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Identification of significant chromatin contacts from HiChIP data by FitHiChIP

Author

Listed:
  • Sourya Bhattacharyya

    (La Jolla Institute for Immunology)

  • Vivek Chandra

    (La Jolla Institute for Immunology)

  • Pandurangan Vijayanand

    (La Jolla Institute for Immunology
    University of Southampton
    University of California San Diego)

  • Ferhat Ay

    (La Jolla Institute for Immunology
    University of California San Diego)

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.

Suggested Citation

  • Sourya Bhattacharyya & Vivek Chandra & Pandurangan Vijayanand & Ferhat Ay, 2019. "Identification of significant chromatin contacts from HiChIP data by FitHiChIP," Nature Communications, Nature, vol. 10(1), pages 1-14, December.
    • Handle: RePEc:nat:natcom:v:10:y:2019:i:1:d:10.1038_s41467-019-11950-y
    DOI: 10.1038/s41467-019-11950-y
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    Cited by:

    1. Brent S. Perlman & Noah Burget & Yeqiao Zhou & Gregory W. Schwartz & Jelena Petrovic & Zora Modrusan & Robert B. Faryabi, 2024. "Enhancer-promoter hubs organize transcriptional networks promoting oncogenesis and drug resistance," Nature Communications, Nature, vol. 15(1), pages 1-21, December.
    2. Mark W. Youngblood & Zeynep Erson-Omay & Chang Li & Hinda Najem & Süleyman Coșkun & Evgeniya Tyrtova & Julio D. Montejo & Danielle F. Miyagishima & Tanyeri Barak & Sayoko Nishimura & Akdes Serin Harma, 2023. "Super-enhancer hijacking drives ectopic expression of hedgehog pathway ligands in meningiomas," Nature Communications, Nature, vol. 14(1), pages 1-16, December.
    3. Theodore Sakellaropoulos & Catherine Do & Guimei Jiang & Giulia Cova & Peter Meyn & Dacia Dimartino & Sitharam Ramaswami & Adriana Heguy & Aristotelis Tsirigos & Jane A. Skok, 2024. "MethNet: a robust approach to identify regulatory hubs and their distal targets from cancer data," Nature Communications, Nature, vol. 15(1), pages 1-15, December.
    4. Umut Berkay Altıntaş & Ji-Heui Seo & Claudia Giambartolomei & Dogancan Ozturan & Brad J. Fortunato & Geoffrey M. Nelson & Seth R. Goldman & Karen Adelman & Faraz Hach & Matthew L. Freedman & Nathan A., 2024. "Decoding the epigenetics and chromatin loop dynamics of androgen receptor-mediated transcription," Nature Communications, Nature, vol. 15(1), pages 1-14, December.

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