title: Genome-Wide Analysis of the Distinct Types of Chromatin Interactions in Arabidopsis thaliana.
abstract: The three-dimensional shapes of chromosomes regulate gene expression and genome function. Our knowledge of the role of chromatin interaction is evolving rapidly. Here, we present a study of global chromatin interaction patterns in Arabidopsis thaliana. High-throughput experimental techniques have been developed to map long-range interactions within chromatin. We have integrated data from multiple experimental sources including Hi-C, BS-seq, ChIP-chip and ChIP-seq data for 17 epigenetic marks and 35 transcription factors. We identified seven groups of interacting loci, which can be distinguished by their epigenetic profiles. Furthermore, the seven groups of interacting loci can be divided into three types of chromatin linkages based on expression status. We observed that two interacting loci sometimes share common epigenetic and transcription factor-binding profiles. Different groups of loci display very different relationships between epigenetic marks and the binding of transcription factors. Distinctive types of chromatin linkages exhibit different gene expression profiles. Our study unveils an entirely unexplored regulatory interaction, linking epigenetic profiles, transcription factor binding and the three-dimensional spatial organization of the Arabidopsis nuclear genome.
authors.affiliation: Department of Bioinformatics, The State Key Laboratory of Plant Physiology and Biochemistry, Institute of Plant Science, PR China.|James D. Watson Institute of Genome Sciences, Zhejiang University, Hangzhou, PR China.|College of Life Sciences, Zhejiang University, Hangzhou, PR China.
authors.forename: Jingjing
authors.initials: J
authors.lastname: Wang
authors.affiliation: Department of Bioinformatics, The State Key Laboratory of Plant Physiology and Biochemistry, Institute of Plant Science, PR China.|College of Life Sciences, Zhejiang University, Hangzhou, PR China.
authors.forename: Yincong
authors.initials: Y
authors.lastname: Zhou
authors.affiliation: Department of Bioinformatics, The State Key Laboratory of Plant Physiology and Biochemistry, Institute of Plant Science, PR China.|James D. Watson Institute of Genome Sciences, Zhejiang University, Hangzhou, PR China.|College of Life Sciences, Zhejiang University, Hangzhou, PR China.
authors.forename: Xue
authors.initials: X
authors.lastname: Li
authors.affiliation: Department of Bioinformatics, The State Key Laboratory of Plant Physiology and Biochemistry, Institute of Plant Science, PR China.|College of Life Sciences, Zhejiang University, Hangzhou, PR China.
authors.forename: Xianwen
authors.initials: X
authors.lastname: Meng
authors.affiliation: Department of Bioinformatics, The State Key Laboratory of Plant Physiology and Biochemistry, Institute of Plant Science, PR China.|Institute of Crop Science, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, PR China.|College of Life Sciences, Zhejiang University, Hangzhou, PR China.
authors.forename: Miao
authors.initials: M
authors.lastname: Fan
authors.affiliation: Department of Bioinformatics, The State Key Laboratory of Plant Physiology and Biochemistry, Institute of Plant Science, PR China.|College of Life Sciences, Zhejiang University, Hangzhou, PR China.
authors.forename: Hongjun
authors.initials: H
authors.lastname: Chen
authors.affiliation: Department of Bioinformatics, The State Key Laboratory of Plant Physiology and Biochemistry, Institute of Plant Science, PR China.|James D. Watson Institute of Genome Sciences, Zhejiang University, Hangzhou, PR China.|College of Life Sciences, Zhejiang University, Hangzhou, PR China.
authors.forename: Jitong
authors.initials: J
authors.lastname: Xue
authors.affiliation: Department of Bioinformatics, The State Key Laboratory of Plant Physiology and Biochemistry, Institute of Plant Science, PR China.|James D. Watson Institute of Genome Sciences, Zhejiang University, Hangzhou, PR China.|College of Life Sciences, Zhejiang University, Hangzhou, PR China.
authors.forename: Ming
authors.initials: M
authors.lastname: Chen
mesh_terms: D017360:Arabidopsis / Q000235:genetics / Q000378:metabolism*; D029681:Arabidopsis Proteins / Q000235:genetics / Q000378:metabolism*; D001665:Binding Sites / Q000235:genetics; D002843:Chromatin / Q000235:genetics / Q000378:metabolism*; D047369:Chromatin Immunoprecipitation; D019175:DNA Methylation; D044127:Epigenesis, Genetic; D057890:Epigenomics / Q000379:methods; D020869:Gene Expression Profiling; D018506:Gene Expression Regulation, Plant; D053263:Gene Regulatory Networks; D018745:Genome, Plant; D006657:Histones / Q000378:metabolism; D008745:Methylation; D008957:Models, Genetic; D011485:Protein Binding; D014157:Transcription Factors / Q000235:genetics / Q000378:metabolism*
chemical_list: D029681:Arabidopsis Proteins; D002843:Chromatin; D006657:Histones; D014157:Transcription Factors
keywords: Chromatin interactions; Epigenetic regulation; Hi-C; Long-range interactions; Three-dimensional organization; Transcription factors