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Differential chromatin profiles partially determine transcription factor binding

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  • Rujian Chen
  • David K Gifford

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.

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  • Rujian Chen & David K Gifford, 2017. "Differential chromatin profiles partially determine transcription factor binding," PLOS ONE, Public Library of Science, vol. 12(7), pages 1-10, July.
    • Handle: RePEc:plo:pone00:0179411
    DOI: 10.1371/journal.pone.0179411
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    References listed on IDEAS

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    1. Rajagopal, 2014. "The Human Factors," Palgrave Macmillan Books, in: Architecting Enterprise, chapter 9, pages 225-249, Palgrave Macmillan.
    2. Shaun Mahony & Matthew D Edwards & Esteban O Mazzoni & Richard I Sherwood & Akshay Kakumanu & Carolyn A Morrison & Hynek Wichterle & David K Gifford, 2014. "An Integrated Model of Multiple-Condition ChIP-Seq Data Reveals Predeterminants of Cdx2 Binding," PLOS Computational Biology, Public Library of Science, vol. 10(3), pages 1-14, March.
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