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Computational modeling of chromatin accessibility identified important epigenomic regulators

Authors
  • Zhao, Yanding1, 1
  • Dong, Yadong1, 1
  • Hong, Wei1, 1
  • Jiang, Chongming1, 1
  • Yao, Kevin2
  • Cheng, Chao1, 1
  • 1 Baylor College of Medicine, Room ICTR 100D, One Baylor Plaza, Baylor College of Medicine, Houston, TX, 77030, USA , Houston (United States)
  • 2 Texas A&M University, College Station, TX, 77843, USA , College Station (United States)
Type
Published Article
Journal
BMC Genomics
Publisher
Springer (Biomed Central Ltd.)
Publication Date
Jan 08, 2022
Volume
23
Issue
1
Identifiers
DOI: 10.1186/s12864-021-08234-5
Source
Springer Nature
Keywords
Disciplines
  • Research
License
Green

Abstract

Chromatin accessibility is essential for transcriptional activation of genomic regions. It is well established that transcription factors (TFs) and histone modifications (HMs) play critical roles in chromatin accessibility regulation. However, there is a lack of studies that quantify these relationships. Here we constructed a two-layer model to predict chromatin accessibility by integrating DNA sequence, TF binding, and HM signals. By applying the model to two human cell lines (GM12878 and HepG2), we found that DNA sequences had limited power for accessibility prediction, while both TF binding and HM signals predicted chromatin accessibility with high accuracy. According to the HM model, HM features determined chromatin accessibility in a cell line shared manner, with the prediction power attributing to five core HM types. Results from the TF model indicated that chromatin accessibility was determined by a subset of informative TFs including both cell line-specific and generic TFs. The combined model of both TF and HM signals did not further improve the prediction accuracy, indicating that they provide redundant information in terms of chromatin accessibility prediction. The TFs and HM models can also distinguish the chromatin accessibility of proximal versus distal transcription start sites with high accuracy.

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