Differential chromatin profiles partially determine transcription factor binding

Rujian Chen and David K Gifford

PLOS ONE, 2017, vol. 12, issue 7, 1-10

Abstract: We characterize how genomic variants that alter chromatin accessibility influence regulatory factor binding with a new method called DeltaBind that predicts condition specific factor binding more accurately than other methods based on DNase-seq data. Using DeltaBind and DNase-seq experiments we predicted the differential binding of 18 factors in K562 and GM12878 cells with an average precision of 28% at 10% recall, with the prediction of individual factors ranging from 5% to 65% precision. We further found that genome variants that alter chromatin accessibility are not necessarily predictive of altering proximal factor binding. Taken together these findings suggest that DNase-seq or ATAC-seq Quantitative Trait Loci (dsQTLs), while important, must be considered in a broader context to establish causality for phenotypic changes.

Date: 2017
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Persistent link: https://EconPapers.repec.org/RePEc:plo:pone00:0179411

DOI: 10.1371/journal.pone.0179411

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