Dynamic remodeling of individual nucleosomes across a eukaryotic genome in response to transcriptional perturbation.
Dynamic remodeling of individual nucleosomes across a eukaryotic genome in response to transcriptional perturbation.
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DOI：
10.1371/journal.pbio.0060065
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发表时间：
2008-03-18
期刊：
影响因子：
9.8
通讯作者：
Iyer VR
中科院分区：
文献类型：
--
作者：
Shivaswamy S;Bhinge A;Zhao Y;Jones S;Hirst M;Iyer VR
真核生物基因组被包装成染色质，核小体构成其基本结构单元，但对于任何基因组，染色质的详细结构及其在单个核小体位置的动态重塑还没有得到完全的实验定义。我们使用超高通量测序技术来描绘在引起全基因组转录变化的生理扰动前后酵母基因组中单个核小体的重塑。近80%的基因组被定位的核小体所覆盖，核小体以与转录区域和转录因子结合位点相关的有限数量的刻板模式出现。对生理扰动作出反应的染色质重塑通常与一个或两个核小体在启动子中的驱逐、出现或重新定位有关，而不是更广泛的区域范围的变化。动态核小体重塑倾向于增加介导转录变化的转录因子结合位点的可及性。然而，即使在没有明显的转录变化的情况下，特定的核小体重排在启动子上也是明显的，这表明在染色质重塑和转录活性之间没有简单的、全球适用的关系。我们的研究提供了酵母基因组中单核小体重塑的详细的、高分辨率的动态图谱及其与全球转录变化的关系。真核生物基因组被包装在一个系统的层次结构中，以适应它在细胞核内的范围。然而，当转录机制必须访问基因组DNA来调节基因表达时，这种堆积对转录机制构成了障碍。基因组包装的一个基本方面是DNA缠绕在核小体周围--核小体是由组蛋白形成的结构--在转录过程中必须将其移位。在这项研究中，我们确定了所有与引起真核生物酿酒酵母全基因组转录变化的生理扰动相关的核小体移位。我们分离了细胞受热休克前后的核小体DNA，然后利用超高通量测序确定了这些DNA片段的末端，从而确定了核小体在基因组中的位置。我们确定了基因启动子上核小体置换的局部模式，发现核小体驱逐通常与激活有关，它们的出现与基因抑制有关。核小体重塑通常会改善DNA对转录调控因子的可及性，从而介导对热休克等应激的反应。然而，并不是所有的核小体重塑都与转录变化有关，这表明核小体重新定位和转录活性之间的关系不仅仅是竞争获得DNA的反映。超高通量测序被用来显示核小体在启动子上的独特的、局部的重新定位模式是整个基因组对生理刺激的转录反应的基础。
The eukaryotic genome is packaged as chromatin with nucleosomes comprising its basic structural unit, but the detailed structure of chromatin and its dynamic remodeling in terms of individual nucleosome positions has not been completely defined experimentally for any genome. We used ultra-high–throughput sequencing to map the remodeling of individual nucleosomes throughout the yeast genome before and after a physiological perturbation that causes genome-wide transcriptional changes. Nearly 80% of the genome is covered by positioned nucleosomes occurring in a limited number of stereotypical patterns in relation to transcribed regions and transcription factor binding sites. Chromatin remodeling in response to physiological perturbation was typically associated with the eviction, appearance, or repositioning of one or two nucleosomes in the promoter, rather than broader region-wide changes. Dynamic nucleosome remodeling tends to increase the accessibility of binding sites for transcription factors that mediate transcriptional changes. However, specific nucleosomal rearrangements were also evident at promoters even when there was no apparent transcriptional change, indicating that there is no simple, globally applicable relationship between chromatin remodeling and transcriptional activity. Our study provides a detailed, high-resolution, dynamic map of single-nucleosome remodeling across the yeast genome and its relation to global transcriptional changes. The eukaryotic genome is packed in a systematic hierarchy to accommodate it within the confines of the cell's nucleus. This packing, however, presents an impediment to the transcription machinery when it must access genomic DNA to regulate gene expression. A fundamental aspect of genome packing is the spooling of DNA around nucleosomes—structures formed from histone proteins—which must be dislodged during transcription. In this study, we identified all the nucleosome displacements associated with a physiological perturbation causing genome-wide transcriptional changes in the eukaryote Saccharomyces cerevisiae. We isolated nucleosomal DNA before and after subjecting cells to heat shock, then identified the ends of these DNA fragments and, thereby, the location of nucleosomes along the genome, using ultra-high–throughput sequencing. We identified localized patterns of nucleosome displacement at gene promoters in response to heat shock, and found that nucleosome eviction was generally associated with activation and their appearance with gene repression. Nucleosome remodeling generally improved the accessibility of DNA to transcriptional regulators mediating the response to stresses like heat shock. However, not all nucleosomal remodeling was associated with transcriptional changes, indicating that the relationship between nucleosome repositioning and transcriptional activity is not merely a reflection of competing access to DNA. Ultra-high-throughput sequencing is used to show that distinct, localized patterns of nucleosome repositioning at promoters underlie the genome-wide transcriptional response to a physiological stimulus.
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