Subtle changes in chromatin loop contact propensity are associated with differential gene regulation and expression

William W. Greenwald, He Li, Paola Benaglio, David Jakubosky, Hiroko Matsui, Anthony Schmitt, Siddarth Selvaraj, Matteo D’Antonio, Agnieszka D’Antonio-Chronowska, Erin N. Smith () and Kelly A. Frazer ()
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William W. Greenwald: University of California, San Diego
He Li: University of California, San Diego
Paola Benaglio: University of California, San Diego
David Jakubosky: University of California, San Diego
Hiroko Matsui: University of California, San Diego
Anthony Schmitt: Arima Genomics
Siddarth Selvaraj: Arima Genomics
Matteo D’Antonio: University of California, San Diego
Agnieszka D’Antonio-Chronowska: University of California, San Diego
Erin N. Smith: University of California, San Diego
Kelly A. Frazer: University of California, San Diego

Nature Communications, 2019, vol. 10, issue 1, 1-17

Abstract: Abstract While genetic variation at chromatin loops is relevant for human disease, the relationships between contact propensity (the probability that loci at loops physically interact), genetics, and gene regulation are unclear. We quantitatively interrogate these relationships by comparing Hi-C and molecular phenotype data across cell types and haplotypes. While chromatin loops consistently form across different cell types, they have subtle quantitative differences in contact frequency that are associated with larger changes in gene expression and H3K27ac. For the vast majority of loci with quantitative differences in contact frequency across haplotypes, the changes in magnitude are smaller than those across cell types; however, the proportional relationships between contact propensity, gene expression, and H3K27ac are consistent. These findings suggest that subtle changes in contact propensity have a biologically meaningful role in gene regulation and could be a mechanism by which regulatory genetic variants in loop anchors mediate effects on expression.

Date: 2019
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Persistent link: https://EconPapers.repec.org/RePEc:nat:natcom:v:10:y:2019:i:1:d:10.1038_s41467-019-08940-5

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DOI: 10.1038/s41467-019-08940-5

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