Discovery and profiling of bovine microRNAs from immune-related and embryonic tissues

Physiological Genomics

Volumn 29, Issue 1, 2007, Pages 35-43

  Coutinho, Luiz L ^b   Matukumalli, Lakshmi K ^a,c   Sonstegard, Tad S ^a   Van Tassell, Curtis P ^a   Gasbarre, Louis C ^a   Capuco, Anthony V ^a   Smith, Timothy P L ^d  

^a AGRICULTURAL RESEARCH SERVICE   (United States)

^b UNIVERSITY OF SÃO PAULO   (Brazil)

^c GEORGE MASON UNIVERSITY   (United States)

^d U S MEAT ANIMAL RESEARCH CENTER   (United States)

Author keywords

Embryo; Immune; MicroRNA; Small RNA

Indexed keywords

COMPLEMENTARY DNA; MICRORNA;

ANIMAL TISSUE; ARTICLE; CALCULATION; COMPARATIVE STUDY; COMPUTER MODEL; CONTROLLED STUDY; COW; DATA BASE; DNA LIBRARY; DNA SEQUENCE; EMBRYO; EMBRYONAL TISSUE; GENE EXPRESSION; IMMUNE RESPONSE; LYMPH NODE; NONHUMAN; PREDICTION; PRIORITY JOURNAL; REVERSE TRANSCRIPTION POLYMERASE CHAIN REACTION; RNA SEQUENCE; SEQUENCE ANALYSIS; SMALL INTESTINE; THYMUS; VALIDATION STUDY;

ANIMALS; BASE PAIRING; BASE SEQUENCE; CATTLE; CLUSTER ANALYSIS; COMPUTATIONAL BIOLOGY; CONSERVED SEQUENCE; EMBRYO; GENE EXPRESSION PROFILING; GENE EXPRESSION REGULATION; GENE LIBRARY; GENOMICS; MICRORNAS; MOLECULAR SEQUENCE DATA; REVERSE TRANSCRIPTASE POLYMERASE CHAIN REACTION; SEQUENCE ALIGNMENT; SEQUENCE ANALYSIS, DNA;

BOVINAE; VERTEBRATA;

EID: 34248178219     PISSN: 10948341     EISSN: 15312267     Source Type: Journal    
DOI: 10.1152/physiolgenomics.00081.2006     Document Type: Article

References (42)

1. Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ. Basic local alignment search tool. J Mol Biol 215: 403-410, 1990.
2. Altuvia Y, Landgraf P, Lithwick G, Elefant N, Pfeffer S, Aravin A, Brownstein MJ, Tuschl T, Margalit H. Clustering and conservation patterns of human microRNAs. Nucleic Acids Res 33: 2697-2706, 2005.
3. Alvarez-Garcia I, Miska EA. MicroRNA functions in animal development and human disease. Development 132: 4653-4662, 2005.
4. Ambros V. microRNAs: tiny regulators with great potential. Cell 107: 823-826, 2001.
5. Ambros V, Bartel B, Bartel DP, Burge CB, Carrington JC, Chen X, Dreyfuss G, Eddy SR, Griffiths-Jones S, Marshall M, Matzke M, Ruvkun G, Tuschl T. A uniform system for microRNA annotation. RNA 9: 277-279, 2003.
6. Barad O, Meiri E, Avniel A, Aharonov R, Barzilai A, Bentwich I, Einav U, Gilad S, Hurban P, Karov Y, Lobenhofer EK, Sharon E, Shiboleth YM, Shtutman M, Bentwich Z, Einat P. MicroRNA expression detected by oligonucleotide microarrays: system establishment and expression profiling in human tissues. Genome Res 14: 2486-2494, 2004.
7. Bartel DP. MicroRNAs: genomics, biogenesis, mechanism, function. Cell 116: 281-297, 2004.
8. Baskerville S, Bartel DP. Microarray profiling of microRNAs reveals frequent coexpression with neighboring miRNAs and host genes. RNA 11: 241-247, 2005.
9. Bentwich I, Avniel A, Karov Y, Aharonov R, Gilad S, Barad O, Barzilai A, Einat P, Einav U, Meiri E, Sharon E, Spector Y, Bentwich Z. Identification of hundreds of conserved and nonconserved human microRNAs. Nat Genet 37: 766-770, 2005.
10. Berezikov E, Guryev V, van de Belt J, Wienholds E, Plasterk RH, Cuppen E. Phylogenetic shadowing and computational identification of human microRNA genes. Cell 120: 21-24, 2005.
11. Chan JA, Krichevsky AM, Kosik KS. MicroRNA-21 is an antiapoptotic factor in human glioblastoma cells. Cancer Res 65: 6029-6033, 2005.
12. Chen CZ, Li L, Lodish HF, Bartel DP. MicroRNAs modulate hematopoietic lineage differentiation. Science 303: 83-86, 2004.
13. Cummins JM, He Y, Leary RJ, Pagliarini R, Diaz LA Jr, Sjoblom T, Barad O, Bentwich Z, Szafranska AE, Labourier E, Raymond CK, Roberts BS, Juhl H, Kinzler KW, Vogelstein B, Velculescu VE. The colorectal microRNAome. Proc Natl Acad Sci USA 103: 3687-3692, 2006.
14. Ewing B, Hillier L, Wendl MC, Green P. Base-calling of automated sequencer traces using phred. I. Accuracy assessment. Genome Res 8: 175-185, 1998.
15. Farh KK, Grimson A, Jan C, Lewis BP, Johnston WK, Lim LP, Burge CB, Bartel DP. The widespread impact of mammalian MicroRNAs on mRNA repression and evolution. Science 310: 1817-1821, 2005.
16. Gibs R, Weinstock G, Kappes S, Schook L, Skow L, Womack J. Bovine Genomic Sequencing Initiative. www.genome.gov/Pages/Research/Sequencing/ SeqProposals/BovineSEQpdf, 2006.
17. Giraldez AJ, Cinalli RM, Glasner ME, Enright AJ, Thomson JM, Baskerville S, Hammond SM, Bartel DP, Schier AF. MicroRNAs regulate brain morphogenesis in zebrafish. Science 308: 833-838, 2005.
18. Griffiths-Jones S, Grocock RJ, van Dongen S, Bateman A, Enright AJ. miRBase: microRNA sequences, targets and gene nomenclature. Nucleic Acids Res 34: D140-D144, 2006.
19. Harfe BD. MicroRNAs in vertebrate development. Curr Opin Genet Dev 15: 410-415, 2005.
20. He L, Hannon GJ. MicroRNAs: small RNAs with a big role in gene regulation. Nat Rev Genet 5: 522-531, 2004.
21. Hsu PW, Huang HD, Hsu SD, Lin LZ, Tsou AP, Tseng CP, Stadler PF, Washietl S, Hofacker IL. miRNAMap: genomic maps of microRNA genes and their target genes in mammalian genomes. Nucleic Acids Res 34: D135-D139, 2006.
22. Khvorova A, Reynolds A, Jayasena SD. Functional siRNAs and miRNAs exhibit strand bias. Cell 115: 209-216, 2003.
23. Lecellier CH, Dunoyer P, Arar K, Lehmann-Che J, Eyquem S, Himber C, Saib A, Voinnet O. A cellular microRNA mediates antiviral defense in human cells. Science 308: 557-560, 2005.
24. Lim LP, Lau NC, Garrett-Engele P, Grimson A, Schelter JM, Castle J, Bartel DP, Linsley PS, Johnson JM. Microarray analysis shows that some microRNAs downregulate large numbers of target mRNAs. Nature 433: 769-773, 2005.
25. Liu CG, Calin GA, Meloon B, Gamliel N, Sevignani C, Ferracin M, Dumitru CD, Shimizu M, Zupo S, Dono M, Alder H, Bullrich F, Negrini M, Croce CM. An oligonucleotide microchip for genome-wide microRNA profiling in human and mouse tissues. Proc Natl Acad Sci USA 101: 9740-9744, 2004.
26. Lu C, Tej SS, Luo S, Haudenschild CD, Meyers BC, Green PJ. Elucidation of the small RNA component of the transcriptome. Science 309: 1567-1569, 2005.
27. Mathews DH, Sabina J, Zuker M, Turner DH. Expanded sequence dependence of thermodynamic parameters improves prediction of RNA secondary structure. J Mol Biol 288: 911-940, 1999.
28. Mineno J, Okamoto S, Ando T, Sato M, Chono H, Izu H, Takayama M, Asada K, Mirochnitchenko O, Inouye M, Kato I. The expression profile of microRNAs in mouse embryos. Nucleic Acids Res 34: 1765-1771, 2006.
29. Monticelli S, Ansel KM, Xiao C, Socci ND, Krichevsky AM, Thai TH, Rajewsky N, Marks DS, Sander C, Rajewsky K, Rao A, Kosik KS. MicroRNA profiling of the murine hematopoietic system. Genome Biol 6: R71, 2005.
30. Pasquinelli AE, Hunter S, Bracht J. MicroRNAs: a developing story. Curr Opin Genet Dev 15: 200-205, 2005.
31. Pillai RS. MicroRNA function: multiple mechanisms for a tiny RNA? RNA 11: 1753-1761, 2005.
32. Poy MN, Eliasson L, Krutzfeldt J, Kuwajima S, Ma X, Macdonald PE, Pfeffer S, Tuschl T, Rajewsky N, Rorsman P, Stoffel M. A pancreatic islet-specific microRNA regulates insulin secretion. Nature 432: 226-230, 2004.
33. Rassenti L, Lu DP, Read RL, Humphreys DT, Battah FM, Martin DIK, Rasko JEJ. PCR-based expression analysis and identification of microRNAs. J RNAi Gene Silencing 1: 44-49, 2005.
34. Sewer A, Paul N, Landgraf P, Aravin A, Pfeffer S, Brownstein MJ, Tuschl T, van Nimwegen E, Zavolan M. Identification of clustered microRNAs using an ab initio prediction method. BMC Bioinformatics 6: 267, 2005.
35. Shingara J, Keiger K, Shelton J, Laosinchai-Wolf W, Powers P, Conrad R, Brown D, Labourier E. An optimized isolation and labeling platform for accurate microRNA expression profiling. RNA 11: 1461-1470, 2005.
36. Suh MR, Lee Y, Kim JY, Kim SK, Moon SH, Lee JY, Cha KY, Chung HM, Yoon HS, Moon SY, Kim VN, Kim KS. Human embryonic stem cells express a unique set of microRNAs. Dev Biol 270: 488-498, 2004.
37. Thomson JM, Parker J, Perou CM, Hammond SM. A custom microarray platform for analysis of microRNA gene expression. Nat Methods 1: 47-53, 2004.
38. Washietl S, Hofacker IL, Stadler PF. Fast and reliable prediction of noncoding RNAs. Proc Natl Acad Sci USA 102: 2454-2459, 2005.
39. Wienholds E, Kloosterman WP, Miska E, Alvarez-Saavedra E, Berezikov E, de Bruijn E, Horvitz HR, Kauppinen S, Plasterk RH. MicroRNA expression in zebrafish embryonic development. Science 309: 310-311, 2005.
40. Wienholds E, Plasterk RH. MicroRNA function in animal development. FEBS Lett 579: 5911-5922, 2005.
41. Zhao Y, Samal E, Srivastava D. Serum response factor regulates a muscle-specific microRNA that targets Hand2 during cardiogenesis. Nature 436: 214-220, 2005.
42. Zuker M. Mfold web server for nucleic acid folding and hybridization prediction. Nucleic Acids Res 31: 3406-3415, 2003.