Prediction of cell-type-specific cohesin-mediated chromatin loops based on chromatin state.

Publisher: Academic Press Country of Publication: United States NLM ID: 9426302 Publication Model: Print-Electronic Cited Medium: Internet ISSN: 1095-9130 (Electronic) Linking ISSN: 10462023 NLM ISO Abbreviation: Methods Subsets: MEDLINE

Publication: Duluth, MN : Academic Press
Original Publication: San Diego : Academic Press, c1990-

Chromosomal Proteins, Non-Histone*/metabolism ; Chromosomal Proteins, Non-Histone*/genetics ; Cell Cycle Proteins*/metabolism ; Cell Cycle Proteins*/genetics ; Chromatin*/metabolism ; Chromatin*/genetics ; Cohesins* ; CCCTC-Binding Factor*/metabolism ; CCCTC-Binding Factor*/genetics; Humans ; YY1 Transcription Factor/metabolism ; YY1 Transcription Factor/genetics ; Nuclear Proteins/metabolism ; Nuclear Proteins/genetics ; Computational Biology/methods ; DNA-Binding Proteins/metabolism ; DNA-Binding Proteins/genetics ; Histones/metabolism ; Histones/genetics ; Phosphoproteins/metabolism ; Phosphoproteins/genetics ; Chromatin Immunoprecipitation Sequencing/methods

Chromatin loop is of crucial importance for the regulation of gene transcription. Cohesin is a type of chromatin-associated protein that mediates the interaction of chromatin through the loop extrusion. Cohesin-mediated chromatin interactions have strong cell-type specificity, posing a challenge for predicting chromatin loops. Existing computational methods perform poorly in predicting cell-type-specific chromatin loops. To address this issue, we propose a random forest model to predict cell-type-specific cohesin-mediated chromatin loops based on chromatin states identified by ChromHMM and the occupancy of related factors. Our results show that chromatin state is responsible for cell-type-specificity of loops. Using only chromatin states as features, the model achieved high accuracy in predicting cell-type-specific loops between two cell types and can be applied to different cell types. Furthermore, when chromatin states are combined with the occurrence frequency of CTCF, RAD21, YY1, and H3K27ac ChIP-seq peaks, more accurate prediction can be achieved. Our feature extraction method provides novel insights into predicting cell-type-specific chromatin loops and reveals the relationship between chromatin state and chromatin loop formation.
Competing Interests: Declaration of competing interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper.
(Copyright © 2024 Elsevier Inc. All rights reserved.)

Keywords: Cell-type-specificity; Chromatin loop; Chromatin state; Cohesin; Computational method

0 (RAD21 protein, human)
0 (CTCF protein, human)

Date Created: 20240426 Date Completed: 20240516 Latest Revision: 20240516

20240517

10.1016/j.ymeth.2024.04.014

38670416