DNA sequence influences hexasome orientation to regulate DNA accessibility
DNA sequence influences hexasome orientation to regulate DNA accessibility
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DOI：
10.1093/nar/gkz283
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发表时间：
2019-06-20
影响因子：
14.9
通讯作者：
Poirier, Michael G.
中科院分区：
文献类型：
--
作者：
Brehove, Matthew;Shatoff, Elan;Poirier, Michael G.
核小体是真核生物基因组的基本组成单位，含有约146个碱基对的DNA，包裹在一个组蛋白H3-H4四聚体和两个组蛋白H2 A-H2 B二聚体周围。通过去除H2 A-H2 B二聚体将核小体转化为六酶体是一个重要的调控事件，但其调控和功能后果尚未得到很好的理解。为了研究六酶体对DNA可及性的影响，我们使用Widom-601核小体定位序列（Nucleosome Positioning Sequence，NPs）的性质在体外形成均匀定向的六酶体。我们发现，在六酶体H2 A-H2 B远端侧的转录因子（TF）的DNA可及性与裸DNA相同，而在H2 A-H2 B近端侧的可及性降低了2倍，这是由于六酶体解包概率降低了2倍。然后，我们确定Widom-601 cDNA的23 bp区域负责形成均匀取向的六酶体。分析已发表的ChIP-exo数据的hexasome含有基因确定了两个DNA序列基序，与hexasome方向在体内，而ExoIII映射研究这些序列显示，他们产生均匀定向的hexasome在体外。这些结果表明，六酶体的方向，这是由潜在的DNA序列在体内的影响，是重要的调节DNA的可及性，以调节转录。
Nucleosomes, the fundamental organizing units of eukaryotic genomes, contain similar to 146 base pairs of DNA wrapped around a histone H3-H4 tetramer and two histone H2A-H2B dimers. Converting nucleosomes into hexasomes by removal of a H2A-H2B dimer is an important regulatory event, but its regulation and functional consequences are not well-understood. To investigate the influence of hexasomes on DNA accessibility, we used the property of the Widom-601 Nucleosome Positioning Sequence (NPS) to form homogeneously oriented hexasomes in vitro. We find that DNA accessibility to transcription factors (TF) on the hexasome H2A-H2B distal side is identical to naked DNA, while the accessibility on the H2A-H2B proximal side is reduced by 2-fold, which is due to a 2-fold reduction in hexasome unwrapping probability. We then determined that a 23 bp region of the Widom-601 NPS is responsible for forming homogeneously oriented hexasomes. Analysis of published ChIP-exo data of hexasome containing genes identified two DNA sequence motifs that correlate with hexasome orientation in vivo, while ExoIII mapping studies of these sequences revealed they generate homogeneously oriented hexasomes in vitro. These results indicate that hexasome orientation, which is influenced by the underlying DNA sequence in vivo, is important for modulating DNA accessibility to regulate transcription.