Ruler elements in chromatin remodelers set nucleosome array spacing and phasing.
Ruler elements in chromatin remodelers set nucleosome array spacing and phasing.
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DOI：
10.1038/s41467-021-23015-0
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发表时间：
2021-05-28
影响因子：
16.6
通讯作者：
Korber P
中科院分区：
文献类型：
--
作者：
Oberbeckmann E;Niebauer V;Watanabe S;Farnung L;Moldt M;Schmid A;Cramer P;Peterson CL;Eustermann S;Hopfner KP;Korber P
有规则间隔的核小体阵列主导染色质，通常通过与参考位点（如活性启动子）对齐而分阶段进行。核小体之间的距离（间距）以及分相位点和核小体之间的距离是如何确定的尚不清楚，特别是，依赖atp的染色质重塑物如何影响这些特征。在这里，我们使用全基因组重构来探索酿酒酵母atp依赖性重塑子如何产生规则间隔核小体的相控阵。我们发现重塑者有一个名为“尺子”的功能元素，它以重塑者特有的方式决定间距和相位。我们使用基于结构的诱变来识别和调整位于INO80重塑复合体的Nhp10和Arp8模块中的标尺元件。一般来说，我们提出一个重塑尺子调节核小体滑动方向偏差，以响应（epi）遗传信息。这最终概念化了重塑体介导的核小体动力学如何决定相对于其他核小体、DNA结合因子、DNA末端和DNA序列元件的稳定稳态核小体定位。尽管染色质重塑器已被证明可以使核小体阵列与屏障对齐，并在阵列内的核小体之间产生间距规则，但如何确定与屏障的距离和间距长度的绝对值仍不清楚。在这里，作者揭示重塑子包含一个“标尺”元素，在生成核小体阵列时设置重塑子特定的排列和间距距离。
Arrays of regularly spaced nucleosomes dominate chromatin and are often phased by alignment to reference sites like active promoters. How the distances between nucleosomes (spacing), and between phasing sites and nucleosomes are determined remains unclear, and specifically, how ATP-dependent chromatin remodelers impact these features. Here, we used genome-wide reconstitution to probe how Saccharomyces cerevisiae ATP-dependent remodelers generate phased arrays of regularly spaced nucleosomes. We find that remodelers bear a functional element named the ‘ruler’ that determines spacing and phasing in a remodeler-specific way. We use structure-based mutagenesis to identify and tune the ruler element residing in the Nhp10 and Arp8 modules of the INO80 remodeler complex. Generally, we propose that a remodeler ruler regulates nucleosome sliding direction bias in response to (epi)genetic information. This finally conceptualizes how remodeler-mediated nucleosome dynamics determine stable steady-state nucleosome positioning relative to other nucleosomes, DNA bound factors, DNA ends and DNA sequence elements. Although chromatin remodelers have been shown to align nucleosome arrays to barriers and to generate spacing regularity among nucleosomes within arrays, it has remained unclear how the distance to barrier and the spacing length are determined in absolute terms. Here, the authors reveal that remodelers contain a ‘ruler’ element that sets remodeler-specific alignment and spacing distances when generating nucleosome arrays.
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影响因子：
16
作者：
Badis, Gwenael;Chan, Esther T.;van Bakel, Harm;Pena-Castillo, Lourdes;Tillo, Desiree;Tsui, Kyle;Carlson, Clayton D.;Gossett, Andrea J.;Hasinoff, Michael J.;Warren, Christopher L.;Gebbia, Marinella;Talukder, Shaheynoor;Yang, Ally;Mnaimneh, Sanie;Terterov, Dimitri;Coburn, David;Yeo, Ai Li;Yeo, Zhen Xuan;Clarke, Neil D.;Lieb, Jason D.;Ansari, Aseem Z.;Nislow, Corey;Hughes, Timothy R.
通讯作者：
Hughes, Timothy R.
影响因子：
5.3
作者：
Gangaraju, Vamsi K.;Bartholomew, Blaine
通讯作者：
Bartholomew, Blaine
Snf2 同源物 Fun30 充当同型二聚体 ATP 依赖性染色质重塑酶。
DOI：
10.1074/jbc.m109.082149
发表时间：
2010-03-26
期刊：
The Journal of biological chemistry
影响因子：
--
作者：
Awad S;Ryan D;Prochasson P;Owen-Hughes T;Hassan AH
通讯作者：
Hassan AH
影响因子：
64.5
作者：
Hartley PD;Madhani HD
通讯作者：
Madhani HD
影响因子：
16.6
作者：
Brahma S;Ngubo M;Paul S;Udugama M;Bartholomew B
通讯作者：
Bartholomew B