ChIPr: accurate prediction of cohesin-mediated 3D genome organization from 2D chromatin features
Open accessPublished version of a preprint
Abstract
The three-dimensional genome organization influences diverse nuclear processes. Here we present Chromatin Interaction Predictor (ChIPr), a suite of regression models based on deep neural networks, random forest, and gradient boosting to predict cohesin-mediated chromatin interaction strength between any two loci in the genome. The predictions of ChIPr correlate well with ChIA-PET data in four cell lines. The standard ChIPr model requires three experimental inputs: ChIP-Seq signals for RAD21, H3K27ac, and H3K27me3 but works well with just RAD21 signal. Integrative analysis reveals novel insights into the role of CTCF motif, its orientation, and CTCF binding on cohesin-mediated chromatin interactions.
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Cites
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- Authors
- Abbas, A., Chandratre, K., Gao, Y., Yuan, J., Zhang, M. Q., & Mani, R. S.
- Affiliations
- The University of Texas Southwestern Medical Center (US)
- The University of Texas at Dallas (US)
- Chinese Academy of Medical Sciences & Peking Union Medical College (CN)
- Harold C. Simmons Comprehensive Cancer Center (US)
- Corresponding author
- Zhang, Michael Q.
- Mani, Ram S.
- Venue
- Genome Biology
- Published
- 2024-01-12
- Volume
- 25
- Issue
- 1
- Pages
- 15-15
- ISSN
- 1465-6906 (ISSN-L)
- 1474-760X
- PMC
- PMC10785520
- OpenAlex
- W4390790903
- Cited by
- 13
- References
- 6
- Citations by year
- 2026: 4 · 2025: 3 · 2024: 6
- FWCI
- 1.76
- Type
- journal article
- Language
- en
- Open access
- gold
- doi.org
- Locations
- Genome biology (publishedVersion, cc-by)
- bioRxiv (Cold Spring Harbor Laboratory) (acceptedVersion, cc-by-nc-nd)
- PubMed Central (publishedVersion, cc-by)
- PubMed (publishedVersion)
- DOAJ (DOAJ: Directory of Open Access Journals) (submittedVersion, cc-by-sa)
- Funders
- NIH (R01CA245294)
- Cancer Prevention and Research Institute of Texas (RP230382)
- U.S. Department of Defense (W81XWH-21-1-0114)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Chromatin Dynamics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Chromatin Remodeling and Cancer
- Life Sciences › Agricultural and Biological Sciences › Plant Science › Chromosomal and Genetic Variations
- Keywords
- 3D genome organization, RAD21, H3K27ac, H3K27me3, CTCF binding, chromatin interaction prediction, deep neural network, gradient boosting, random forest, ChIA-PET
- MeSH terms
- CCCTC-Binding Factor, Cohesins, Chromatin, Chromosomal Proteins, Non-Histone, Cell Cycle Proteins
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