Measuring DNA mechanics on the genome scale.
Measuring DNA mechanics on the genome scale.
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在基因组规模上测量 DNA 力学。
DOI：
10.1038/s41586-020-03052-3
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发表时间：
2021-01
期刊：
影响因子：
64.8
通讯作者：
Ha T
中科院分区：
文献类型：
--
作者：
Basu A;Bobrovnikov DG;Qureshi Z;Kayikcioglu T;Ngo TTM;Ranjan A;Eustermann S;Cieza B;Morgan MT;Hejna M;Rube HT;Hopfner KP;Wolberger C;Song JS;Ha T
DNA的机械变形（如弯曲）是普遍存在的，并与多种细胞功能有关。然而，缺乏高通量的工具，直接测量DNA的机械性能限制了我们的理解是否以及如何DNA序列调节DNA力学和相关的染色质交易全基因组。我们开发了一种称为loop-seq的检测方法，用于高通量测量DNA的内在环化性-DNA弯曲性的代表。我们测量了270，806个50 bp DNA片段的内在环化率，这些片段跨越了S.酿酒酵母染色体V和其他基因组区域的序列，并且还包括随机序列。我们发现了转录起始位点（TSS）上游的序列编码区域具有异常低的可弯曲性。这些区域不利于核小体形成所需的急剧DNA弯曲，并且与已知的核小体耗尽区（NDRs）共中心。我们表明，生物化学低弯曲的接头DNA位于约40 bp远离核小体边缘抑制核小体滑入接头的染色质重塑INO 80。该观察解释了INO 80如何在没有任何其他因素的情况下通过阅读DNA机械景观来创建启动子近端核小体阵列。我们发现，染色体范围内，核小体的特点是高DNA弯曲附近的二分体和低弯曲附近的连接。这种对比度增加的核小体更深的基因体，这表明DNA力学在组织核小体远离TSS，其中核小体重塑占主导地位的一个以前不受重视的作用。重要的是，同义密码子的随机替换并不能保留这种对比，这表明密码子选择的进化受到选择压力的影响，以保留基因中序列编码的机械调节沿着。我们还提供了证据表明，通过TSS近端核小体的转录是由本地DNA力学的影响。总的来说，这第一个基因组规模的DNA力学地图暗示了具有广泛功能意义的“机械代码”。
Mechanical deformations of DNA such as bending are ubiquitous and implicated in diverse cellular functions. However, the lack of high-throughput tools to directly measure the mechanical properties of DNA limits our understanding of whether and how DNA sequences modulate DNA mechanics and associated chromatin transactions genome-wide. We developed an assay called loop-seq to measure the intrinsic cyclizability of DNA – a proxy for DNA bendability – in high throughput. We measured the intrinsic cyclizabilities of 270,806 50 bp DNA fragments that span the entire length of S. cerevisiae chromosome V and other genomic regions, and also include random sequences. We discovered sequence-encoded regions of unusually low bendability upstream of Transcription Start Sites (TSSs). These regions disfavor the sharp DNA bending required for nucleosome formation and are co-centric with known Nucleosome Depleted Regions (NDRs). We show biochemically that low bendability of linker DNA located about 40 bp away from a nucleosome edge inhibits nucleosome sliding into the linker by the chromatin remodeler INO80. The observation explains how INO80 can create promoter-proximal nucleosomal arrays in the absence of any other factors by reading the DNA mechanical landscape. We show that chromosome wide, nucleosomes are characterized by high DNA bendability near dyads and low bendability near the linkers. This contrast increases for nucleosomes deeper into gene bodies, suggesting that DNA mechanics plays a previously unappreciated role in organizing nucleosomes far from the TSS, where nucleosome remodelers predominate. Importantly, random substitution of synonymous codons does not preserve this contrast, suggesting that the evolution of codon choice has been impacted by selective pressure to preserve sequence-encoded mechanical modulations along genes. We also provide evidence that transcription through the TSS-proximal nucleosomes is impacted by local DNA mechanics. Overall, this first genome-scale map of DNA mechanics hints at a ‘mechanical code’ with broad functional implications.
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