Circadian transcription in liver

Bio Systems
K BozekH Herzel

Abstract

Circadian rhythms regulate a wide range of cellular, physiological, metabolic and behavioral activities in mammals. The complexity of tissue- and day-time specific regulation of thousands of clock controlled genes (CCGs) suggests that many transcriptional regulators are involved. Our bioinformatic analysis is based on two published DNA-array studies from mouse liver. We search overrepresented transcription factor binding sites in promoter regions of CCGs using GC-matched controls. Analyzing a large set of CCG promoters, we find known motifs such as E-boxes, D-boxes and cAMP responsive elements. In addition, we find overrepresented GC-rich motifs (Sp1, ETF, Nrf1), AT-rich motifs (TBP, Fox04, MEF-2), Y-box motifs (NF-Y, C/EBP) and cell cycle regulators (E2F, Elk-1). In a subset of system-driven genes, we find overrepresented motifs of the serum response factor SRF and the estrogen receptor ER. The analysis of published ChIP data reveals that some of our predicted regulators (C/EBP, E2F, HNF-1, Myc, MEF-2) target relatively many clock controlled genes. Our analysis of CCG promoters contributes to an understanding of the complex transcriptional regulation of circadian rhythms in liver.

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Citations

Nov 2, 2011·Proceedings of the National Academy of Sciences of the United States of America·Ann AtwoodSteve A Kay
Sep 7, 2012·PloS One·Yi-Qiao XuCurtis D Klaassen
Jul 31, 2013·Journal of Molecular Endocrinology·Margarita M IvanovaCarolyn M Klinge
Mar 1, 2016·Journal of Hepatology·Yuyan HanGianfranco Alpini
Apr 4, 2017·Nature Communications·Andrew S P LimPhilip L De Jager
Apr 20, 2021·FASEB Journal : Official Publication of the Federation of American Societies for Experimental Biology·Soumyaditya GhoshRoman V Kondratov
Dec 9, 2015·Molecular and Cellular Biology·Sandra SchickVijay K Tiwari

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