Genetic and Epigenomic Mechanisms of Mammalian Circadian Transcription

Overview

Journal Nat Struct Mol Biol

Specialties Cell Biology
Molecular Biology

Date 2016 Dec 7

PMID 27922611

Citations 43

Authors

Romeo Papazyan

Yuxiang Zhang

Mitchell A Lazar

Affiliations

Soon will be listed here.

Abstract

The mammalian molecular clock comprises a complex network of transcriptional programs that integrates environmental signals with physiological pathways in a tissue-specific manner. Emerging technologies are extending knowledge of basic clock features by uncovering their underlying molecular mechanisms, thus setting the stage for a 'systems' view of the molecular clock. Here we discuss how recent data from genome-wide genetic and epigenetic studies have informed the understanding of clock function. In addition to its importance in human physiology and disease, the clock mechanism provides an ideal model to assess general principles of dynamic transcription regulation in vivo.

Citing Articles

Checkpoint kinases regulate the circadian clock after DNA damage by influencing chromatin dynamics.

Yang Y, Duan Z, Liu X, Li Z, Shen Z, Gong S Nucleic Acids Res. 2025; 53(5).

PMID: 40052820 PMC: 11886795. DOI: 10.1093/nar/gkaf162.

Altered circadian expression of clock genes and clock-regulatory epigenetic modifiers in saliva of children with fetal alcohol spectrum disorders.

Das U, Thomas J, Tarale P, Soja J, Inkelis S, Chambers C Sci Rep. 2024; 14(1):19886.

PMID: 39191924 PMC: 11349991. DOI: 10.1038/s41598-024-71023-z.

Importance of Circadian Rhythms in the Ocular Surface.

Zhang X, Jie Y Biomolecules. 2024; 14(7).

PMID: 39062510 PMC: 11274730. DOI: 10.3390/biom14070796.

Phenotype Design Space Provides a Mechanistic Framework Relating Molecular Parameters to Phenotype Diversity Available for Selection.

Savageau M J Mol Evol. 2023; 91(5):687-710.

PMID: 37620617 PMC: 10598110. DOI: 10.1007/s00239-023-10127-y.

International Union of Basic and Clinical Pharmacology CXIII: Nuclear Receptor Superfamily-Update 2023.

Burris T, de Vera I, Cote I, Flaveny C, Wanninayake U, Chatterjee A Pharmacol Rev. 2023; 75(6):1233-1318.

PMID: 37586884 PMC: 10595025. DOI: 10.1124/pharmrev.121.000436.

References

Le Martelot G, Canella D, Symul L, Migliavacca E, Gilardi F, Liechti R . Genome-wide RNA polymerase II profiles and RNA accumulation reveal kinetics of transcription and associated epigenetic changes during diurnal cycles. PLoS Biol. 2012; 10(11):e1001442. PMC: 3507959. DOI: 10.1371/journal.pbio.1001442. View

Oberoi J, Fairall L, Watson P, Yang J, Czimmerer Z, Kampmann T . Structural basis for the assembly of the SMRT/NCoR core transcriptional repression machinery. Nat Struct Mol Biol. 2011; 18(2):177-84. PMC: 3232451. DOI: 10.1038/nsmb.1983. View

Whitfield T, Wang J, Collins P, Partridge E, Force Aldred S, Trinklein N . Functional analysis of transcription factor binding sites in human promoters. Genome Biol. 2012; 13(9):R50. PMC: 3491394. DOI: 10.1186/gb-2012-13-9-r50. View

Woldt E, Sebti Y, Solt L, Duhem C, Lancel S, Eeckhoute J . Rev-erb-α modulates skeletal muscle oxidative capacity by regulating mitochondrial biogenesis and autophagy. Nat Med. 2013; 19(8):1039-46. PMC: 3737409. DOI: 10.1038/nm.3213. View

Brown S . Circadian rhythms. A new histone code for clocks?. Science. 2011; 333(6051):1833-4. DOI: 10.1126/science.1212842. View

Zhu B, Gates L, Stashi E, Dasgupta S, Gonzales N, Dean A . Coactivator-Dependent Oscillation of Chromatin Accessibility Dictates Circadian Gene Amplitude via REV-ERB Loading. Mol Cell. 2015; 60(5):769-783. PMC: 4671835. DOI: 10.1016/j.molcel.2015.10.024. View

Harding H, Lazar M . The orphan receptor Rev-ErbA alpha activates transcription via a novel response element. Mol Cell Biol. 1993; 13(5):3113-21. PMC: 359704. DOI: 10.1128/mcb.13.5.3113-3121.1993. View

Balsalobre A, Marcacci L, Schibler U . Multiple signaling pathways elicit circadian gene expression in cultured Rat-1 fibroblasts. Curr Biol. 2000; 10(20):1291-4. DOI: 10.1016/s0960-9822(00)00758-2. View

Korge S, Grudziecki A, Kramer A . Highly Efficient Genome Editing via CRISPR/Cas9 to Create Clock Gene Knockout Cells. J Biol Rhythms. 2015; 30(5):389-95. DOI: 10.1177/0748730415597519. View

10.

King D, Zhao Y, Sangoram A, Wilsbacher L, Tanaka M, Antoch M . Positional cloning of the mouse circadian clock gene. Cell. 1997; 89(4):641-53. PMC: 3815553. DOI: 10.1016/s0092-8674(00)80245-7. View

11.

Bickmore W, van Steensel B . Genome architecture: domain organization of interphase chromosomes. Cell. 2013; 152(6):1270-84. DOI: 10.1016/j.cell.2013.02.001. View

12.

Valekunja U, Edgar R, Oklejewicz M, van der Horst G, ONeill J, Tamanini F . Histone methyltransferase MLL3 contributes to genome-scale circadian transcription. Proc Natl Acad Sci U S A. 2013; 110(4):1554-9. PMC: 3557088. DOI: 10.1073/pnas.1214168110. View

13.

Dumas B, Harding H, Choi H, Lehmann K, Chung M, Lazar M . A new orphan member of the nuclear hormone receptor superfamily closely related to Rev-Erb. Mol Endocrinol. 1994; 8(8):996-1005. DOI: 10.1210/mend.8.8.7997240. View

14.

Nakahata Y, Kaluzova M, Grimaldi B, Sahar S, Hirayama J, Chen D . The NAD+-dependent deacetylase SIRT1 modulates CLOCK-mediated chromatin remodeling and circadian control. Cell. 2008; 134(2):329-40. PMC: 3526943. DOI: 10.1016/j.cell.2008.07.002. View

15.

Zhang Y, Fang B, Emmett M, Damle M, Sun Z, Feng D . GENE REGULATION. Discrete functions of nuclear receptor Rev-erbα couple metabolism to the clock. Science. 2015; 348(6242):1488-92. PMC: 4613749. DOI: 10.1126/science.aab3021. View

16.

Ripperger J, Schibler U . Rhythmic CLOCK-BMAL1 binding to multiple E-box motifs drives circadian Dbp transcription and chromatin transitions. Nat Genet. 2006; 38(3):369-74. DOI: 10.1038/ng1738. View

17.

Curtis A, Seo S, Westgate E, Rudic R, Smyth E, Chakravarti D . Histone acetyltransferase-dependent chromatin remodeling and the vascular clock. J Biol Chem. 2003; 279(8):7091-7. DOI: 10.1074/jbc.M311973200. View

18.

Menet J, Pescatore S, Rosbash M . CLOCK:BMAL1 is a pioneer-like transcription factor. Genes Dev. 2014; 28(1):8-13. PMC: 3894415. DOI: 10.1101/gad.228536.113. View

19.

Shalev M, Aviram R, Adamovich Y, Kraut-Cohen J, Shamia T, Ben-Dor S . The PXDLS linear motif regulates circadian rhythmicity through protein-protein interactions. Nucleic Acids Res. 2014; 42(19):11879-90. PMC: 4231743. DOI: 10.1093/nar/gku873. View

20.

Gordan R, Shen N, Dror I, Zhou T, Horton J, Rohs R . Genomic regions flanking E-box binding sites influence DNA binding specificity of bHLH transcription factors through DNA shape. Cell Rep. 2013; 3(4):1093-104. PMC: 3640701. DOI: 10.1016/j.celrep.2013.03.014. View