Transcription factor activity rhythms and tissue-specific chromatin interactions explain circadian gene expression across organs.

Details

Serval ID
serval:BIB_B99C34A1E160
Type
Article: article from journal or magazin.
Collection
Publications
Title
Transcription factor activity rhythms and tissue-specific chromatin interactions explain circadian gene expression across organs.
Journal
Genome research
Author(s)
Yeung Jake, Mermet Jerome, Jouffe Celine, Marquis Julien, Charpagne Aline, Gachon Frederic, Naef Felix
Publication state
Published
Issued date
02/2018
Volume
28
Number
2
Pages
182-191
Language
english
Abstract
Temporal control of physiology requires the interplay between gene networks involved in daily timekeeping and tissue function across different organs. How the circadian clock interweaves with tissue-specific transcriptional programs is poorly understood. Here, we dissected temporal and tissue-specific regulation at multiple gene regulatory layers by examining mouse tissues with an intact or disrupted clock over time. Integrated analysis uncovered two distinct regulatory modes underlying tissue-specific rhythms: tissue-specific oscillations in transcription factor (TF) activity, which were linked to feeding-fasting cycles in liver and sodium homeostasis in kidney; and colocalized binding of clock and tissue-specific transcription factors at distal enhancers. Chromosome conformation capture (4C-seq) in liver and kidney identified liver-specific chromatin loops that recruited clock-bound enhancers to promoters to regulate liver-specific transcriptional rhythms. Furthermore, this looping was remarkably promoter-specific on the scale of less than 10 kilobases (kb). Enhancers can contact a rhythmic promoter while looping out nearby nonrhythmic alternative promoters, confining rhythmic enhancer activity to specific promoters. These findings suggest that chromatin folding enables the clock to regulate rhythmic transcription of specific promoters to output temporal transcriptional programs tailored to different tissues.
Keywords
Animals, Mice, Promoter Regions, Genetic, Chromatin/genetics, Circadian Clocks/*genetics, Circadian Rhythm/*genetics, Enhancer Elements, Genetic/*genetics, Gene Expression Regulation/genetics, Kidney/metabolism, Liver/metabolism, Organ Specificity/genetics, Transcription Factors/*genetics
Pubmed
Create date
19/02/2020 12:23
Last modification date
20/02/2020 6:26
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