XRNA-methylation-dependent RNA processing controls the speed of the circadian clock

Cell

Volumn 155, Issue 4, 2013, Pages 793-

  Fustin, Jean Michel ^a   Doi, Masao ^a   Yamaguchi, Yoshiaki ^a   Hida, Hayashi ^a   Nishimura, Shinichi ^a   Yoshida, Minoru ^b   Isagawa, Takayuki ^c   Morioka, Masaki Suimye ^c   Kakeya, Hideaki ^a   Manabe, Ichiro ^c   Okamura, Hitoshi ^a  

^a KYOTO UNIVERSITY   (Japan)

^b RIKEN   (Japan)

^c UNIVERSITY OF TOKYO   (Japan)

Author keywords

[No Author keywords available]

Indexed keywords

3 DEAZAADENOSINE; MESSENGER RNA; RNA; TRANSCRIPTOME;

ANIMAL CELL; ARTICLE; CELL TYPE; CIRCADIAN RHYTHM; CONTROLLED STUDY; EMBRYO; GENE SILENCING; HUMAN; HUMAN CELL; LIVER; LOCOMOTION; MOUSE; NONHUMAN; PRIORITY JOURNAL; RNA METHYLATION; RNA PROCESSING; RNA SEQUENCE; RNA TRANSLATION; SUPRACHIASMATIC NUCLEUS; TRANSCRIPTION REGULATION;

EUKARYOTA;

EID: 84887875528     PISSN: 00928674     EISSN: 10974172     Source Type: Journal    
DOI: 10.1016/j.cell.2013.10.026     Document Type: Article

References (42)

1. R.A. Akhtar, A.B. Reddy, E.S. Maywood, J.D. Clayton, V.M. King, A.G. Smith, T.W. Gant, M.H. Hastings, and C.P. Kyriacou Circadian cycling of the mouse liver transcriptome, as revealed by cDNA microarray, is driven by the suprachiasmatic nucleus Curr. Biol. 12 2002 540 550
2. G. Asher, D. Gatfield, M. Stratmann, H. Reinke, C. Dibner, F. Kreppel, R. Mostoslavsky, F.W. Alt, and U. Schibler SIRT1 regulates circadian clock gene expression through PER2 deacetylation Cell 134 2008 317 328
3. S. Audic, and J.M. Claverie The significance of digital gene expression profiles Genome Res. 7 1997 986 995
4. P.S. Backlund Jr., D. Carotti, and G.L. Cantoni Effects of the S-adenosylhomocysteine hydrolase inhibitors 3-deazaadenosine and 3-deazaaristeromycin on RNA methylation and synthesis Eur. J. Biochem. 160 1986 245 251
5. J.M. Bujnicki, M. Feder, M. Radlinska, and R.M. Blumenthal Structure prediction and phylogenetic analysis of a functionally diverse family of proteins homologous to the MT-A70 subunit of the human mRNA:m(6)A methyltransferase J. Mol. Evol. 55 2002 431 444
6. R. Carmel, and D.W. Jacobsen Homocysteine in health and disease 2001 Cambridge University Press Cambridge
7. S.R. Carmody, and S.R. Wente mRNA nuclear export at a glance J. Cell Sci. 122 2009 1933 1937
8. R. Chen, A. Schirmer, Y. Lee, H. Lee, V. Kumar, S.H. Yoo, J.S. Takahashi, and C. Lee Rhythmic PER abundance defines a critical nodal point for negative feedback within the circadian clock mechanism Mol. Cell 36 2009 417 430
9. P.K. Chiang Biological effects of inhibitors of S-adenosylhomocysteine hydrolase Pharmacol. Ther. 77 1998 115 134
10. M.J. Clancy, M.E. Shambaugh, C.S. Timpte, and J.A. Bokar Induction of sporulation in Saccharomyces cerevisiae leads to the formation of N6-methyladenosine in mRNA: a potential mechanism for the activity of the IME4 gene Nucleic Acids Res. 30 2002 4509 4518
11. M.D. Cole, and V.H. Cowling Specific regulation of mRNA cap methylation by the c-Myc and E2F1 transcription factors Oncogene 28 2009 1169 1175
12. V.H. Cowling Myc up-regulates formation of the mRNA methyl cap Biochem. Soc. Trans. 38 2010 1598 1601
13. C. Dibner, D. Sage, M. Unser, C. Bauer, T. d'Eysmond, F. Naef, and U. Schibler Circadian gene expression is resilient to large fluctuations in overall transcription rates EMBO J. 28 2009 123 134
14. M. Doi, A. Ishida, A. Miyake, M. Sato, R. Komatsu, F. Yamazaki, I. Kimura, S. Tsuchiya, H. Kori, and K. Seo Circadian regulation of intracellular G-protein signalling mediates intercellular synchrony and rhythmicity in the suprachiasmatic nucleus Nat. Commun. 2 2011 327
15. D. Dominissini, S. Moshitch-Moshkovitz, S. Schwartz, M. Salmon-Divon, L. Ungar, S. Osenberg, K. Cesarkas, J. Jacob-Hirsch, N. Amariglio, and M. Kupiec Topology of the human and mouse m6A RNA methylomes revealed by m6A-seq Nature 485 2012 201 206
16. K.L. Eckel-Mahan, V.R. Patel, R.P. Mohney, K.S. Vignola, P. Baldi, and P. Sassone-Corsi Coordination of the transcriptome and metabolome by the circadian clock Proc. Natl. Acad. Sci. USA 109 2012 5541 5546
17. E. Eden, D. Lipson, S. Yogev, and Z. Yakhini Discovering motifs in ranked lists of DNA sequences PLoS Comput. Biol. 3 2007 e39
18. E. Eden, R. Navon, I. Steinfeld, D. Lipson, and Z. Yakhini GOrilla: a tool for discovery and visualization of enriched GO terms in ranked gene lists BMC Bioinformatics 10 2009 48
19. M.E. Fernandez-Sanchez, T. Gonatopoulos-Pournatzis, G. Preston, M.A. Lawlor, and V.H. Cowling S-adenosyl homocysteine hydrolase is required for Myc-induced mRNA cap methylation, protein synthesis, and cell proliferation Mol. Cell. Biol. 29 2009 6182 6191
20. G. Jia, Y. Fu, X. Zhao, Q. Dai, G. Zheng, Y. Yang, C. Yi, T. Lindahl, T. Pan, Y.G. Yang, and C. He N6-methyladenosine in nuclear RNA is a major substrate of the obesity-associated FTO Nat. Chem. Biol. 7 2011 885 887
21. X. Jiao, J.H. Chang, T. Kilic, L. Tong, and M. Kiledjian A mammalian pre-mRNA 5′ end capping quality control mechanism and an unexpected link of capping to pre-mRNA processing Mol. Cell 50 2013 104 115
22. D. Kaida, H. Motoyoshi, E. Tashiro, T. Nojima, M. Hagiwara, K. Ishigami, H. Watanabe, T. Kitahara, T. Yoshida, and H. Nakajima Spliceostatin A targets SF3b and inhibits both splicing and nuclear retention of pre-mRNA Nat. Chem. Biol. 3 2007 576 583
23. S. Katada, and P. Sassone-Corsi The histone methyltransferase MLL1 permits the oscillation of circadian gene expression Nat. Struct. Mol. Biol. 17 2010 1414 1421
24. N. Koike, S.H. Yoo, H.C. Huang, V. Kumar, C. Lee, T.K. Kim, and J.S. Takahashi Transcriptional architecture and chromatin landscape of the core circadian clock in mammals Science 338 2012 349 354
25. K.D. Meyer, Y. Saletore, P. Zumbo, O. Elemento, C.E. Mason, and S.R. Jaffrey Comprehensive analysis of mRNA methylation reveals enrichment in 3′ UTRs and near stop codons Cell 149 2012 1635 1646
26. K. Miyazaki, M. Wakabayashi, S. Chikahisa, H. Sei, and N. Ishida PER2 controls circadian periods through nuclear localization in the suprachiasmatic nucleus Genes Cells 12 2007 1225 1234
27. Y. Nakahata, M. Kaluzova, B. Grimaldi, S. Sahar, J. Hirayama, D. Chen, L.P. Guarente, and P. Sassone-Corsi The NAD+-dependent deacetylase SIRT1 modulates CLOCK-mediated chromatin remodeling and circadian control Cell 134 2008 329 340
28. J.D. Plautz, M. Straume, R. Stanewsky, C.F. Jamison, C. Brandes, H.B. Dowse, J.C. Hall, and S.A. Kay Quantitative analysis of Drosophila period gene transcription in living animals J. Biol. Rhythms 12 1997 204 217
29. A.R. Quinlan, and I.M. Hall BEDTools: a flexible suite of utilities for comparing genomic features Bioinformatics 26 2010 841 842
30. J.A. Ripperger, and M. Merrow Perfect timing: epigenetic regulation of the circadian clock FEBS Lett. 585 2011 1406 1411
31. M.D. Robinson, and G.K. Smyth Moderated statistical tests for assessing differences in tag abundance Bioinformatics 23 2007 2881 2887
32. M. Rosbash Molecular control of circadian rhythms Curr. Opin. Genet. Dev. 5 1995 662 668
33. K.L. Schalinske, and R.D. Steele Variations in S-adenosylmethionine, S-adenosylhomocysteine and adenosine concentrations in rat liver Biofactors 3 1992 265 268
34. C. Trapnell, L. Pachter, and S.L. Salzberg TopHat: discovering splice junctions with RNA-Seq Bioinformatics 25 2009 1105 1111
35. U.K. Valekunja, R.S. Edgar, M. Oklejewicz, G.T. van der Horst, J.S. O'Neill, F. Tamanini, D.J. Turner, and A.B. Reddy Histone methyltransferase MLL3 contributes to genome-scale circadian transcription Proc. Natl. Acad. Sci. USA 110 2013 1554 1559
36. C. Vollmers, R.J. Schmitz, J. Nathanson, G. Yeo, J.R. Ecker, and S. Panda Circadian oscillations of protein-coding and regulatory RNAs in a highly dynamic mammalian liver epigenome Cell Metab. 16 2012 833 845
37. A.K. Wilkins, P.I. Barton, and B. Tidor The Per2 negative feedback loop sets the period in the mammalian circadian clock mechanism PLoS Comput. Biol. 3 2007 e242
38. K.C. Woo, T.D. Kim, K.H. Lee, D.Y. Kim, W. Kim, K.Y. Lee, and K.T. Kim Mouse period 2 mRNA circadian oscillation is modulated by PTB-mediated rhythmic mRNA degradation Nucleic Acids Res. 37 2009 26 37
39. S. Yamaguchi, S. Mitsui, S. Miyake, L. Yan, H. Onishi, K. Yagita, M. Suzuki, S. Shibata, M. Kobayashi, and H. Okamura The 5′ upstream region of mPer1 gene contains two promoters and is responsible for circadian oscillation Curr. Biol. 10 2000 873 876
40. S.H. Yoo, S. Yamazaki, P.L. Lowrey, K. Shimomura, C.H. Ko, E.D. Buhr, S.M. Siepka, H.K. Hong, W.J. Oh, and O.J. Yoo PERIOD2:LUCIFERASE real-time reporting of circadian dynamics reveals persistent circadian oscillations in mouse peripheral tissues Proc. Natl. Acad. Sci. USA 101 2004 5339 5346
41. E.E. Zhang, A.C. Liu, T. Hirota, L.J. Miraglia, G. Welch, P.Y. Pongsawakul, X. Liu, A. Atwood, J.W. Huss 3rd, and J. Janes A genome-wide RNAi screen for modifiers of the circadian clock in human cells Cell 139 2009 199 210
42. G. Zheng, J.A. Dahl, Y. Niu, P. Fedorcsak, C.M. Huang, C.J. Li, C.B. Vågbø, Y. Shi, W.L. Wang, and S.H. Song ALKBH5 is a mammalian RNA demethylase that impacts RNA metabolism and mouse fertility Mol. Cell 49 2013 18 29