Differential chromatin profiles partially determine transcription factor binding
Name
journal.pone.0179411.pdf
Size
3.37 MB
Format
Adobe PDF
Checksum (MD5)
f11f03d03d2982045f616dd168477e5c
Author(s)
Chen, Rujian
Gifford, David K
Date Issued
July 2017
Journal
PLOS ONE
Publisher
Public Library of Science
Citation
Chen, Rujian, and Gifford, David K. “Differential Chromatin Profiles Partially Determine Transcription Factor Binding.” Edited by Roberto Mantovani. PLOS ONE 12, 7 (July 2017): e0179411 © 2017 Chen and Gifford
Version
Final published version
Abstract
This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited. 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.
MIT Department
Massachusetts Institute of Technology. Computer Science and Artificial Intelligence Laboratory
Massachusetts Institute of Technology. Department of Electrical Engineering and Computer Science
Terms of Use
Creative Commons Attribution 4.0 International License
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DOI of Published Version
https://doi.org/10.1371/JOURNAL.PONE.0179411
