Comprehensive analysis of microRNA-mRNA co-expression in circadian rhythm

Experimental and Molecular Medicine

Volumn 41, Issue 9, 2009, Pages 638-647

  Na, Young Ji ^a,b   Jung, Hwan Sung ^c   Suk, Chan Lee ^d   Lee, Young Ju ^a   Yeun, Joo Choi ^a   Park, Woong Yang ^a   Hee, Sup Shin ^d   Ju, Han Kim ^a  

^a Seoul National University College of Medicine   (South Korea)

^b Seoul National University   (South Korea)

^c HARVARD MEDICAL SCHOOL   (United States)

^d Korea Institute of Science and Technology   (South Korea)

Author keywords

Circadian rhythm; Gene expression profiling; Gene expression regulation; Liver; Mice; microRNA

Indexed keywords

MESSENGER RNA; MICRORNA; PROTEIN BMAL1; TRANSCRIPTION FACTOR CLOCK;

ANIMAL EXPERIMENT; ANIMAL TISSUE; ARTICLE; CIRCADIAN RHYTHM; CONTROLLED STUDY; EXON; GENE CONTROL; GENE EXPRESSION; GENE LOCATION; GENE SEQUENCE; GENE TARGETING; GENOMICS; MALE; MOUSE; NONHUMAN; PROTEIN EXPRESSION; RNA FINGERPRINTING;

MUS;

EID: 70349469700     PISSN: 12263613     EISSN: 20926413     Source Type: Journal    
DOI: 10.3858/emm.2009.41.9.070     Document Type: Article

References (32)

1. Bartel DP. MicroRNAs: genomics, biogenesis, mechanism, and function. Cell 2004;116:281-297
2. Bolstad BM, Irizarry RA, Astrand M, Speed TP. A comparison of normalization methods for high density oligonucleotide array data based on variance and bias. Bioinformatics 2003;19:185-193 (Pubitemid 36181903)
3. Bunger MK, Wilsbacher LD, Moran SM, Clendenin C, Radcliffe LA, Hogenesch JB, Simon MC, Takahashi JS, Bradfield CA. Mop3 is an essential component of the master circadian pacemaker in mammals. Cell 2000;103:1009-1017 (Pubitemid 32037390)
4. Cheng HY, Papp JW, Varlamova O, Dziema H, Russell B, Curfman JP, Nakazawa T, Shimizu K, Okamura H, Impey S, Obrietan K. microRNA modulation of circadian-clock period and entrainment. Neuron 2007;54:813-829 (Pubitemid 46843524)
5. Gekakis N, Staknis D, Nguyen HB, Davis FC, Wilsbacher LD, King DP, Takahashi JS, Weitz CJ. Role of the CLOCK protein in the mammalian circadian mechanism. Science 1998;280:1564-1569 (Pubitemid 28277694)
6. Griffiths-Jones S. The microRNA Registry. Nucleic Acids Res 2004;32:D109-11
7. Griffiths-Jones S, Grocock RJ, van Dongen S, Bateman A, Enright AJ. miRBase: microRNA sequences, targets and gene nomenclature. Nucleic Acids Res 2006;34:D140-4
8. Hornstein E, Mansfield JH, Yekta S, Hu JK, Harfe BD, McManus MT, Baskerville S, Bartel DP, Tabin CJ. The microRNA miR-196 acts upstream of Hoxb8 and Shh in limb development. Nature 2005;438:671-674 (Pubitemid 41740577)
9. John B, Enright AJ, Aravin A, Tuschl T, Sander C, Marks DS. Human MicroRNA targets. PLoS Biol 2004;2:e363
10. Kiriakidou M, Nelson PT, Kouranov A, Fitziev P, Bouyioukos C, Mourelatos Z, Hatzigeorgiou A. A combined computational-experimental approach predicts human microRNA targets. Genes Dev 2004;18:1165-1178 (Pubitemid 38669037)
11. Krek A, Grun D, Poy MN, Wolf R, Rosenberg L, Epstein EJ, MacMenamin P, da Piedade I, Gunsalus KC, Stoffel M, Rajewsky N. Combinatorial microRNA target predictions. Nat Genet 2005;37:495-500
12. Kuhn K, Baker SC, Chudin E, Lieu MH, Oeser S, Bennett H, Rigault P, Barker D, McDaniel TK, Chee MS. A novel, high-performance random array platform for quantitative gene expression profiling. Genome Res 2004;14:2347-2356 (Pubitemid 39517342)
13. Lagos-Quintana M, Rauhut R, Lendeckel W, Tuschl T. Identification of novel genes coding for small expressed RNAs. Science 2001;294:853-858 (Pubitemid 33032103)
14. Lau NC, Lim LP, Weinstein EG, Bartel DP. An abundant class of tiny RNAs with probable regulatory roles in Caenorhabditis elegans. Science 2001;294:858-862
15. Lee RC, Feinbaum RL, Ambros V. The C. elegans heterochronic gene lin-4 encodes small RNAs with antisense complementarity to lin-14. Cell 1993;75:843-854 (Pubitemid 24014542)
16. Lee RC, Ambros V. An extensive class of small RNAs in Caenorhabditis elegans. Science 2001;294:862-864 (Pubitemid 33032105)
17. Lewis BP, Shih IH, Jones-Rhoades MW, Bartel DP, Burge CB. Prediction of mammalian microRNA targets. Cell 2003;115:787-798
18. Lewis BP, Burge CB, Bartel DP. Conserved seed pairing, often flanked by adenosines, indicates that thousands of human genes are microRNA targets. Cell 2005;120:15-20
19. Lin SL, Miller JD, Ying SY. Intronic MicroRNA (miRNA). J Biomed Biotechnol 2006;2006:26818
20. Lowrey PL, Takahashi JS. Mammalian circadian biology: elucidating genome-wide levels of temporal organization. Annu Rev Genomics Hum Genet 2004;5:407-441
21. Pasquinelli AE, Reinhart BJ, Slack F, Martindale MQ, Kuroda MI, Maller B, Hayward DC, Ball EE, Degnan B, Muller P, Spring J, Srinivasan A, Fishman M, Finnerty J, Corbo J, Levine M, Leahy P, Davidson E, Ruvkun G. Conservation of the sequence and temporal expression of let-7 heterochronic regulatory RNA. Nature 2000;408:86-89 (Pubitemid 30828264)
22. Pegoraro M, Tauber E. The role of microRNAs (miRNA) in circadian rhythmicity. J Genet 2008;87:505-511
23. Place RF, Li LC, Pookot D, Noonan EJ, Dahiya R. MicroRNA-373 induces expression of genes with complementary promoter sequences. Proc Natl Acad Sci U S A 2008;105:1608-1613 (Pubitemid 351346562)
24. Reddy AB, Karp NA, Maywood ES, Sage EA, Deery M, O'Neill JS, Wong GK, Chesham J, Odell M, Lilley KS, Kyriacou CP, Hastings MH. Circadian orchestration of the hepatic proteome. Curr Biol 2006;16:1107-1115
25. Reppert SM, Weaver DR. Molecular analysis of mammalian circadian rhythms. Annu Rev Physiol 2001;63:647-676 (Pubitemid 32304333)
26. Sethupathy P, Corda B, Hatzigeorgiou AG. TarBase: A comprehensive database of experimentally supported animal microRNA targets. RNA 2006;12:192-197 (Pubitemid 43121923)
27. Shearman LP, Jin X, Lee C, Reppert SM, Weaver DR. Targeted disruption of the mPer3 gene: subtle effects on circadian clock function. Mol Cell Biol 2000;20:6269-6275 (Pubitemid 30650213)
28. Siepka SM, Yoo SH, Park J, Song W, Kumar V, Hu Y, Lee C, Takahashi JS. Circadian mutant Overtime reveals F-box protein FBXL3 regulation of cryptochrome and period gene expression. Cell 2007;129:1011-1023 (Pubitemid 46802705)
29. Thomson JM, Parker J, Perou CM, Hammond SM. A custom microarray platform for analysis of microRNA gene expression. Nat Methods 2004;1:47-53
30. Weber MJ. New human and mouse microRNA genes found by homology search. FEBS J 2005;272:59-73
31. Wienholds E, Plasterk RH. MicroRNA function in animal development. FEBS Lett 2005;579:5911-5922
32. Yang M, Lee JE, Padgett RW, Edery I. Circadian regulation of a limited set of conserved microRNAs in Drosophila. BMC Genomics 2008;9:83 (Pubitemid 351356776)