Maps: Model-based analysis of long-range chromatin interactions from PLAC-seq and HiChIP experiments

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  • Juric, I.
    • Other Affiliation: Cleveland Clinic Foundation
  • Yu, M.
    • Other Affiliation: Ludwig Institute for Cancer Research
  • Abnousi, A.
    • Other Affiliation: Cleveland Clinic Foundation
  • Raviram, R.
    • Other Affiliation: Ludwig Institute for Cancer Research
  • Fang, R.
    • Other Affiliation: University of California, San Diego
  • Zhao, Y.
    • Other Affiliation: University of California, San Diego
  • Zhang, Y.
    • Other Affiliation: Ludwig Institute for Cancer Research
  • Qiu, Y.
    • Other Affiliation: University of California, San Diego
  • Yang, Y.
    • Affiliation: School of Medicine, Department of Genetics
  • Li, Y.
    • Affiliation: School of Medicine, Department of Genetics
  • Ren, B.
    • Other Affiliation: University of California, San Diego
  • Hu, M.
    • Other Affiliation: Cleveland Clinic Foundation
Abstract
  • Hi-C and chromatin immunoprecipitation (ChIP) have been combined to identify long-range chromatin interactions genome-wide at reduced cost and enhanced resolution, but extracting information from the resulting datasets has been challenging. Here we describe a computational method, MAPS, Model-based Analysis of PLAC-seq and HiChIP, to process the data from such experiments and identify long-range chromatin interactions. MAPS adopts a zero-truncated Poisson regression framework to explicitly remove systematic biases in the PLAC-seq and HiChIP datasets, and then uses the normalized chromatin contact frequencies to identify significant chromatin interactions anchored at genomic regions bound by the protein of interest. MAPS shows superior performance over existing software tools in the analysis of chromatin interactions from multiple PLAC-seq and HiChIP datasets centered on different transcriptional factors and histone marks.
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  • Article
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  • In Copyright
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  • Attribution 3.0 United States
Journal title
  • PLoS Computational Biology
Journal volume
  • 15
Journal issue
  • 4
Language
  • English
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  • Publisher
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  • 1553-734X
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  • Public Library of Science

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