title: De novo deciphering three-dimensional chromatin interaction and topological domains by wavelet transformation of epigenetic profiles.
abstract: Defining chromatin interaction frequencies and topological domains is a great challenge for the annotations of genome structures. Although the chromosome conformation capture (3C) and its derivative methods have been developed for exploring the global interactome, they are limited by high experimental complexity and costs. Here we describe a novel computational method, called CITD, for de novo prediction of the chromatin interaction map by integrating histone modification data. We used the public epigenomic data from human fibroblast IMR90 cell and embryonic stem cell (H1) to develop and test CITD, which can not only successfully reconstruct the chromatin interaction frequencies discovered by the Hi-C technology, but also provide additional novel details of chromosomal organizations. We predicted the chromatin interaction frequencies, topological domains and their states (e.g. active or repressive) for 98 additional cell types from Roadmap Epigenomics and ENCODE projects. A total of 131 protein-coding genes located near 78 preserved boundaries among 100 cell types are found to be significantly enriched in functional categories of the nucleosome organization and chromatin assembly. CITD and its predicted results can be used for complementing the topological domains derived from limited Hi-C data and facilitating the understanding of spatial principles underlying the chromosomal organization.
authors.affiliation: Department of Biological Sciences, Center for Systems Biology, The University of Texas at Dallas, Richardson, TX 75080, USA.
authors.forename: Yong
authors.initials: Y
authors.lastname: Chen
authors.affiliation: Department of Biological Sciences, Center for Systems Biology, The University of Texas at Dallas, Richardson, TX 75080, USA.
authors.forename: Yunfei
authors.initials: Y
authors.lastname: Wang
authors.affiliation: Department of Biological Sciences, Center for Systems Biology, The University of Texas at Dallas, Richardson, TX 75080, USA.
authors.forename: Zhenyu
authors.initials: Z
authors.lastname: Xuan
authors.affiliation: Department of Mathematical Sciences, The University of Texas at Dallas, Richardson, TX 75080, USA.
authors.forename: Min
authors.identifier: 0000-0002-4029-8716
authors.initials: M
authors.lastname: Chen
authors.affiliation: Department of Biological Sciences, Center for Systems Biology, The University of Texas at Dallas, Richardson, TX 75080, USA MOE Key Laboratory of Bioinformatics and Bioinformatics Division, Center for Synthetic and System Biology, TNLIST/Department Automation, Tsinghua University, Beijing 100084, China michael.zhang@utdallas.edu.
authors.forename: Michael Q
authors.initials: MQ
authors.lastname: Zhang
mesh_terms: D001665:Binding Sites; D002454:Cell Differentiation / Q000235:genetics; D002843:Chromatin / Q000737:chemistry* / Q000378:metabolism; D042002:Chromatin Assembly and Disassembly; D019295:Computational Biology / Q000379:methods; D030561:Databases, Nucleic Acid; D044127:Epigenesis, Genetic; D057890:Epigenomics / Q000379:methods; D006657:Histones / Q000378:metabolism; D006801:Humans; D015203:Reproducibility of Results; D014157:Transcription Factors
chemical_list: D002843:Chromatin; D006657:Histones; D014157:Transcription Factors