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For: Sobel JA, Krier I, Andersin T, Raghav S, Canella D, Gilardi F, Kalantzi AS, Rey G, Weger B, Gachon F, Dal Peraro M, Hernandez N, Schibler U, Deplancke B, Naef F, CycliX consortium. Transcriptional regulatory logic of the diurnal cycle in the mouse liver. PLoS Biol 2017;15:e2001069. [PMID: 28414715 PMCID: PMC5393560 DOI: 10.1371/journal.pbio.2001069] [Citation(s) in RCA: 57] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2016] [Accepted: 03/10/2017] [Indexed: 12/11/2022]  Open
Number Cited by Other Article(s)
1
Tong CY, Li C, Hurni C, Jacq A, Nie XY, Guy CR, Suh JH, Wong RKW, Merlin C, Naef F, Menet JS, Jiang Y. Single-Cell Multiomic Analysis of Circadian Rhythmicity in Mouse Liver. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2025:2025.04.03.647044. [PMID: 40291723 PMCID: PMC12026578 DOI: 10.1101/2025.04.03.647044] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/30/2025]
2
Hunter AL, Bechtold DA. The metabolic significance of peripheral tissue clocks. Commun Biol 2025;8:497. [PMID: 40140664 PMCID: PMC11947457 DOI: 10.1038/s42003-025-07932-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2024] [Accepted: 03/12/2025] [Indexed: 03/28/2025]  Open
3
He W, Loganathan N, Belsham DD. IGF1 Signaling Regulates Neuropeptide Expression in Hypothalamic Neurons Under Physiological and Pathological Conditions. Endocrinology 2025;166:bqaf051. [PMID: 40105689 PMCID: PMC11949690 DOI: 10.1210/endocr/bqaf051] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/29/2025] [Revised: 02/28/2025] [Accepted: 03/17/2025] [Indexed: 03/20/2025]
4
Mustafa AF, He W, Belsham DD. Transforming growth factor β-2 is rhythmically expressed in both WT and BMAL1-deficient hypothalamic neurons and regulates neuropeptide Y: Disruption by palmitate. Mol Cell Endocrinol 2025;595:112411. [PMID: 39522861 DOI: 10.1016/j.mce.2024.112411] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/13/2024] [Revised: 11/06/2024] [Accepted: 11/07/2024] [Indexed: 11/16/2024]
5
Zee A, Deng DZ, DiTacchio L, Vollmers C. The Circadian Isoform Landscape of Mouse Livers. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.10.16.618716. [PMID: 39464136 PMCID: PMC11507890 DOI: 10.1101/2024.10.16.618716] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 10/29/2024]
6
Pacheco-Bernal I, Becerril-Pérez F, Bustamante-Zepeda M, González-Suárez M, Olmedo-Suárez MA, Hernández-Barrientos LR, Alarcón-Del-Carmen A, Escalante-Covarrubias Q, Mendoza-Viveros L, Hernández-Lemus E, León-Del-Río A, de la Rosa-Velázquez IA, Orozco-Solis R, Aguilar-Arnal L. Transitions in chromatin conformation shaped by fatty acids and the circadian clock underlie hepatic transcriptional reorganization in obese mice. Cell Mol Life Sci 2024;81:309. [PMID: 39060446 PMCID: PMC11335233 DOI: 10.1007/s00018-024-05364-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2024] [Revised: 06/25/2024] [Accepted: 07/12/2024] [Indexed: 07/28/2024]
7
Litwin C, Koronowski KB. Liver as a nexus of daily metabolic cross talk. INTERNATIONAL REVIEW OF CELL AND MOLECULAR BIOLOGY 2024;393:95-139. [PMID: 40390465 DOI: 10.1016/bs.ircmb.2024.06.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/21/2025]
8
Nie XY, Menet JS. Circadian regulation of stereotypic chromatin conformations at enhancers. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.04.24.590818. [PMID: 38712031 PMCID: PMC11071494 DOI: 10.1101/2024.04.24.590818] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/08/2024]
9
Sharma D, Partch CL. PAS Dimerization at the Nexus of the Mammalian Circadian Clock. J Mol Biol 2024;436:168341. [PMID: 37924861 PMCID: PMC11729053 DOI: 10.1016/j.jmb.2023.168341] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2023] [Revised: 10/23/2023] [Accepted: 10/29/2023] [Indexed: 11/06/2023]
10
Maehara H, Kokaji T, Hatano A, Suzuki Y, Matsumoto M, Nakayama KI, Egami R, Tsuchiya T, Ozaki H, Morita K, Shirai M, Li D, Terakawa A, Uematsu S, Hironaka KI, Ohno S, Kubota H, Araki H, Miura F, Ito T, Kuroda S. DNA hypomethylation characterizes genes encoding tissue-dominant functional proteins in liver and skeletal muscle. Sci Rep 2023;13:19118. [PMID: 37926704 PMCID: PMC10625943 DOI: 10.1038/s41598-023-46393-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2023] [Accepted: 10/31/2023] [Indexed: 11/07/2023]  Open
11
Zhang Y, Chen G, Deng L, Gao B, Yang J, Ding C, Zhang Q, Ouyang W, Guo M, Wang W, Liu B, Zhang Q, Sung WK, Yan J, Li G, Li X. Integrated 3D genome, epigenome and transcriptome analyses reveal transcriptional coordination of circadian rhythm in rice. Nucleic Acids Res 2023;51:9001-9018. [PMID: 37572350 PMCID: PMC10516653 DOI: 10.1093/nar/gkad658] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2022] [Revised: 07/11/2023] [Accepted: 08/01/2023] [Indexed: 08/14/2023]  Open
12
Halawani D, Wang Y, Ramakrishnan A, Estill M, He X, Shen L, Friedel RH, Zou H. Circadian clock regulator Bmal1 gates axon regeneration via Tet3 epigenetics in mouse sensory neurons. Nat Commun 2023;14:5165. [PMID: 37620297 PMCID: PMC10449865 DOI: 10.1038/s41467-023-40816-7] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2022] [Accepted: 08/11/2023] [Indexed: 08/26/2023]  Open
13
Michael AK, Stoos L, Crosby P, Eggers N, Nie XY, Makasheva K, Minnich M, Healy KL, Weiss J, Kempf G, Cavadini S, Kater L, Seebacher J, Vecchia L, Chakraborty D, Isbel L, Grand RS, Andersch F, Fribourgh JL, Schübeler D, Zuber J, Liu AC, Becker PB, Fierz B, Partch CL, Menet JS, Thomä NH. Cooperation between bHLH transcription factors and histones for DNA access. Nature 2023;619:385-393. [PMID: 37407816 PMCID: PMC10338342 DOI: 10.1038/s41586-023-06282-3] [Citation(s) in RCA: 38] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2022] [Accepted: 06/02/2023] [Indexed: 07/07/2023]
14
Bafna A, Banks G, Hastings MH, Nolan PM. Dynamic modulation of genomic enhancer elements in the suprachiasmatic nucleus, the site of the mammalian circadian clock. Genome Res 2023;33:673-688. [PMID: 37156620 PMCID: PMC10317116 DOI: 10.1101/gr.277581.122] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2022] [Accepted: 05/03/2023] [Indexed: 05/10/2023]
15
Obodo D, Outland EH, Hughey JJ. Sex Inclusion in Transcriptome Studies of Daily Rhythms. J Biol Rhythms 2023;38:3-14. [PMID: 36419398 PMCID: PMC9903005 DOI: 10.1177/07487304221134160] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
16
Martini T, Naef F, Tchorz JS. Spatiotemporal Metabolic Liver Zonation and Consequences on Pathophysiology. ANNUAL REVIEW OF PATHOLOGY 2023;18:439-466. [PMID: 36693201 DOI: 10.1146/annurev-pathmechdis-031521-024831] [Citation(s) in RCA: 27] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
17
Comprehensive analysis of the circadian nuclear and cytoplasmic transcriptome in mouse liver. PLoS Genet 2022;18:e1009903. [PMID: 35921362 PMCID: PMC9377612 DOI: 10.1371/journal.pgen.1009903] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2021] [Revised: 08/15/2022] [Accepted: 07/06/2022] [Indexed: 11/19/2022]  Open
18
Liu N, Tian H, Yu Z, Zhao H, Li W, Sang D, Lin K, Cui Y, Liao M, Xu Z, Chen C, Guo Y, Wang Y, Huang HW, Wang J, Zhang H, Wu W, Huang H, Lv S, Guo Z, Wang W, Zheng S, Wang F, Zhang Y, Cai T, Zhang EE. A highland-adaptation mutation of the Epas1 protein increases its stability and disrupts the circadian clock in the plateau pika. Cell Rep 2022;39:110816. [PMID: 35584682 DOI: 10.1016/j.celrep.2022.110816] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2020] [Revised: 02/07/2022] [Accepted: 04/20/2022] [Indexed: 11/30/2022]  Open
19
Hunter AL, Poolman TM, Kim D, Gonzalez FJ, Bechtold DA, Loudon ASI, Iqbal M, Ray DW. HNF4A modulates glucocorticoid action in the liver. Cell Rep 2022;39:110697. [PMID: 35443180 PMCID: PMC9380254 DOI: 10.1016/j.celrep.2022.110697] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2021] [Revised: 01/24/2022] [Accepted: 03/29/2022] [Indexed: 12/13/2022]  Open
20
Tartour K, Padmanabhan K. The Clock Takes Shape-24 h Dynamics in Genome Topology. Front Cell Dev Biol 2022;9:799971. [PMID: 35047508 PMCID: PMC8762244 DOI: 10.3389/fcell.2021.799971] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2021] [Accepted: 12/14/2021] [Indexed: 11/20/2022]  Open
21
Greulich F, Bielefeld KA, Scheundel R, Mechtidou A, Strickland B, Uhlenhaut NH. Enhancer RNA Expression in Response to Glucocorticoid Treatment in Murine Macrophages. Cells 2021;11:28. [PMID: 35011590 PMCID: PMC8744892 DOI: 10.3390/cells11010028] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2021] [Revised: 12/17/2021] [Accepted: 12/20/2021] [Indexed: 12/15/2022]  Open
22
Briggs P, Hunter AL, Yang SH, Sharrocks AD, Iqbal M. PEGS: An efficient tool for gene set enrichment within defined sets of genomic intervals. F1000Res 2021;10:570. [PMID: 34504687 PMCID: PMC8406447 DOI: 10.12688/f1000research.53926.2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 10/25/2021] [Indexed: 11/28/2022]  Open
23
Præstholm SM, Correia CM, Goitea VE, Siersbæk MS, Jørgensen M, Havelund JF, Pedersen TÅ, Færgeman NJ, Grøntved L. Impaired glucocorticoid receptor expression in liver disrupts feeding-induced gene expression, glucose uptake, and glycogen storage. Cell Rep 2021;37:109938. [PMID: 34731602 DOI: 10.1016/j.celrep.2021.109938] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2021] [Revised: 09/08/2021] [Accepted: 10/13/2021] [Indexed: 10/19/2022]  Open
24
Greco CM, Koronowski KB, Smith JG, Shi J, Kunderfranco P, Carriero R, Chen S, Samad M, Welz PS, Zinna VM, Mortimer T, Chun SK, Shimaji K, Sato T, Petrus P, Kumar A, Vaca-Dempere M, Deryagian O, Van C, Kuhn JMM, Lutter D, Seldin MM, Masri S, Li W, Baldi P, Dyar KA, Muñoz-Cánoves P, Benitah SA, Sassone-Corsi P. Integration of feeding behavior by the liver circadian clock reveals network dependency of metabolic rhythms. SCIENCE ADVANCES 2021;7:eabi7828. [PMID: 34550736 PMCID: PMC8457671 DOI: 10.1126/sciadv.abi7828] [Citation(s) in RCA: 43] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/30/2021] [Accepted: 07/29/2021] [Indexed: 05/28/2023]
25
Judd J, Sanderson H, Feschotte C. Evolution of mouse circadian enhancers from transposable elements. Genome Biol 2021;22:193. [PMID: 34187518 PMCID: PMC8240256 DOI: 10.1186/s13059-021-02409-9] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2020] [Accepted: 06/10/2021] [Indexed: 12/13/2022]  Open
26
Kinouchi K, Mikami Y, Kanai T, Itoh H. Circadian rhythms in the tissue-specificity from metabolism to immunity; insights from omics studies. Mol Aspects Med 2021;80:100984. [PMID: 34158177 DOI: 10.1016/j.mam.2021.100984] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2021] [Revised: 05/04/2021] [Accepted: 06/07/2021] [Indexed: 12/31/2022]
27
Furlan-Magaril M, Ando-Kuri M, Arzate-Mejía RG, Morf J, Cairns J, Román-Figueroa A, Tenorio-Hernández L, Poot-Hernández AC, Andrews S, Várnai C, Virk B, Wingett SW, Fraser P. The global and promoter-centric 3D genome organization temporally resolved during a circadian cycle. Genome Biol 2021;22:162. [PMID: 34099014 PMCID: PMC8185950 DOI: 10.1186/s13059-021-02374-3] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2020] [Accepted: 05/05/2021] [Indexed: 12/17/2022]  Open
28
Scrt1, a transcriptional regulator of β-cell proliferation identified by differential chromatin accessibility during islet maturation. Sci Rep 2021;11:8800. [PMID: 33888791 PMCID: PMC8062533 DOI: 10.1038/s41598-021-88003-2] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2020] [Accepted: 03/25/2021] [Indexed: 12/12/2022]  Open
29
Wang Y, Mao Y, Zhao Y, Yi X, Ding G, Yu C, Sheng J, Liu X, Meng Y, Huang H. Early-life undernutrition induces enhancer RNA remodeling in mice liver. Epigenetics Chromatin 2021;14:18. [PMID: 33789751 PMCID: PMC8011416 DOI: 10.1186/s13072-021-00392-w] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2020] [Accepted: 03/19/2021] [Indexed: 01/10/2023]  Open
30
Mermet J, Yeung J, Naef F. Oscillating and stable genome topologies underlie hepatic physiological rhythms during the circadian cycle. PLoS Genet 2021;17:e1009350. [PMID: 33524027 PMCID: PMC7877755 DOI: 10.1371/journal.pgen.1009350] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2020] [Revised: 02/11/2021] [Accepted: 01/08/2021] [Indexed: 01/08/2023]  Open
31
Weger BD, Gobet C, David FPA, Atger F, Martin E, Phillips NE, Charpagne A, Weger M, Naef F, Gachon F. Systematic analysis of differential rhythmic liver gene expression mediated by the circadian clock and feeding rhythms. Proc Natl Acad Sci U S A 2021;118:e2015803118. [PMID: 33452134 PMCID: PMC7826335 DOI: 10.1073/pnas.2015803118] [Citation(s) in RCA: 94] [Impact Index Per Article: 23.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]  Open
32
Droin C, Kholtei JE, Bahar Halpern K, Hurni C, Rozenberg M, Muvkadi S, Itzkovitz S, Naef F. Space-time logic of liver gene expression at sub-lobular scale. Nat Metab 2021;3:43-58. [PMID: 33432202 PMCID: PMC7116850 DOI: 10.1038/s42255-020-00323-1] [Citation(s) in RCA: 85] [Impact Index Per Article: 21.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/05/2020] [Accepted: 11/12/2020] [Indexed: 01/29/2023]
33
Unruh BA, Kojima S. The Making and Breaking of RNAs: Dynamics of Rhythmic RNA Expression in Mammals. J Biol Rhythms 2020;35:519-529. [PMID: 32965157 PMCID: PMC9250146 DOI: 10.1177/0748730420957498] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/08/2023]
34
Hu H, Chen Z, Ji L, Wang Y, Yang M, Lai R, Zhong Y, Zhang X, Wang L. ARID1A-dependent permissive chromatin accessibility licenses estrogen-receptor signaling to regulate circadian rhythms genes in endometrial cancer. Cancer Lett 2020;492:162-173. [PMID: 32858102 DOI: 10.1016/j.canlet.2020.08.034] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2020] [Revised: 08/10/2020] [Accepted: 08/21/2020] [Indexed: 01/22/2023]
35
Nuclear receptor REVERBα is a state-dependent regulator of liver energy metabolism. Proc Natl Acad Sci U S A 2020;117:25869-25879. [PMID: 32989157 PMCID: PMC7568238 DOI: 10.1073/pnas.2005330117] [Citation(s) in RCA: 40] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]  Open
36
Chowdhury D, Wang C, Lu A, Zhu H. Identifying Transcription Factor Combinations to Modulate Circadian Rhythms by Leveraging Virtual Knockouts on Transcription Networks. iScience 2020;23:101490. [PMID: 32920484 PMCID: PMC7492989 DOI: 10.1016/j.isci.2020.101490] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2020] [Revised: 07/24/2020] [Accepted: 08/19/2020] [Indexed: 02/02/2023]  Open
37
Kelley DR. Cross-species regulatory sequence activity prediction. PLoS Comput Biol 2020;16:e1008050. [PMID: 32687525 PMCID: PMC7392335 DOI: 10.1371/journal.pcbi.1008050] [Citation(s) in RCA: 116] [Impact Index Per Article: 23.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2019] [Revised: 07/30/2020] [Accepted: 06/12/2020] [Indexed: 12/22/2022]  Open
38
Levine DC, Hong H, Weidemann BJ, Ramsey KM, Affinati AH, Schmidt MS, Cedernaes J, Omura C, Braun R, Lee C, Brenner C, Peek CB, Bass J. NAD+ Controls Circadian Reprogramming through PER2 Nuclear Translocation to Counter Aging. Mol Cell 2020;78:835-849.e7. [PMID: 32369735 PMCID: PMC7275919 DOI: 10.1016/j.molcel.2020.04.010] [Citation(s) in RCA: 121] [Impact Index Per Article: 24.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2019] [Revised: 02/12/2020] [Accepted: 04/07/2020] [Indexed: 12/18/2022]
39
hnRNP K Supports High-Amplitude D Site-Binding Protein mRNA (Dbp mRNA) Oscillation To Sustain Circadian Rhythms. Mol Cell Biol 2020;40:MCB.00537-19. [PMID: 31907279 DOI: 10.1128/mcb.00537-19] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2019] [Accepted: 12/20/2019] [Indexed: 01/24/2023]  Open
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Genomics of circadian rhythms in health and disease. Genome Med 2019;11:82. [PMID: 31847894 PMCID: PMC6916512 DOI: 10.1186/s13073-019-0704-0] [Citation(s) in RCA: 314] [Impact Index Per Article: 52.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2019] [Accepted: 12/09/2019] [Indexed: 12/29/2022]  Open
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Hor CN, Yeung J, Jan M, Emmenegger Y, Hubbard J, Xenarios I, Naef F, Franken P. Sleep-wake-driven and circadian contributions to daily rhythms in gene expression and chromatin accessibility in the murine cortex. Proc Natl Acad Sci U S A 2019;116:25773-25783. [PMID: 31776259 PMCID: PMC6925978 DOI: 10.1073/pnas.1910590116] [Citation(s) in RCA: 58] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]  Open
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Zhang CZ, Sun HZ, Zhang CH, Jin L, Sang D, Li SL. Effects of photoperiod on circadian clock genes in skin contribute to the regulation of hair follicle cycling of Inner Mongolia white cashmere goats. Anim Sci J 2019;91:e13320. [PMID: 31845459 DOI: 10.1111/asj.13320] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2019] [Revised: 08/03/2019] [Accepted: 10/29/2019] [Indexed: 12/21/2022]
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Kinouchi K, Magnan C, Ceglia N, Liu Y, Cervantes M, Pastore N, Huynh T, Ballabio A, Baldi P, Masri S, Sassone-Corsi P. Fasting Imparts a Switch to Alternative Daily Pathways in Liver and Muscle. Cell Rep 2019;25:3299-3314.e6. [PMID: 30566858 DOI: 10.1016/j.celrep.2018.11.077] [Citation(s) in RCA: 95] [Impact Index Per Article: 15.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2017] [Revised: 09/08/2018] [Accepted: 11/19/2018] [Indexed: 01/09/2023]  Open
44
Molecular mechanisms and physiological importance of circadian rhythms. Nat Rev Mol Cell Biol 2019;21:67-84. [PMID: 31768006 DOI: 10.1038/s41580-019-0179-2] [Citation(s) in RCA: 745] [Impact Index Per Article: 124.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/19/2019] [Indexed: 12/12/2022]
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Circadian Clock Regulation of Hepatic Energy Metabolism Regulatory Circuits. BIOLOGY 2019;8:biology8040079. [PMID: 31635079 PMCID: PMC6956161 DOI: 10.3390/biology8040079] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/14/2019] [Revised: 10/13/2019] [Accepted: 10/15/2019] [Indexed: 01/03/2023]
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Beytebiere JR, Greenwell BJ, Sahasrabudhe A, Menet JS. Clock-controlled rhythmic transcription: is the clock enough and how does it work? Transcription 2019;10:212-221. [PMID: 31595813 DOI: 10.1080/21541264.2019.1673636] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]  Open
47
Chowdhury D, Wang C, Lu AP, Zhu HL. Understanding Quantitative Circadian Regulations Are Crucial Towards Advancing Chronotherapy. Cells 2019;8:cells8080883. [PMID: 31412622 PMCID: PMC6721722 DOI: 10.3390/cells8080883] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2019] [Revised: 08/01/2019] [Accepted: 08/09/2019] [Indexed: 12/19/2022]  Open
48
Lugena AB, Zhang Y, Menet JS, Merlin C. Genome-wide discovery of the daily transcriptome, DNA regulatory elements and transcription factor occupancy in the monarch butterfly brain. PLoS Genet 2019;15:e1008265. [PMID: 31335862 PMCID: PMC6677324 DOI: 10.1371/journal.pgen.1008265] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2018] [Revised: 08/02/2019] [Accepted: 06/21/2019] [Indexed: 12/20/2022]  Open
49
Petkau N, Budak H, Zhou X, Oster H, Eichele G. Acetylation of BMAL1 by TIP60 controls BRD4-P-TEFb recruitment to circadian promoters. eLife 2019;8:e43235. [PMID: 31294688 PMCID: PMC6650244 DOI: 10.7554/elife.43235] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2018] [Accepted: 07/10/2019] [Indexed: 12/22/2022]  Open
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Adamovich Y, Ladeuix B, Sobel J, Manella G, Neufeld-Cohen A, Assadi MH, Golik M, Kuperman Y, Tarasiuk A, Koeners MP, Asher G. Oxygen and Carbon Dioxide Rhythms Are Circadian Clock Controlled and Differentially Directed by Behavioral Signals. Cell Metab 2019;29:1092-1103.e3. [PMID: 30773466 DOI: 10.1016/j.cmet.2019.01.007] [Citation(s) in RCA: 86] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/04/2017] [Revised: 11/13/2018] [Accepted: 01/16/2019] [Indexed: 12/25/2022]
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