Chromatin Dynamics of Circadian Transcription

Overview

Journal Curr Mol Biol Rep

Specialty Biochemistry

Date 2016 Mar 26

PMID 27014564

Citations 6

Authors

Lorena Aguilar-Arnal

Paolo Sassone-Corsi

Affiliations

Soon will be listed here.

Abstract

The molecular circadian clock orchestrates the daily cyclical expression of thousands of genes. Disruption of this transcriptional program leads to a variety of pathologies, including insomnia, depression and metabolic disorders. Circadian rhythms in gene expression rely on specific chromatin transitions which are ultimately coordinated by the molecular clock. As a consequence, a highly plastic and dynamic circadian epigenome can be delineated across different tissues and cell types. Intriguingly, genome topology appears to coordinate cyclic transcription at circadian interactomes, in which circadian genes are in physical contact within the cell nucleus in a time-specific manner. Moreover, the clock machinery shows functional interplays with key metabolic regulators, thereby connecting the circadian epigenome to cellular metabolism. Unraveling the molecular aspects of such interplays is likely to reveal new therapeutic strategies towards the treatment of metabolic disorders.

Citing Articles

Spatial Organization of the Gene Regulatory Program: An Information Theoretical Approach to Breast Cancer Transcriptomics.

Anda-Jauregui G, Espinal-Enriquez J, Hernandez-Lemus E Entropy (Basel). 2020; 21(2).

PMID: 33266910 PMC: 7514677. DOI: 10.3390/e21020195.

The Circadian Clock as an Essential Molecular Link Between Host Physiology and Microorganisms.

Murakami M, Tognini P Front Cell Infect Microbiol. 2020; 9:469.

PMID: 32039048 PMC: 6987142. DOI: 10.3389/fcimb.2019.00469.

The social evolution of sleep: sex differences, intragenomic conflicts and clinical pathologies.

Faria G, Varela S, Gardner A Proc Biol Sci. 2019; 286(1894):20182188.

PMID: 30963856 PMC: 6367171. DOI: 10.1098/rspb.2018.2188.

Rosiglitazone reverses high fat diet-induced changes in BMAL1 function in muscle, fat, and liver tissue in mice.

Ribas-Latre A, Fekry B, Kwok C, Baumgartner C, Shivshankar S, Sun K Int J Obes (Lond). 2018; 43(3):567-580.

PMID: 29795456 PMC: 6351224. DOI: 10.1038/s41366-018-0090-5.

Circadian Metabolomics in Time and Space.

Dyar K, Eckel-Mahan K Front Neurosci. 2017; 11:369.

PMID: 28744188 PMC: 5504240. DOI: 10.3389/fnins.2017.00369.

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

Schmalen I, Reischl S, Wallach T, Klemz R, Grudziecki A, Prabu J . Interaction of circadian clock proteins CRY1 and PER2 is modulated by zinc binding and disulfide bond formation. Cell. 2014; 157(5):1203-15. DOI: 10.1016/j.cell.2014.03.057. View

Hatori M, Vollmers C, Zarrinpar A, DiTacchio L, Bushong E, Gill S . Time-restricted feeding without reducing caloric intake prevents metabolic diseases in mice fed a high-fat diet. Cell Metab. 2012; 15(6):848-60. PMC: 3491655. DOI: 10.1016/j.cmet.2012.04.019. View

Ramsey K, Yoshino J, Brace C, Abrassart D, Kobayashi Y, Marcheva B . Circadian clock feedback cycle through NAMPT-mediated NAD+ biosynthesis. Science. 2009; 324(5927):651-4. PMC: 2738420. DOI: 10.1126/science.1171641. View

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

Takahata S, Ozaki T, Mimura J, Kikuchi Y, Sogawa K, Fujii-Kuriyama Y . Transactivation mechanisms of mouse clock transcription factors, mClock and mArnt3. Genes Cells. 2000; 5(9):739-47. DOI: 10.1046/j.1365-2443.2000.00363.x. View

Masri S, Patel V, Eckel-Mahan K, Peleg S, Forne I, Ladurner A . Circadian acetylome reveals regulation of mitochondrial metabolic pathways. Proc Natl Acad Sci U S A. 2013; 110(9):3339-44. PMC: 3587221. DOI: 10.1073/pnas.1217632110. View

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

Libert S, Bonkowski M, Pointer K, Pletcher S, Guarente L . Deviation of innate circadian period from 24 h reduces longevity in mice. Aging Cell. 2012; 11(5):794-800. PMC: 3526942. DOI: 10.1111/j.1474-9726.2012.00846.x. View

10.

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

11.

Hebert A, Dittenhafer-Reed K, Yu W, Bailey D, Selen E, Boersma M . Calorie restriction and SIRT3 trigger global reprogramming of the mitochondrial protein acetylome. Mol Cell. 2012; 49(1):186-99. PMC: 3704155. DOI: 10.1016/j.molcel.2012.10.024. View

12.

LeGates T, Fernandez D, Hattar S . Light as a central modulator of circadian rhythms, sleep and affect. Nat Rev Neurosci. 2014; 15(7):443-54. PMC: 4254760. DOI: 10.1038/nrn3743. View

13.

Hirano A, Yumimoto K, Tsunematsu R, Matsumoto M, Oyama M, Kozuka-Hata H . FBXL21 regulates oscillation of the circadian clock through ubiquitination and stabilization of cryptochromes. Cell. 2013; 152(5):1106-18. DOI: 10.1016/j.cell.2013.01.054. View

14.

McGlincy N, Valomon A, Chesham J, Maywood E, Hastings M, Ule J . Regulation of alternative splicing by the circadian clock and food related cues. Genome Biol. 2012; 13(6):R54. PMC: 3446320. DOI: 10.1186/gb-2012-13-6-r54. View

15.

Kume K, Zylka M, Sriram S, Shearman L, Weaver D, Jin X . mCRY1 and mCRY2 are essential components of the negative limb of the circadian clock feedback loop. Cell. 1999; 98(2):193-205. DOI: 10.1016/s0092-8674(00)81014-4. View

16.

Ciabrelli F, Cavalli G . Chromatin-driven behavior of topologically associating domains. J Mol Biol. 2014; 427(3):608-25. DOI: 10.1016/j.jmb.2014.09.013. View

17.

Sahar S, Sassone-Corsi P . Regulation of metabolism: the circadian clock dictates the time. Trends Endocrinol Metab. 2011; 23(1):1-8. PMC: 3259741. DOI: 10.1016/j.tem.2011.10.005. View

18.

Chang H, Guarente L . SIRT1 mediates central circadian control in the SCN by a mechanism that decays with aging. Cell. 2013; 153(7):1448-60. PMC: 3748806. DOI: 10.1016/j.cell.2013.05.027. View

19.

Xing W, Busino L, Hinds T, Marionni S, Saifee N, Bush M . SCF(FBXL3) ubiquitin ligase targets cryptochromes at their cofactor pocket. Nature. 2013; 496(7443):64-8. PMC: 3618506. DOI: 10.1038/nature11964. View

20.

Doi M, Hirayama J, Sassone-Corsi P . Circadian regulator CLOCK is a histone acetyltransferase. Cell. 2006; 125(3):497-508. DOI: 10.1016/j.cell.2006.03.033. View