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Mapping accessible chromatin regions using Sono-Seq

机译:使用Sono-Seq映射可访问的染色质区域

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摘要

Disruptions in local chromatin structure often indicate features of biological interest such as regulatory regions. We find that soni-cation of cross-linked chromatin, when combined with a size-selection step and massively parallel short-read sequencing, can be used as a method (Sono-Seq) to map locations of high chromatin accessibility in promoter regions. Sono-Seq sites frequently correspond to actively transcribed promoter regions, as evidenced by their co-association with RNA Polymerase II ChIP regions, transcription start sites, histone H3 lysine 4 trimethylation (H3K4me3) marks, and CpG islands; signals over other sites, such as those bound by the CTCF insulator, are also observed. The pattern of breakage by Sono-Seq overlaps with, but is distinct from, that observed for FAIRE and DNase I hypersensitive sites. Our results demonstrate that Sono-Seq can be a useful and simple method by which to map many local alterations in chromatin structure. Furthermore, our results provide insights into the mapping of binding sites by using ChlP-Seq experiments and the value of reference samples that should be used in such experiments.
机译:局部染色质结构的破坏通常表明具有生物学意义的特征,例如调节区。我们发现,与尺寸选择步骤和大规模平行的短读测序结合使用时,交联染色质的超声可作为一种方法(Sono-Seq)来绘制启动子区域中高染色质可及性的位置。 Sono-Seq位点通常对应于活跃转录的启动子区域,如它们与RNA聚合酶II ChIP区,转录起始位点,组蛋白H3赖氨酸4三甲基化(H3K4me3)标记和CpG岛的共同关联所证明。还可以观察到其他位置(例如,由CTCF绝缘子束缚的位置)上的信号。 Sono-Seq的破坏模式与FAIRE和DNase I超敏位点所观察到的模式重叠,但与之不同。我们的结果表明,Sono-Seq可以是一种有用且简单的方法,通过它可以绘制染色质结构的许多局部变化。此外,我们的结果提供了通过ChlP-Seq实验对结合位点作图的了解,以及在此类实验中应使用的参考样品的价值。

著录项

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  • 作者单位

    Program in Computational Biology and Departments , Yale University, New Haven, CT 06520;

    Molecular, Cellular and Developmental Biology, Yale University, New Haven, CT 06520;

    Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520;

    Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115;

    Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115;

    Molecular, Cellular and Developmental Biology, Yale University, New Haven, CT 06520;

    Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115;

    Program in Computational Biology and Departments , Yale University, New Haven, CT 06520 Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520;

    Program in Computational Biology and Departments , Yale University, New Haven, CT 06520 Molecular, Cellular and Developmental Biology, Yale University, New Haven, CT 06520;

  • 收录信息 美国《科学引文索引》(SCI);美国《生物学医学文摘》(MEDLINE);美国《化学文摘》(CA);
  • 原文格式 PDF
  • 正文语种 eng
  • 中图分类
  • 关键词

    ChlP-Seq; ENCODE; formaldehyde cross-linking; sonication; DNA sequencing;

    机译:ChlP-Seq;编码甲醛交联;声波处理DNA测序;

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