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Cited by 238Genomics and Chromatin DynamicsChromatin Remodeling and CancerChromosomal and Genetic Variations

Identification of significant chromatin contacts from HiChIP data by FitHiChIP

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Bhattacharyya, Sourya, Chandra, Vivek, Vijayanand, Pandurangan, Ay, Ferhat·2019·Nature Communications
DOI 10.1038/s41467-019-11950-yPMC PMC6748947

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Abstract

HiChIP/PLAC-seq is increasingly becoming popular for profiling 3D chromatin contacts among regulatory elements and for annotating functions of genetic variants. Here we describe FitHiChIP, a computational method for loop calling from HiChIP/PLAC-seq data, which jointly models the non-uniform coverage and genomic distance scaling of contact counts to compute statistical significance estimates. We also develop a technique to filter putative bystander loops that can be explained by stronger adjacent loops. Compared to existing methods, FitHiChIP performs better in recovering contacts reported by Hi-C, promoter capture Hi-C and ChIA-PET experiments and in capturing previously validated promoter-enhancer interactions. FitHiChIP loop calls are reproducible among replicates and are consistent across different experimental settings. Our work also provides a framework for differential HiChIP analysis with an option to utilize ChIP-seq data for further characterizing differential loops. Even though designed for HiChIP, FitHiChIP is also applicable to other conformation capture assays.

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  • Many computational algorithms for Hi-C analysis explicitly correct for distance decay, identifying significant interactions based on how unusual their contact frequency is at a given distance.

    “many computational algorithms for the analysis of data from Hi-C and related techniques explicitly correct for distance decay, identifying “significant interactions” based on how unusual their contact frequency is at a given distance [277, 468–471].”

    From Transcriptional enhancers and their communication with gene promoters (2021) · cites this paper as [469]

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References 53 · Cited by 238

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Authors
Bhattacharyya, S., Chandra, V., Vijayanand, P., & Ay, F.
Affiliations
La Jolla Institute for Immunology (US)
Corresponding author
Ay, Ferhat
ORCID
Venue
Nature Communications
Publisher
Springer Science and Business Media LLC
Published
2019-09-17
Volume
10
Issue
1
Pages
4221-4221
ISSN
2041-1723 (ISSN-L)
DOI
10.1038/s41467-019-11950-y
PMC
PMC6748947
OpenAlex
W2973702082
Cited by
238
References
53
Citations by year
2026: 30 · 2025: 30 · 2024: 61 · 2023: 39 · 2022: 28 · 2021: 32 · 2020: 12 · 2019: 6
FWCI
6.78
Type
journal article
Language
en
Open access
Licence
Locations
  • Nature Communications (publishedVersion, cc-by)
  • bioRxiv (Cold Spring Harbor Laboratory) (acceptedVersion, cc-by-nc-nd)
  • Europe PMC (PubMed Central) (publishedVersion, cc-by)
  • PubMed Central (publishedVersion, cc-by)
  • PubMed (publishedVersion)
  • ePrints Soton (University of Southampton) (acceptedVersion)
  • RePEc: Research Papers in Economics (submittedVersion)
  • DOAJ (DOAJ: Directory of Open Access Journals) (submittedVersion, cc-by-sa)
  • DOAJ (DOAJ: Directory of Open Access Journals) (submittedVersion)
Funders
U.S. Department of Health & Human Services | National Institutes of Health (R35-GM128938, R24-AI108564)
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
HiChIP, enhancer-promoter interactions, regulatory elements
MeSH terms
Animals, Binding Sites, Chromatin, Enhancer Elements, Genetic, Promoter Regions, Genetic, Computational Biology, Genomics, Chromatin Immunoprecipitation, Mice

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