) 26-36
35. Bonnet E., Wuyts J., Rouze P., and Van de Peer Y. Evidence that microRNA precursors, unlike other non-coding RNAs, have lower folding free energies than random sequences. Bioinformatics 20 (2004) 2911-2917
36. Jiang P., et al. MiPred: classification of real and pseudo microRNA precursors using random forest prediction model with combined features. Nucleic Acids Res. 35 (2007) W339-W344
37. Kuhn R.M. The UCSC Genome Browser Database: update 2009. Nucleic Acids Res. 37 (2009) D755-D761
38. Altuvia Y. Clustering and conservation patterns of human microRNAs. Nucleic Acids Res. 33 (2005) 2697-2706
39. Lagos-Quintana M., Rauhut R., Lendeckel W., and Tuschl T. Identification of novel genes coding for small expressed RNAs. Science 294 (2001) 853-858
40. Lagos-Quintana M., Rauhut R., Meyer J., Borkhardt A., and Tuschl T. New microRNAs from mouse and human. RNA 9 (2003) 175-179
41. Yu J., et al. Human embryonic stem cells reprogram myeloid precursors following cell-cell fusion. Stem Cells 24 (2006) 168-176
42. Lee Y., Jeon K., Lee J.T., Kim S., and Kim V.N. MicroRNA maturation: stepwise processing and subcellular localization. EMBO J. 21 (2002) 4663-4670
43. Thatcher E.J., Flynt A.S., Li N., Patton J.R., and Patton J.G. MiRNA expression analysis during normal zebrafish development and following inhibition of the Hedgehog and Notch signaling pathways. Dev. Dyn. 236 (2007) 2172-2180
44. Gitlin L., Stone J.K., and Andino R. Poliovirus escape from RNA interference: short interfering RNA-target recognition and implications for therapeutic approaches. J. Virol. 79 (2005) 1027-1035
45. Seitz H., et al. A large imprinted microRNA gene cluster at the mouse Dlk1-Gtl2 domain. Genome Res. 14 (2004) 1741-1748
46. Mathews D.H., Sabina J., Zuker M., and Turner D.H. Expanded sequence dependence of thermodynamic parameters improves prediction of RNA secondary structure. J. Mol. Biol. 288 (1999) 911-940
47. Zuker M. Mfold web server for nucleic acid folding and hybridization prediction. Nucleic Acids Res. 31 (2003) 3406-3415