Usf1, a suppressor of the circadian Clock mutant, reveals the nature of the DNA-binding of the CLOCK:BMAL1 complex in mice

eLife

Volumn 2013, Issue 2, 2013, Pages

  Shimomura, Kazuhiro ^a   Kumar, Vivek ^b   Koike, Nobuya ^c   Kim, Tae Kyung ^c   Chong, Jason ^d   Buhr, Ethan D ^d   Whiteley, Andrew R ^d   Low, Sharon S ^d,g   Omura, Chiaki ^d   Fenner, Deborah ^d   Owens, Joseph R ^a   Richards, Marc ^d   Yoo, Seung Hee ^b   Hong, Hee Kyung ^d   Vitaterna, Martha H ^a   Bass, Joseph ^a   Pletcher, Mathew T ^e,h   Wiltshire, Tim ^e,i   Hogenesch, John ^f   Lowrey, Phillip L ^d,j   Takahashi, Joseph S ^b   more..

^a NORTHWESTERN UNIVERSITY   (United States)

^b HOWARD HUGHES MEDICAL INSTITUTE   (United States)

^c UNIVERSITY OF TEXAS SOUTHWESTERN MEDICAL CENTER   (United States)

^d NORTHWESTERN UNIVERSITY   (United States)

^e GENOMICS INSTITUTE OF THE NOVARTIS RESEARCH FOUNDATION   (United States)

^f UNIVERSITY OF PENNSYLVANIA   (United States)

^g NATIONAL INSTITUTES OF HEALTH   (United States)

^h PFIZER INC   (United States)

ⁱ University of North Carolina   (United States)

^j RIDER UNIVERSITY   (United States)

more..

Author keywords

[No Author keywords available]

Indexed keywords

PER1 PROTEIN; PER2 PROTEIN; PROTEIN BMAL1; TRANSCRIPTION FACTOR CLOCK; ARNTL PROTEIN, MOUSE; CLOCK PROTEIN, MOUSE; DNA; MESSENGER RNA; TRANSCRIPTION FACTOR ARNTL; UPSTREAM STIMULATORY FACTOR; USF1 PROTEIN, MOUSE;

ANIMAL EXPERIMENT; ANIMAL TISSUE; ARTICLE; BINDING AFFINITY; BIOLUMINESCENCE; CIRCADIAN RHYTHM; CLOCK GENE; CONTROLLED STUDY; DNA BINDING; E BOX ELEMENT; FEMALE; GEL MOBILITY SHIFT ASSAY; GENE; GENE EXPRESSION; GENE MUTATION; HAPLOTYPE; HUMAN; HUMAN CELL; LOCOMOTION; MALE; MOUSE; NONHUMAN; PHENOTYPE; POLYMERASE CHAIN REACTION; PROTEIN EXPRESSION; SINGLE NUCLEOTIDE POLYMORPHISM; SUPPRESSOR GENE; USF1 GENE; ANIMAL; BAGG ALBINO MOUSE; BINDING COMPETITION; BINDING SITE; C57BL MOUSE; COMPARATIVE STUDY; GENE EXPRESSION REGULATION; GENETIC TRANSCRIPTION; GENETICS; GENOTYPE; METABOLISM; MUTATION; PROMOTER REGION; PROTEIN DOMAIN; SIGNAL TRANSDUCTION; SPECIES DIFFERENCE; TIME FACTOR; TRANSCRIPTION INITIATION; TRANSGENIC MOUSE;

ANIMALS; ARNTL TRANSCRIPTION FACTORS; BINDING SITES; BINDING, COMPETITIVE; CIRCADIAN CLOCKS; CIRCADIAN RHYTHM; CLOCK PROTEINS; DNA; E-BOX ELEMENTS; GENE EXPRESSION REGULATION; GENOTYPE; MICE; MICE, INBRED BALB C; MICE, INBRED C57BL; MICE, TRANSGENIC; MUTATION; PHENOTYPE; POLYMORPHISM, SINGLE NUCLEOTIDE; PROMOTER REGIONS, GENETIC; PROTEIN INTERACTION DOMAINS AND MOTIFS; RNA, MESSENGER; SIGNAL TRANSDUCTION; SPECIES SPECIFICITY; TIME FACTORS; TRANSCRIPTION, GENETIC; TRANSCRIPTIONAL ACTIVATION; UPSTREAM STIMULATORY FACTORS;

EID: 84879068462     PISSN: None     EISSN: 2050084X     Source Type: Journal    
DOI: 10.7554/eLife.00426     Document Type: Article

References (43)

1. Bass J, Takahashi JS. 2010. Circadian integration of metabolism and energetics. Science 330:1349-54. doi: 10.1126/science.1195027.
2. Bunger MK, Wilsbacher LD, Moran SM, Clendenin C, Radcliffe LA, Hogenesch JB, et al. 2000. Mop3 is an essential component of the master circadian pacemaker in mammals. Cell 103:1009-17. doi: 10.1016/S0092-8674(00)00205-1.
3. Cho H, Zhao X, Hatori M, Yu RT, Barish GD, Lam MT, et al. 2012. Regulation of circadian behaviour and metabolism by REV-ERB-α and REV-ERB-β. Nature 485:123-7. doi: 10.1038/nature11048.
4. Churchill GA, Airey DC, Allayee H, Angel JM, Attie AD, Beatty J, et al. 2004. The collaborative cross, a community resource for the genetic analysis of complex traits. Nat Genet 36:1133-7. doi: 10.1038/ng1104-1133.
5. Corre S, Galibert MD. 2005. Upstream stimulating factors: highly versatile stress-responsive transcription factors. Pigment Cell Res 18:337-48. doi: 10.1111/j.1600-0749.2005.00262.x.
6. Cowles CR, Hirschhorn JN, Altshuler D, Lander ES. 2002. Detection of regulatory variation in mouse genes. Nat Genet 32:432-7. doi: 10.1038/ng992.
7. Darvasi A, Soller M. 1995. Advanced intercross lines, an experimental population for fine genetic mapping. Genetics 141:1199-207.
8. Ferré-D'Amaré AR, Pognonec P, Roeder RG, Burley SK. 1994. Structure and function of the b/HLH/Z domain of USF. EMBO J 13:180-9.
9. Frazer KA, Eskin E, Kang HM, Bogue MA, Hinds DA, Beilharz EJ, et al. 2007. A sequence-based variation map of 8.27 million SNPs in inbred mouse strains. Nature 448:1050-3. doi: 10.1038/nature06067.
10. Gekakis N, Staknis D, Nguyen HB, Davis FC, Wilsbacher LD, King DP, et al. 1998. Role of the CLOCK protein in the mammalian circadian mechanism. Science 280:1564-9. doi: 10.1126/science.280.5369.1564.
11. Heinz S, Benner C, Spann N, Bertolino E, Lin YC, Laslo P, et al. 2010. Simple combinations of lineage-determining transcription factors prime cis-regulatory elements required for macrophage and B cell identities. Mol Cell 38:576-89. doi: 10.1016/j.molcel.2010.05.004.
12. Hogenesch JB, Gu YZ, Jain S, Bradfield CA. 1998. The basic-helix-loop-helix-PAS orphan MOP3 forms transcriptionally active complexes with circadian and hypoxia factors. Proc Natl Acad Sci USA 95:5474-9.
13. Hong HK, Chong JL, Song W, Song EJ, Jyawook AA, Schook AC, et al. 2007. Inducible and reversible Clock gene expression in brain using the tTA system for the study of circadian behavior. PLoS Genet 3:e33. doi: 10.1371/journal.pgen.0030033.
14. Huang N, Chelliah Y, Shan Y, Taylor CA, Yoo SH, Partch C, et al. 2012. Crystal structure of the heterodimeric CLOCK: BMAL1 transcriptional activator complex. Science 337:189-94. doi: 10.1126/science.1222804.
15. Kim TK, Hemberg M, Gray JM, Costa AM, Bear DM, Wu J, et al. 2010. Widespread transcription at neuronal activity-regulated enhancers. Nature 465:182-7. doi: 10.1038/nature09033.
16. King DP, Zhao Y, Sangoram AM, Wilsbacher LD, Tanaka M, Antoch MP, et al. 1997. Positional cloning of the mouse circadian Clock gene. Cell 89:641-53. doi: 10.1016/S0092-8674(00)80245-7.
17. Koike N, Yoo SH, Huang HC, Kumar V, Lee C, Kim TK, et al. 2012. Transcriptional architecture and chromatin landscape of the core circadian clock in mammals. Science 338:349-54. doi: 10.1126/science.1226339.
18. Kume K, Zylka MJ, Sriram S, Shearman LP, Weaver DR, Jin X, et al. 1999. mCRY1 and mCRY2 are essential components of the negative limb of the circadian clock feedback loop. Cell 98:193-205. doi: 10.1016/S0092-8674(00)81014-4.
19. Lee C, Etchegaray JP, Cagampang FR, Loudon AS, Reppert SM. 2001. Posttranslational mechanisms regulate the mammalian circadian clock. Cell 107:855-67. doi: 10.1016/S0092-8674(01)00610-9.
20. Lowrey PL, Takahashi JS. 2011. Genetics of circadian rhythms in mammalian model organisms. Adv Genet 74:175-230. doi: 10.1016/B978-0-12-387690-4.00006-4.
21. Nadeau JH, Frankel WN. 2000. The roads from phenotypic variation to gene discovery: mutagenesis versus QTLs. Nat Genet 25:381-4. doi: 10.1038/78051.
22. Nadeau JH, Topol EJ. 2006. The genetics of health. Nat Genet 38:1095-8. doi: 10.1038/ng1006-1095.
23. Preitner N, Damiola F, Lopez-Molina L, Zakany J, Duboule D, Albrecht U, et al. 2002. The orphan nuclear receptor REV-ERBalpha controls circadian transcription within the positive limb of the mammalian circadian oscillator. Cell 110:251-60. doi: 10.1016/S0092-8674(02)00825-5.
24. Reppert SM, Weaver DR. 2002. Coordination of circadian timing in mammals. Nature 418:935-41. doi: 10.1038/nature00965.
25. Rey G, Cesbron F, Rougemont J, Reinke H, Brunner M, Naef F. 2011. Genome-wide and phase-specific DNA-binding rhythms of BMAL1 control circadian output functions in mouse liver. PLoS Biol 9:e1000595. doi: 10.1371/journal.pbio.1000595.
26. Ripperger JA, Schibler U. 2006. Rhythmic CLOCK-BMAL1 binding to multiple E-box motifs drives circadian Dbp transcription and chromatin transitions. Nat Genet 38:369-74. doi: 10.1038/ng1738.
27. Salmon-Divon M, Dvinge H, Tammoja K, Bertone P. 2010. PeakAnalyzer: genome-wide annotation of chromatin binding and modification loci. BMC Bioinformatics 11:415. doi: 10.1186/1471-2105-11-415.
28. Sato TK, Panda S, Miraglia LJ, Reyes TM, Rudic RD, McNamara P, et al. 2004. A functional genomics strategy reveals Rora as a component of the mammalian circadian clock. Neuron 43:527-37. doi: 10.1016/j.neuron.2004.07.018.
29. Shimomura K, Low-Zeddies SS, King DP, Steeves TD, Whiteley A, Kushla J, et al. 2001. Genome-wide epistatic interaction analysis reveals complex genetic determinants of circadian behavior in mice. Genome Res 11:959-80. doi: 10.1101/gr.171601.
30. Takahashi JS. 2004. Finding new clock components: past and future. J Biol Rhythms 19:339-47. doi: 10.1177/0748730404269151.
31. Tomida S, Mamiya T, Sakamaki H, Miura M, Aosaki T, Masuda M, et al. 2009. Usp46 is a quantitative trait gene regulating mouse immobile behavior in the tail suspension and forced swimming tests. Nat Genet 41:688-95. doi: 10.1038/ng.344.
32. Ueda HR, Hayashi S, Chen W, Sano M, Machida M, Shigeyoshi Y, et al. 2005. System-level identification of transcriptional circuits underlying mammalian circadian clocks. Nat Genet 37:187-92. doi: 10.1038/ng1504.
33. Uno K, Ueda HR. 2007. Microarrays: quality control and hybridization protocol. Methods Mol Biol 362:225-43.
34. Valdar W, Solberg LC, Gauguier D, Burnett S, Klenerman P, Cookson WO, et al. 2006. Genome-wide genetic association of complex traits in heterogeneous stock mice. Nat Genet 38:879-87. doi: 10.1038/ng1840.
35. Vitaterna MH, King DP, Chang AM, Kornhauser JM, Lowrey PL, McDonald JD, et al. 1994. Mutagenesis and mapping of a mouse gene, Clock, essential for circadian behavior. Science 264:719-25. doi: 10.1126/science.8171325.
36. Wade CM, Kulbokas EJ III, Kirby AW, Zody MC, Mullikin JC, Lander ES, et al. 2002. The mosaic structure of variation in the laboratory mouse genome. Nature 420:574-8. doi: 10.1038/nature01252.
37. Watanabe A, Toyota T, Owada Y, Hayashi T, Iwayama Y, Matsumata M, et al. 2007. Fabp7 maps to a quantitative trait locus for a schizophrenia endophenotype. PLoS Biol 5:e297. doi: 10.1371/journal.pbio.0050297.
38. Yalcin B, Willis-Owen SA, Fullerton J, Meesaq A, Deacon RM, Rawlins JN, et al. 2004. Genetic dissection of a behavioral quantitative trait locus shows that Rgs2 modulates anxiety in mice. Nat Genet 36:1197-202. doi: 10.1038/ng1450.
39. Yamazaki S, Takahashi JS. 2005. Real-time luminescence reporting of circadian gene expression in mammals. Meth Enzymol 393:288-301. doi: 10.1016/S0076-6879(05)93012-7.
40. Yang H, Wang JR, Didion JP, Buus RJ, Welsh CE, Bonhomme F, et al. 2011. Subspecific origin and haplotype diversity in the laboratory mouse. Nat Genet 43:648-55. doi: 10.1038/ng.847.
41. Yoo SH, Yamazaki S, Lowrey PL, Shimomura K, Ko CH, Buhr ED, et al. 2004. PERIOD2::LUCIFERASE real-time reporting of circadian dynamics reveals persistent circadian oscillations in mouse peripheral tissues. Proc Natl Acad Sci USA 101:5339-46. doi: 10.1073/pnas.0308709101.
42. Yoshitane H, Takao T, Satomi Y, Du NH, Okano T, Fukada Y. 2009. Roles of CLOCK phosphorylation in suppression of E-box-dependent transcription. Mol Cell Biol 29:3675-86. doi: 10.1128/MCB.01864-08.
43. Zhang Y, Liu T, Meyer CA, Eeckhoute J, Johnson DS, Bernstein BE, et al. 2008. Model-based analysis of ChIP-Seq (MACS). Genome Biol 9:R137. doi: 10.1186/gb-2008-9-9-r137.