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H3K4me2 reliably defines transcription factor binding regions in different cells

机译：H3K4ME2可靠地定义不同细胞中的转录因子结合区域

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摘要

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.
机译：组蛋白修饰（HM）模式被广泛应用于鉴定转录因子结合区域（TFBR）。 然而，TFBRS与富含某些类型的HMS的基因组区域重叠的TFBR重叠频率，并且哪些HM标记更有效地确定TFBRS的TFBRS尚未得到系统地研究。 为了解决这些问题，我们在三个细胞系中研究了149个转录因子（TF）芯片-SEQ数据集和33 HM芯片SEQ数据集。 我们发现，平均约90％的TFBRS与H3K4ME2丰富的地区重叠。 此外，具有较强的H3K4ME2富集信号的H3K4ME2富集的区域更可能与TFBR重叠而不是具有较弱信号的TFBR。 此外，我们表明，H3K4ME2富集的地区与H3K27AC富集的地区一起可以大大减少TFBR的假阳性预测。 我们的研究揭示了使用HEK4ME富集的地区综合发现TFBR的综合发现，特别是当不存在TF的良好抗体时。

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  • 来源
    《Genomics》 |2014年第3期|共7页
  • 作者

    WangY.; LiX.; HuH.;

  • 作者单位

    Department of Electric Engineering and Computer Science University of Central Florida Orlando FL;

    Burnett School of Biomedical Science University of Central Florida Orlando FL 32816 United;

    Department of Electric Engineering and Computer Science University of Central Florida Orlando FL;

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  • 原文格式 PDF
  • 正文语种 eng
  • 中图分类 医学遗传学;
  • 关键词

    ChIP-seq; H3K4me2; Histone modification; Transcription factor binding regions;

    机译：芯片SEQ;H3K4ME2;组蛋白修饰;转录因子结合区域;

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