Regulation of Pol II Pausing Is Involved in Daily Gene Transcription in the Mouse Liver

Journal of Biological Rhythms
Jialou ZhuXiaodong Li

Abstract

The circadian clock orchestrates gene expression rhythms. Regulation at the level of gene transcription is essential for molecular and cellular rhythms. Pol II pause release is a critical step of transcription regulation. However, whether and how Pol II pause release is regulated during daily transcription have not been characterized. In this study, we performed Pol II ChIP-seq across the day in the mouse liver and quantitatively analyzed binding signals within the transcription start site (TSS) region and the gene body. We frequently found discordant changes between Pol II near the TSS ([Pol II]TSS, paused Pol II) and that within the gene body ([Pol II]GB, transcribing Pol II) across the genome, with only [Pol II]GB always reflecting transcription of clock and clock-controlled genes. Accordingly, Pol II traveling ratios of more than 7000 genes showed significant daily changes (>1.5-fold). Therefore, there is widespread regulation of Pol II pausing in the mouse liver. Interestingly, gene transcription rhythms exhibited a bimodal phase distribution. The transcription of ~400 genes peaked near ZT0, coincident with a genome-wide increase in [Pol II]TSS and traveling ratio (TR). The transcription of ~300 other genes peaked ~12 h la...Continue Reading

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Citations

Jul 25, 2021·International Journal of Molecular Sciences·Jamison B BurchettBrian J Altman

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Methods Mentioned

BETA
ChIP-seq
density gradient centrifugation
ChIPs
ChIP
ubiquitination

Software Mentioned

Integrative Genomic Viewer ( IGV )
BEDTools
Excel
CYCLE
JTK
Bowtie
MACS
SAM
bedcov
Samtools

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