Identification of baboon microRNAs expressed in liver and lymphocytes

Journal of Biomedical Science

Volumn 17, Issue 1, 2010, Pages

  Karere, Genesio M ^a   Glenn, Jeremy P ^a   Vandeberg, John L ^a,b   Cox, Laura A ^a,b  

^a SOUTHWEST FOUNDATION FOR BIOMEDICAL RESEARCH   (United States)

^b SOUTHWEST NATIONAL PRIMATE RESEARCH CENTER   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

MICRORNA; PRIMER DNA;

ANIMAL CELL; ANIMAL EXPERIMENT; ANIMAL MODEL; ANIMAL TISSUE; ARTICLE; ATHEROSCLEROSIS; BABOON; COMPARATIVE GENOMIC HYBRIDIZATION; COMPUTER MODEL; CONTROLLED STUDY; DYSLIPIDEMIA; GENOME; HUMAN; LIVER; LYMPHOCYTE; MICROARRAY ANALYSIS; NONHUMAN; PREDICTOR VARIABLE; PRIMATE; PRIORITY JOURNAL; REVERSE TRANSCRIPTION POLYMERASE CHAIN REACTION; RNA ANALYSIS; SEQUENCE ALIGNMENT; ANIMAL; CARDIOVASCULAR DISEASE; GENE EXPRESSION PROFILING; GENE EXPRESSION REGULATION; GENETICS; METABOLISM;

PAPIO; PRIMATES;

ANIMALS; CARDIOVASCULAR DISEASES; COMPARATIVE GENOMIC HYBRIDIZATION; DNA PRIMERS; GENE EXPRESSION PROFILING; GENE EXPRESSION REGULATION; HUMANS; LIVER; LYMPHOCYTES; MICRORNAS; PAPIO; REVERSE TRANSCRIPTASE POLYMERASE CHAIN REACTION;

EID: 77954079355     PISSN: 10217770     EISSN: 14230127     Source Type: Journal    
DOI: 10.1186/1423-0127-17-54     Document Type: Article

References (44)

1. Identification of mammalian microRNA host genes and transcription units. A Rodriguez S Griffiths-Jones JL Ashurst A Bradley, Genome Res 2004 14 10A 1902 1910 10.1101/gr.2722704 15364901
2. The C. elegans heterochronic gene lin-4 encodes small RNAs with antisense complementarity to lin-14. RC Lee RL Feinbaum V Ambros, Cell 1993 75 5 843 854 10.1016/0092-8674(93)90529-Y 8252621
3. MicroRNA genes are transcribed by RNA polymerase II. Y Lee M Kim J Han KH Yeom S Lee SH Baek VN Kim, EMBO J 2004 23 20 4051 4060 10.1038/sj.emboj.7600385 15372072
4. Human microRNAs are processed from capped, polyadenylated transcripts that can also function as mRNAs. X Cai CH Hagedorn BR Cullen, RNA 2004 10 12 1957 1966 10.1261/rna.7135204 15525708
5. Exportin 5 is a RanGTP-dependent dsRNA-binding protein that mediates nuclear export of pre-miRNAs. MT Bohnsack K Czaplinski D Gorlich, RNA 2004 10 2 185 191 10.1261/rna.5167604 14730017
6. Exportin-5 mediates the nuclear export of pre-microRNAs and short hairpin RNAs. R Yi Y Qin IG Macara BR Cullen, Genes Dev 2003 17 24 3011 3016 10.1101/gad.1158803 14681208
7. A human, ATP-independent, RISC assembly machine fueled by pre-miRNA. E Maniataki Z Mourelatos, Genes Dev 2005 19 24 2979 2990 10.1101/gad.1384005 16357216
8. The functions of animal microRNAs. V Ambros, Nature 2004 431 7006 350 355 10.1038/nature02871 15372042
9. The Microprocessor complex mediates the genesis of microRNAs. RI Gregory KP Yan G Amuthan T Chendrimada B Doratotaj N Cooch R Shiekhattar, Nature 2004 432 7014 235 240 10.1038/nature03120 15531877
10. A pattern-based method for the identification of MicroRNA binding sites and their corresponding heteroduplexes. KC Miranda T Huynh Y Tay YS Ang WL Tam AM Thomson B Lim I Rigoutsos, Cell 2006 126 6 1203 1217 10.1016/j.cell.2006.07. 031 16990141
11. MicroRNA expression signature and antisense-mediated depletion reveal an essential role of MicroRNA in vascular neointimal lesion formation. R Ji Y Cheng J Yue J Yang X Liu H Chen DB Dean C Zhang, Circ Res 2007 100 11 1579 1588 10.1161/CIRCRESAHA.106.141986 17478730
12. MicroRNAs regulate brain morphogenesis in zebrafish. AJ Giraldez RM Cinalli ME Glasner AJ Enright JM Thomson S Baskerville SM Hammond DP Bartel AF Schier, Science 2005 308 5723 833 838 10.1126/science.1109020 15774722
13. Emerging role of microRNAs in cardiovascular biology. MV Latronico D Catalucci G Condorelli, Circ Res 2007 101 12 1225 1236 10.1161/CIRCRESAHA.107. 163147 18063818
14. A necessary role of miR-221 and miR-222 in vascular smooth muscle cell proliferation and neointimal hyperplasia. X Liu Y Cheng S Zhang Y Lin J Yang C Zhang, Circ Res 2009 104 4 476 487 10.1161/CIRCRESAHA.108.185363 19150885
15. Diagnostic and prognostic implications of microRNAs in human hepatocellular carcinoma. W Li L Xie X He J Li K Tu L Wei J Wu Y Guo X Ma P Zhang Z Pan X Hu Y Zhao H Xie G Jiang T Chen J Wang S Zheng J Cheng D Wan S Yang Y Li J Gu, Int J Cancer 2008 123 7 1616 1622 10.1002/ijc.23693 18649363
16. MicroRNA-133 controls cardiac hypertrophy. A Care D Catalucci F Felicetti D Bonci A Addario P Gallo ML Bang P Segnalini Y Gu ND Dalton L Elia MV Latronico M Hoydal C Autore MA Russo GW Dorn O Ellingsen P Ruiz-Lozano KL Peterson CM Croce C Peschle G Condorelli, Nat Med 2007 13 5 613 618 10.1038/nm1582 17468766
17. MicroRNAs play an essential role in the development of cardiac hypertrophy. D Sayed C Hong IY Chen J Lypowy M Abdellatif, Circ Res 2007 100 3 416 424 10.1161/01.RES.0000257913.42552.23 17234972
18. The up-regulation of microRNA-335 is associated with lipid metabolism in liver and white adipose tissue of genetically obese mice. N Nakanishi Y Nakagawa N Tokushige N Aoki T Matsuzaka K Ishii N Yahagi K Kobayashi S Yatoh A Takahashi H Suzuki O Urayama N Yamada H Shimano, Biochem Biophys Res Commun 2009 385 4 492 496 10.1016/j.bbrc.2009.05.058 19460359
19. miR-122 regulation of lipid metabolism revealed by in vivo antisense targeting. C Esau S Davis SF Murray XX Yu SK Pandey M Pear L Watts SL Booten M Graham R McKay A Subramaniam S Propp BA Lollo S Freier CF Bennett S Bhanot BP Monia, Cell Metab 2006 3 2 87 98 10.1016/j.cmet.2006.01.005 16459310
20. A microRNA expression signature of human solid tumors defines cancer gene targets. S Volinia GA Calin CG Liu S Ambs A Cimmino F Petrocca R Visone M Iorio C Roldo M Ferracin RL Prueitt N Yanaihara G Lanza A Scarpa A Vecchione M Negrini CC Harris CM Croce, Proc Natl Acad Sci USA 2006 103 7 2257 2261 10.1073/pnas.0510565103 16461460
21. Unique microRNA molecular profiles in lung cancer diagnosis and prognosis. N Yanaihara N Caplen E Bowman M Seike K Kumamoto M Yi RM Stephens A Okamoto J Yokota T Tanaka GA Calin CG Liu CM Croce CC Harris, Cancer Cell 2006 9 3 189 198 10.1016/j.ccr.2006.01.025 16530703
22. Conserved seed pairing, often flanked by adenosines, indicates that thousands of human genes are microRNA targets. BP Lewis CB Burge DP Bartel, Cell 2005 120 1 15 20 10.1016/j.cell.2004.12.035 15652477
23. Most mammalian mRNAs are conserved targets of microRNAs. RC Friedman KK Farh CB Burge DP Bartel, Genome Res 2009 19 1 92 105 10.1101/gr.082701.108 18955434
24. miRBase: the microRNA sequence database. S Griffiths-Jones, Methods Mol Biol 2006 342 129 138 16957372
25. A genetic screen implicates miRNA-372 and miRNA-373 as oncogenes in testicular germ cell tumors. PM Voorhoeve C le Sage M Schrier AJ Gillis H Stoop R Nagel YP Liu J van Duijse J Drost A Griekspoor E Zlotorynski N Yabuta G De Vita H Nojima LH Looijenga R Agami, Cell 2006 124 6 1169 1181 10.1016/j.cell.2006.02.037 16564011
26. The UCSC Genome Browser Database. D Karolchik R Baertsch M Diekhans TS Furey A Hinrichs YT Lu KM Roskin M Schwartz CW Sugnet DJ Thomas RJ Weber D Haussler WJ Kent University of California Santa Cruz, Nucleic Acids Res 2003 31 1 51 54 10.1093/nar/gkg129 12519945
27. The human genome browser at UCSC. WJ Kent CW Sugnet TS Furey KM Roskin TH Pringle AM Zahler D Haussler, Genome Res 2002 12 6 996 1006 12045153
28. The UCSC Table Browser data retrieval tool. D Karolchik AS Hinrichs TS Furey KM Roskin CW Sugnet D Haussler WJ Kent, Nucleic Acids Res 2004 32 Database 493 6 10.1093/nar/gkh103 14681465
29. The microRNA Registry. S Griffiths-Jones, Nucleic Acids Res 2004 32 Database 109 11 10.1093/nar/gkh023 14681370
30. Basic local alignment search tool. SF Altschul W Gish W Miller EW Myers DJ Lipman, J Mol Biol 1990 215 3 403 410 2231712
31. Real-time quantification of microRNAs by stem-loop RT-PCR. C Chen DA Ridzon AJ Broomer Z Zhou DH Lee JT Nguyen M Barbisin NL Xu VR Mahuvakar MR Andersen KQ Lao KJ Livak KJ Guegler, Nucleic Acids Res 2005 33 20 179 10.1093/nar/gni178 16314309
32. Clustering and conservation patterns of human microRNAs. Y Altuvia P Landgraf G Lithwick N Elefant S Pfeffer A Aravin MJ Brownstein T Tuschl H Margalit, Nucleic Acids Res 2005 33 8 2697 2706 10.1093/nar/gki567 15891114
33. Prediction and validation of microRNAs and their targets. I Bentwich, FEBS Lett 2005 579 26 5904 5910 10.1016/j.febslet.2005.09.040 16214134
34. Expression profiling of mammalian microRNAs uncovers a subset of brain-expressed microRNAs with possible roles in murine and human neuronal differentiation. LF Sempere S Freemantle I Pitha-Rowe E Moss E Dmitrovsky V Ambros, Genome Biol 2004 5 3 13 10.1186/gb-2004-5-3-r13 15003116
35. Microarray analysis of microRNA expression in the developing mammalian brain. EA Miska E Alvarez-Saavedra M Townsend A Yoshii N Sestan P Rakic M Constantine-Paton HR Horvitz, Genome Biol 2004 5 9 68 10.1186/gb-2004-5-9-r68 15345052
36. Identification of novel homologous microRNA genes in the rhesus macaque genome. J Yue Y Sheng KE Orwig, BMC Genomics 2008 9 8 10.1186/1471-2164-9-8 18186931
37. Cloning and sequencing of baboon and cynomolgus monkey intra-acrosomal protein SP-10: homology with human SP-10 and a mouse sperm antigen (MSA-63). AJ Freemerman RM Wright CJ Flickinger JC Herr, Mol Reprod Dev 1993 34 2 140 148 10.1002/mrd.1080340205 8442953
38. Identification and characteristics of microRNAs from Bombyx mori. PA He Z Nie J Chen J Chen Z Lv Q Sheng S Zhou X Gao L Kong X Wu Y Jin Y Zhang, BMC Genomics 2008 9 248 10.1186/1471-2164-9-248 18507836
39. MicroRNA expression in zebrafish embryonic development. E Wienholds WP Kloosterman E Miska E Alvarez-Saavedra E Berezikov E de Bruijn HR Horvitz S Kauppinen RH Plasterk, Science 2005 309 5732 310 311 10.1126/science.1114519 15919954
40. New human and mouse microRNA genes found by homology search. MJ Weber, FEBS J 2005 272 1 59 73 10.1111/j.1432-1033.2004.04389.x 15634332
41. Identification of hundreds of conserved and nonconserved human microRNAs. I Bentwich A Avniel Y Karov R Aharonov S Gilad O Barad A Barzilai P Einat U Einav E Meiri E Sharon Y Spector Z Bentwich, Nat Genet 2005 37 7 766 770 10.1038/ng1590 15965474
42. A second-generation genetic linkage map of the baboon (Papio hamadryas) genome. LA Cox MC Mahaney JL Vandeberg J Rogers, Genomics 2006 88 3 274 281 10.1016/j.ygeno.2006.03.020 16697552
43. A genetic linkage map of the baboon (Papio hamadryas) genome based on human microsatellite polymorphisms. J Rogers MC Mahaney SM Witte S Nair D Newman S Wedel LA Rodriguez KS Rice SH Slifer A Perelygin M Slifer P Palladino-Negro T Newman K Chambers G Joslyn P Parry PA Morin, Genomics 2000 67 3 237 247 10.1006/geno.2000.6245 10936045
44. Rapid evolution of an X-linked microRNA cluster in primates. R Zhang Y Peng W Wang B Su, Genome Res 2007 17 5 612 617 10.1101/gr.6146507 17416744