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Genome-Wide and Phase-Specific DNA-Binding Rhythms of BMAL1 Control Circadian Output Functions in Mouse Liver
Open accessAbstract
The mammalian circadian clock uses interlocked negative feedback loops in which the heterodimeric basic helix-loop-helix transcription factor BMAL1/CLOCK is a master regulator. While there is prominent control of liver functions by the circadian clock, the detailed links between circadian regulators and downstream targets are poorly known. Using chromatin immunoprecipitation combined with deep sequencing we obtained a time-resolved and genome-wide map of BMAL1 binding in mouse liver, which allowed us to identify over 2,000 binding sites, with peak binding narrowly centered around Zeitgeber time 6. Annotation of BMAL1 targets confirms carbohydrate and lipid metabolism as the major output of the circadian clock in mouse liver. Moreover, transcription regulators are largely overrepresented, several of which also exhibit circadian activity. Genes of the core circadian oscillator stand out as strongly bound, often at promoter and distal sites. Genomic sequence analysis of the sites identified E-boxes and tandem E1-E2 consensus elements. Electromobility shift assays showed that E1-E2 sites are bound by a dimer of BMAL1/CLOCK heterodimers with a spacing-dependent cooperative interaction, a finding that was further validated in transactivation assays. BMAL1 target genes showed cyclic mRNA expression profiles with a phase distribution centered at Zeitgeber time 10. Importantly, sites with E1-E2 elements showed tighter phases both in binding and mRNA accumulation. Finally, analyzing the temporal profiles of BMAL1 binding, precursor mRNA and mature mRNA levels showed how transcriptional and post-transcriptional regulation contribute differentially to circadian expression phase. Together, our analysis of a dynamic protein-DNA interactome uncovered how genes of the core circadian oscillator crosstalk and drive phase-specific circadian output programs in a complex tissue.
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Citations
Cites
Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources
Huang, D. W., Sherman, B. T., & Lempicki, R. A. (2009) · Nature Protocols · doi:10.1038/nprot.2008.211 · Cited by 35,890
Ultrafast and memory-efficient alignment of short DNA sequences to the human genome.
Langmead, B., Trapnell, C., Pop, M., & Salzberg, S. L. (2009) · Genome Biology · doi:10.1186/gb-2009-10-3-r25 · Cited by 21,849
Model-based Analysis of ChIP-Seq (MACS)
Zhang, Y., Liu, T., Meyer, C. A., Eeckhoute, J., Johnson, D. S., Bernstein, B. E., Nusbaum, C., Myers, R. M., Brown, M., Li, W., et al. (2008) · Genome Biology · doi:10.1186/gb-2008-9-9-r137 · Cited by 18,386
Mapping and quantifying mammalian transcriptomes by RNA-Seq
Mortazavi, A., Williams, B. A., McCue, K., Schaeffer, L., & Wold, B. (2008) · Nature Methods · doi:10.1038/nmeth.1226 · Cited by 13,696
DAVID: Database for Annotation, Visualization, and Integrated Discovery
Dennis, G., Sherman, B. T., Hosack, D. A., Yang, J., Gao, W., Lane, H. C., & Lempicki, R. A. (2003) · Genome Biology · doi:10.1186/gb-2003-4-5-p3 · Cited by 9,327
Coordination of circadian timing in mammals
Reppert, S. M., & Weaver, D. R. (2002) · Nature · doi:10.1038/nature00965 · Cited by 4,379
Evolutionarily conserved elements in vertebrate, insect, worm, and yeast genomes
Siepel, A., Bejerano, G., Pedersen, J. S., Hinrichs, A. S., Hou, M., Rosenbloom, K., Clawson, H., Spieth, J., Hillier, L. W., Richards, S., et al. (2005) · Genome Research · doi:10.1101/gr.3715005 · Cited by 3,971 · cited 2×
“DNA sequences and placental mammals PhastCons conservation scores [85] in windows of 650 bp around the center of each binding site were retrieved from Ensembl and the UCSC Genome Browser database, respectively.”
MEME: discovering and analyzing DNA and protein sequence motifs
Bailey, T. L., Williams, N., Misleh, C., & Li, W. W. (2006) · Nucleic Acids Research · doi:10.1093/nar/gkl198 · Cited by 2,670
Obesity and Metabolic Syndrome in Circadian Clock Mutant Mice
Turek, F. W., Joshu, C., Kohsaka, A., Lin, E., Ivanova, G., McDearmon, E., Laposky, A., Losee-Olson, S., Easton, A., Jensen, D. R., et al. (2005) · Science · doi:10.1126/science.1108750 · Cited by 2,485
Coordinated Transcription of Key Pathways in the Mouse by the Circadian Clock
Panda, S., Antoch, M. P., Miller, B. H., Su, A. I., Schook, A. B., Straume, M., Schultz, P. G., Kay, S. A., Takahashi, J. S., & Hogenesch, J. B. (2002) · Cell · doi:10.1016/s0092-8674(02)00722-5 · Cited by 2,290
Preitner, N., Damiola, F., Luis-Lopez-Molina, Zakany, J., Duboule, D., Albrecht, U., & Schibler, U. (2002) · Cell · doi:10.1016/s0092-8674(02)00825-5 · Cited by 2,198
Role of the CLOCK Protein in the Mammalian Circadian Mechanism
Gekakis, N., Staknis, D., Nguyen, H. B., Davis, F. C., Wilsbacher, L. D., King, D. P., Takahashi, J. S., & Weitz, C. J. (1998) · Science · doi:10.1126/science.280.5369.1564 · Cited by 2,013
Structure and function of the feed-forward loop network motif
Mangan, S., & Alon, U. (2003) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.2133841100 · Cited by 1,827
An oestrogen-receptor-α-bound human chromatin interactome
Fullwood, M. J., Liu, M. H., Pan, Y. F., Liu, J., Xu, H., Mohamed, Y. B., Orlov, Y. L., Velkov, S., Ho, A., Mei, P. H., et al. (2009) · Nature · doi:10.1038/nature08497 · Cited by 1,721
Molecular components of the mammalian circadian clock
Ko, C. H., & Takahashi, J. S. (2006) · Human Molecular Genetics · doi:10.1093/hmg/ddl207 · Cited by 1,656
Mop3 is an essential component of the master circadian pacemaker in mammals.
Bunger, M. K., Wilsbacher, L. D., Moran, S. M., Clendenin, C., Radcliffe, L. A., Hogenesch, J. B., Simon, M. C., Takahashi, J. S., & Bradfield, C. A. (2000) · Cell · doi:10.1016/s0092-8674(00)00205-1 · Cited by 1,621
mCRY1 and mCRY2 are essential components of the negative limb of the circadian clock feedback loop
Kume, K., Zylka, M. J., Sriram, S., Shearman, L. P., Weaver, D. R., Jin, X., Maywood, E. S., Hastings, M. H., & Reppert, S. M. (1999) · Cell · doi:10.1016/s0092-8674(00)81014-4 · Cited by 1,617
Disruption of the clock components CLOCK and BMAL1 leads to hypoinsulinaemia and diabetes
Marcheva, B., Ramsey, K. M., Buhr, E. D., Kobayashi, Y., Su, H., Ko, C. H., Ivanova, G., Omura, C., Mo, S., Vitaterna, M. H., et al. (2010) · Nature · doi:10.1038/nature09253 · Cited by 1,525
Extensive and divergent circadian gene expression in liver and heart
Storch, K.-F., Lipan, O., Leykin, I., Viswanathan, N., Davis, F. C., Wong, W. H., & Weitz, C. J. (2002) · Nature · doi:10.1038/nature744 · Cited by 1,510
Interacting molecular loops in the mammalian circadian clock
Shearman, L. P., Sriram, S., Weaver, D. R., Maywood, E. S., Chaves, I., Zheng, B., Kume, K., Lee, C. C., van der, G. T. J., Horst, et al. (2000) · Science · doi:10.1126/science.288.5468.1013 · Cited by 1,367
Circadian Control of the NAD + Salvage Pathway by CLOCK-SIRT1
Nakahata, Y., Sahar, S., Astarita, G., Kaluzova, M., & Sassone-Corsi, P. (2009) · Science · doi:10.1126/science.1170803 · Cited by 1,198
Posttranslational Mechanisms Regulate the Mammalian Circadian Clock
Lee, C., Etchegaray, J.-P., Cagampang, F. R. A., Loudon, A. S. I., & Reppert, S. M. (2001) · Cell · doi:10.1016/s0092-8674(01)00610-9 · Cited by 1,160
Control Mechanism of the Circadian Clock for Timing of Cell Division in Vivo
Matsuo, T., Yamaguchi, S., Mitsui, S., Emi, A., Shimoda, F., & Okamura, H. (2003) · Science · doi:10.1126/science.1086271 · Cited by 1,131
Bucher, P. (1990) · Journal of Molecular Biology · doi:10.1016/0022-2836(90)90223-9 · Cited by 1,126
Circadian Clock Feedback Cycle Through NAMPT-Mediated NAD + Biosynthesis
Ramsey, K. M., Yoshino, J., Brace, C. S., Abrassart, D., Kobayashi, Y., Marcheva, B., Hong, H.-K., Chong, J. L., Buhr, E. D., Lee, C., et al. (2009) · Science · doi:10.1126/science.1171641 · Cited by 1,126
Rudic, R. D., McNamara, P., Curtis, A.-M., Boston, R. C., Panda, S., Hogenesch, J. B., & FitzGerald, G. A. (2004) · PLoS Biology · doi:10.1371/journal.pbio.0020377 · Cited by 1,059
Physiological significance of a peripheral tissue circadian clock
Lamia, K. A., Storch, K.-F., & Weitz, C. J. (2008) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0806717105 · Cited by 1,048
Circadian Gene Expression in Individual Fibroblasts
Nagoshi, E., Saini, C., Bauer, C., Laroche, T., Naef, F., & Schibler, U. (2004) · Cell · doi:10.1016/j.cell.2004.11.015 · Cited by 982
Self-citationNuclear Receptor Expression Links the Circadian Clock to Metabolism
Yang, X., Downes, M., Yu, R. T., Bookout, A. L., He, W., Straume, M., Mangelsdorf, D. J., & Evans, R. M. (2006) · Cell · doi:10.1016/j.cell.2006.06.050 · Cited by 934
Green, C. B., Takahashi, J. S., & Bass, J. (2008) · Cell · doi:10.1016/j.cell.2008.08.022 · Cited by 902 · cited 1×
“and tissue-specific gene expression or metabolic programs [1–4].”
Hogenesch, J. B., Gu, Y.-Z., Jain, S., & Bradfield, C. A. (1998) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.95.10.5474 · Cited by 787
Five-Vertebrate ChIP-seq Reveals the Evolutionary Dynamics of Transcription Factor Binding
Schmidt, D., Wilson, M. D., Ballester, B., Schwalie, P. C., Brown, G. D., Marshall, A., Kutter, C., Watt, S., Martinez-Jimenez, C. P., Mackay, S., et al. (2010) · Science · doi:10.1126/science.1186176 · Cited by 700
Dec1 and Dec2 are regulators of the mammalian molecular clock
Honma, S., Kawamoto, T., Takagi, Y., Fujimoto, K., Sato, F., Noshiro, M., Kato, Y., & Honma, K.-I. (2002) · Nature · doi:10.1038/nature01123 · Cited by 692
Rhythmic histone acetylation underlies transcription in the mammalian circadian clock
Etchegaray, J.-P., Lee, C., Wade, P. A., & Reppert, S. M. (2003) · Nature · doi:10.1038/nature01314 · Cited by 679
Tests of significance in harmonic analysis
Fisher, R. A. (1929) · Proceedings of the Royal Society of London. Series A, Containing Papers of a Mathematical and Physical Character · doi:10.1098/rspa.1929.0151 · Cited by 672
Harmonics of Circadian Gene Transcription in Mammals
Hughes, M. E., DiTacchio, L., Hayes, K. R., Vollmers, C., Pulivarthy, S., Baggs, J. E., Panda, S., & Hogenesch, J. B. (2009) · PLoS Genetics · doi:10.1371/journal.pgen.1000442 · Cited by 671
Kornmann, B., Schaad, O., Bujard, H., Takahashi, J. S., & Schibler, U. (2007) · PLoS Biology · doi:10.1371/journal.pbio.0050034 · Cited by 658
Light-Independent Role of CRY1 and CRY2 in the Mammalian Circadian Clock
Griffin, E. A., Staknis, D., & Weitz, C. J. (1999) · Science · doi:10.1126/science.286.5440.768 · Cited by 646
Circadian Rhythms: Mechanisms and Therapeutic Implications
Levi, F., & Schibler, U. (2007) · Annual Review of Pharmacology and Toxicology · doi:10.1146/annurev.pharmtox.47.120505.105208 · Cited by 645
Ripperger, J. A., & Schibler, U. (2006) · Nature Genetics · doi:10.1038/ng1738 · Cited by 599
Sharova, L. V., Sharov, A. A., Nedorezov, T., Piao, Y., Shaik, N., & Ko, M. S. H. (2009) · DNA Research · doi:10.1093/dnares/dsn030 · Cited by 591 · cited 2×
“(B) mRNA half-lives from mouse embryonic stem cells [61] and mouse fibroblasts [62] for the genes in Figure 7A–7C and (A).”
NPAS2: an analog of clock operative in the mammalian forebrain
Reick, M., Garcia, J. A., Dudley, C., & McKnight, S. L. (2001) · Science · doi:10.1126/science.1060699 · Cited by 572
Circadian and CLOCK-controlled regulation of the mouse transcriptome and cell proliferation
Miller, B. H., McDearmon, E. L., Panda, S., Hayes, K. R., Zhang, J., Andrews, J. L., Antoch, M. P., Walker, J. R., Esser, K. A., Hogenesch, J. B., et al. (2007) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0611724104 · Cited by 518
Gachon, F., Olela, F. F., Schaad, O., Descombes, P., & Schibler, U. (2006) · Cell Metabolism · doi:10.1016/j.cmet.2006.04.015 · Cited by 512
REV-ERBα Participates in Circadian SREBP Signaling and Bile Acid Homeostasis
Le Martelot, G., Claudel, T., Gatfield, D., Schaad, O., Kornmann, B., Sasso, G. L., Moschetta, A., & Schibler, U. (2009) · PLoS Biology · doi:10.1371/journal.pbio.1000181 · Cited by 447
A clock shock: mouse CLOCK is not required for circadian oscillator function
DeBruyne, J. P., Noton, E., Lambert, C. M., Maywood, E. S., Weaver, D. R., & Reppert, S. M. (2006) · Neuron · doi:10.1016/j.neuron.2006.03.041 · Cited by 430
Ripperger, J. A., Shearman, L. P., Reppert, S. M., & Schibler, U. (2000) · Genes & Development · doi:10.1101/gad.14.6.679 · Cited by 428
The FANTOM Consortium, & Riken Omics Science Center (2009) · Nature Genetics · doi:10.1038/ng.375 · Cited by 427
Liu, A. C., Tran, H. G., Zhang, E. E., Priest, A. A., Welsh, D. K., & Kay, S. A. (2008) · PLoS Genetics · doi:10.1371/journal.pgen.1000023 · Cited by 394
Schmutz, I., Ripperger, J. A., Baeriswyl-Aebischer, S., & Albrecht, U. (2010) · Genes & Development · doi:10.1101/gad.564110 · Cited by 361 · cited 2×
“, Pck1 and Glut2 [7], as well as G6Pase [44], are identified as putative targets.”
Canaple, L., Rambaud, J., Dkhissi-Benyahya, O., Rayet, B., Tan, N. S., Michalik, L., Delaunay, F., Wahli, W., & Laudet, V. (2006) · Molecular Endocrinology · doi:10.1210/me.2006-0052 · Cited by 352
A Daily Rhythm in Glucose Tolerance
la Fleur, S. E., Kalsbeek, A., Wortel, J., Fekkes, M. L., & Buijs, R. M. (2001) · Diabetes · doi:10.2337/diabetes.50.6.1237 · Cited by 337
Lemberger, T., Saladin, R., Vázquez, M., Assimacopoulos, F., Staels, B., Desvergne, B., Wahli, W., & Auwerx, J. (1996) · Journal of Biological Chemistry · doi:10.1074/jbc.271.3.1764 · Cited by 329
Duffield, G. E., Best, J. D., Meurers, B. H., Bittner, A., Loros, J. J., & Dunlap, J. C. (2002) · Current Biology · doi:10.1016/s0960-9822(02)00765-0 · Cited by 328
Gréchez-Cassiau, A., Rayet, B., Guillaumond, F., Teboul, M., & Delaunay, F. (2008) · Journal of Biological Chemistry · doi:10.1074/jbc.m705576200 · Cited by 312
Analysis of Gene Regulatory Networks in the Mammalian Circadian Rhythm
Yan, J., Wang, H., Liu, Y., & Shao, C. (2008) · PLoS Computational Biology · doi:10.1371/journal.pcbi.1000193 · Cited by 297
OISHI, K., SHIRAI, H., & ISHIDA, N. (2005) · Biochemical Journal · doi:10.1042/bj20041150 · Cited by 295
Regulation of Clock-Controlled Genes in Mammals
Bozek, K., Relógio, A., Kielbasa, S. M., Heine, M., Dame, C., Kramer, A., & Herzel, H. (2009) · PLoS ONE · doi:10.1371/journal.pone.0004882 · Cited by 284
Molecular clock is involved in predictive circadian adjustment of renal function
Zuber, A. M., Centeno, G., Pradervand, S., Nikolaeva, S., Maquelin, L., Cardinaux, L., Bonny, O., & Firsov, D. (2009) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0904890106 · Cited by 274
Statistical mechanical modeling of genome-wide transcription factor occupancy data by MatrixREDUCE
Foat, B. C., Morozov, A. V., & Bussemaker, H. J. (2006) · Bioinformatics · doi:10.1093/bioinformatics/btl223 · Cited by 274
Conserved principles of mammalian transcriptional regulation revealed by RNA half-life
Friedel, C. C., Dölken, L., Ruzsics, Z., Koszinowski, U. H., & Zimmer, R. (2009) · Nucleic Acids Research · doi:10.1093/nar/gkp542 · Cited by 230
Reinke, H., Saini, C., Fleury-Olela, F., Dibner, C., Benjamin, I. J., & Schibler, U. (2008) · Genes & Development · doi:10.1101/gad.453808 · Cited by 227
Self-citationChen, R., Schirmer, A., Lee, Y., Lee, H., Kumar, V., Yoo, S.-H., Takahashi, J. S., & Lee, C. (2009) · Molecular Cell · doi:10.1016/j.molcel.2009.10.012 · Cited by 225
Edwards, P. A., Muroya, H., & Gould, R. G. (1972) · Journal of Lipid Research · doi:10.1016/s0022-2275(20)39403-7 · Cited by 217
Agostinelli, C., & Ulric, L. (2004) · ARCA (Università Ca' Foscari Venezia) · Cited by 215
Emergence of Noise-Induced Oscillations in the Central Circadian Pacemaker
Ko, C. H., Yamada, Y. R., Welsh, D. K., Buhr, E. D., Liu, A. C., Zhang, E. E., Ralph, M. R., Kay, S. A., Forger, D. B., & Takahashi, J. S. (2010) · PLoS Biology · doi:10.1371/journal.pbio.1000513 · Cited by 212
Smith, K. M., Sancar, G., Dekhang, R., Sullivan, C. M., Li, S., Tag, A. G., Sancar, C., Bredeweg, E. L., Priest, H. D., McCormick, R. F., et al. (2010) · Eukaryotic Cell · doi:10.1128/ec.00154-10 · Cited by 210
Self-citationNakahata, Y., Yoshida, M., Takano, A., Soma, H., Yamamoto, T., Yasuda, A., Nakatsu, T., & Takumi, T. (2008) · BMC Molecular Biology · doi:10.1186/1471-2199-9-1 · Cited by 200
DEC1 Modulates the Circadian Phase of Clock Gene Expression
Nakashima, A., Kawamoto, T., Honda, K. K., Ueshima, T., Noshiro, M., Iwata, T., Fujimoto, K., Kubo, H., Honma, S., Yorioka, N., et al. (2008) · Molecular and Cellular Biology · doi:10.1128/mcb.02168-07 · Cited by 162
Doi, R., Oishi, K., & Ishida, N. (2010) · Journal of Biological Chemistry · doi:10.1074/jbc.m110.110361 · Cited by 157
Schmidt, E. E., & Schibler, U. (1995) · The Journal of Cell Biology · doi:10.1083/jcb.128.4.467 · Cited by 156
Circadian Clock Gene Bmal1 Is Not Essential; Functional Replacement with its Paralog, Bmal2
Shi, S.-Q., Hida, A., McGuinness, O. P., Wasserman, D. H., Yamazaki, S., & Johnson, C. H. (2010) · Current Biology · doi:10.1016/j.cub.2009.12.034 · Cited by 154
Roles of CLOCK Phosphorylation in Suppression of E-Box-Dependent Transcription
Yoshitane, H., Takao, T., Satomi, Y., Du, N., Okano, T., & Fukada, Y. (2009) · Molecular and Cellular Biology · doi:10.1128/mcb.01864-08 · Cited by 141
Hatanaka, F., Matsubara, C., Myung, J., Yoritaka, T., Kamimura, N., Tsutsumi, S., Kanai, A., Suzuki, Y., Sassone‐Corsi, P., Aburatani, H., et al. (2010) · Molecular and Cellular Biology · doi:10.1128/mcb.00781-10 · Cited by 141
Cellular oscillators: rhythmic gene expression and metabolism
Schibler, U., & Naef, F. (2005) · Current Opinion in Cell Biology · doi:10.1016/j.ceb.2005.01.007 · Cited by 139
Self-citationDynamic PER repression mechanisms in the Drosophila circadian clock: from on-DNA to off-DNAPreprint
Menet, J. S., Abruzzi, K. C., Desrochers, J., Rodriguez, J., & Rosbash, M. (2010) · Genes & Development · doi:10.1101/gad.1883910 · Cited by 136
Hogenesch, J. B., Gu, Y.-Z., Moran, S. M., Shimomura, K., Radcliffe, L. A., Takahashi, J. S., & Bradfield, C. A. (2000) · Journal of Neuroscience · doi:10.1523/jneurosci.20-13-j0002.2000 · Cited by 121
Dual role of the CLOCK/BMAL1 circadian complex in transcriptional regulation
Kondratov, R. V., Kanagal‐Shamanna, R., Kondratova, A. A., Gorbacheva, V., & Antoch, M. P. (2006) · The FASEB Journal · doi:10.1096/fj.05-5321fje · Cited by 114
Proof-by-synthesis of the transcriptional logic of mammalian circadian clocks
Ukai‐Tadenuma, M., Kasukawa, T., & Ueda, H. R. (2008) · Nature Cell Biology · doi:10.1038/ncb1775 · Cited by 104
Circadian clocks: Neural and peripheral pacemakers that impact upon the cell division cycle
Reddy, A. B., Wong, G. K. Y., O'Neill, J. S., Maywood, E. S., & Hastings, M. H. (2005) · Mutation research. Fundamental and molecular mechanisms of mutagenesis · doi:10.1016/j.mrfmmm.2005.01.024 · Cited by 87
Analysis and synthesis of high-amplitude Cis -elements in the mammalian circadian clock
Kumaki, Y., Ukai‐Tadenuma, M., Uno, K. D., Nishio, J., Masumoto, K., Nagano, M., Komori, T., Shigeyoshi, Y., Hogenesch, J. B., & Ueda, H. R. (2008) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0802636105 · Cited by 77
Stratmann, M., Stadler, F., Tamanini, F., van der Horst, G. T. J., & Ripperger, J. A. (2010) · Genes & Development · doi:10.1101/gad.578810 · Cited by 74
Sasaki, M., Yoshitane, H., Du, N., Okano, T., & Fukada, Y. (2009) · Journal of Biological Chemistry · doi:10.1074/jbc.m109.040758 · Cited by 65
Ghorbel, M. T., Coulson, J. M., & Murphy, D. (2003) · Molecular and Cellular Neuroscience · doi:10.1016/s1044-7431(02)00019-2 · Cited by 55
Molecular and Statistical Tools for Circadian Transcript Profiling
Wijnen, H., Naef, F., & Young, M. W. (2005) · Methods in enzymology on CD-ROM/Methods in enzymology · doi:10.1016/s0076-6879(05)93015-2 · Cited by 52
Self-citationA wheel of time: the circadian clock, nuclear receptors, and physiology: Figure 1.Preprint
Yang, X. (2010) · Genes & Development · doi:10.1101/gad.1920710 · Cited by 44
Modeling an Evolutionary Conserved Circadian Cis-Element
Paquet, É. R., Rey, G., & Naef, F. (2005) · PLoS Computational Biology · doi:10.1371/journal.pcbi.0040038 · Cited by 33
Self-citationCircadian transcription in liver
Bożek, K., Rosahl, A. L., Gaub, S., Lorenzen, S., & Herzel, H. (2010) · Biosystems · doi:10.1016/j.biosystems.2010.07.010 · Cited by 18
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Metadata
- Authors
- Rey, G., Cesbron, F., Rougemont, J., Reinke, H., Brunner, M., & Naef, F.
- Venue
- PLoS Biology
- Publisher
- Public Library of Science (PLoS)
- Published
- 2011-02-22
- Volume
- 9
- Issue
- 2
- Pages
- e1000595
- ISSN
- 1544-9173 (ISSN-L)
- 1545-7885
- OpenAlex
- W2150076905
- Cited by
- 474
- References
- 88
- FWCI
- 15.28
- Type
- journal article
- Language
- en
- Open access
- gold
About these checks
Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.
Statistics and arithmetic are recomputed, not judged.
Confidence bands are shown only for fields calibrated on our annotated test set. None is calibrated yet, so no band is shown.
What counts as a claim ›How we measure confidence ›How we check this ›
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Data sources
Bibliographic data: Semantic Scholar, OpenAlex, Crossref.
Contains information from the Semantic Scholar Academic Graph Datasets, made available under the ODC Attribution License (ODC-BY 1.0).
Semantic Scholar’s data is described in: Kinney, R., et al. (2023). The Semantic Scholar Open Data Platform. arXiv:2301.10140.
