The global and promoter-centric 3D genome organization temporally resolved during a circadian cycle.

Genome Biology
Mayra Furlan-MagarilPeter Fraser

Abstract

Circadian gene expression is essential for organisms to adjust their physiology and anticipate daily changes in the environment. The molecular mechanisms controlling circadian gene transcription are still under investigation. In particular, how chromatin conformation at different genomic scales and regulatory elements impact rhythmic gene expression has been poorly characterized. Here we measure changes in the spatial chromatin conformation in mouse liver using genome-wide and promoter-capture Hi-C alongside daily oscillations in gene transcription. We find topologically associating domains harboring circadian genes that switch assignments between the transcriptionally active and inactive compartment at different hours of the day, while their boundaries stably maintain their structure over time. To study chromatin contacts of promoters at high resolution over time, we apply promoter capture Hi-C. We find circadian gene promoters displayed a maximal number of chromatin contacts at the time of their peak transcriptional output. Furthermore, circadian genes, as well as contacted and transcribed regulatory elements, reach maximal expression at the same timepoints. Anchor sites of circadian gene promoter loops are enriched in DNA bi...Continue Reading

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Citations

Jul 10, 2021·Genome Biology·Geoffrey J Faulkner
Aug 21, 2021·Cellular and Molecular Life Sciences : CMLS·Helen Ray-Jones, Mikhail Spivakov

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Software Mentioned

Deeptools
Juicer
StringTie
MACS2
DAVID
FastQC
Intervene
Bowtie2
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Juicebox

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