H3K4me2 reliably defines transcription factor binding regions in different cells

    Authors

    Y. Wang; X. M. Li;H. Y. Hu

    Comments

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    Abbreviated Journal Title

    Genomics

    Keywords

    ChIP-seq; Transcription factor binding regions; Histone modification; H3K4me2; CHIP-SEQ DATA; HUMAN GENOME; REGULATORY ELEMENTS; CHROMATIN-STRUCTURE; MOTIF DISCOVERY; DNA; REVEALS; IDENTIFICATION; DETERMINANTS; ORGANIZATION; Biotechnology & Applied Microbiology; Genetics & Heredity

    Abstract

    Histone modification (HM) patterns are widely applied to identify transcription factor binding regions (TFBRs). However, how frequently the TFBRs overlap with genomic regions enriched with certain types of HMs and which HM marker is more effective to pinpoint the TFBRs have not been systematically investigated. To address these problems, we studied 149 transcription factor (TF) ChIP-seq datasets and 33 HM ChIP-seq datasets in three cell lines. We found that on average about 90% of the TFBRs overlap with the H3K4me2-enriched regions. Moreover, the H3K4me2-enriched regions with stronger signals of H3K4me2 enrichment more likely overlap with the TFBRs than those with weaker signals. In addition, we showed that the H3K4me2-enriched regions together with the H3K27ac-enriched regions can greatly reduce false positive predictions of the TFBRs. Our study sheds light on the comprehensive discovery of the TFBRs using the HeK4me-enriched regions, especially when no good antibody to a TF exists. (C) 2014 The Authors. Published by Elsevier Inc. This is an open access article under the CC BY-NC-ND license (http://creativecommons.org/licenses/by-nc-nd/3.0/).

    Journal Title

    Genomics

    Volume

    103

    Issue/Number

    2-3

    Publication Date

    1-1-2014

    Document Type

    Article

    Language

    English

    First Page

    222

    Last Page

    228

    WOS Identifier

    WOS:000334823500008

    ISSN

    0888-7543

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