小柯机器人

科学家解析酿酒酵母基因的蛋白构架
2021-03-11 13:53

美国宾州州立大学B. Franklin Pugh小组在最新研究中,绘制出酿酒酵母基因组的高分辨蛋白构架图谱。2021年3月10日,《自然》杂志在线发表了这项成果。

研究人员介绍,染色质相关蛋白维持染色体完整性和基因调控,但这些蛋白在全基因组范围的构架尚不清楚。

研究人员使用染色质免疫沉淀、核酸外切酶消化和DNA测序(ChIP-exo/seq)来定义了酿酒酵母中的这种构架。研究人员确定21套图谱,由大约400种不同的蛋白质组成,这些蛋白质与DNA复制、着丝粒、亚端粒,转座子和RNA聚合酶(Pol)I、II和III的转录有关。复制蛋白包裹核小体,着丝粒缺少核小体,而阻抑蛋白在亚端粒X元件处包含三个核小体。
 
研究人员发现与Pol II相关的大多数启动子进化为调控区域的缺失,并且只有一个核心启动子。这些组成型启动子包含与+1核小体相邻的短无核小体区域(NFR),它们一起结合转录起始因子TFIID,从而形成预起始复合物。位置确定的绝缘子可以保护核心启动子免受上游事件的影响。一小部分启动子进化出了可诱导性的体系结构,从而序列特异性转录因子(ssTFs)形成了一个不同于NFR的核小体缺失区(NDR)。研究人员描述了ssTFs之间的结构相互作用、其同源辅因子和基因组。这些相互作用包括核小体和转录调节子RPD3-L、SAGA、NuA4、Tup1、中介体和SWI-SNF。
 
令人惊讶的是,研究人员没有检测到ssTFs和TFIID之间的相互作用,这表明这种相互作用不是稳定发生的。这项研究建立的基因诱导模型包含了ssTFs、辅因子和通用因子,例如TBP和TFIIB,但不包括TFIID。相比之下,组成型转录涉及TFIID,但不涉及与其辅因子结合的ssTF。由此,研究人员定义了一个由ssTFs调控的高度集成网络。 
 
附:英文原文

Title: A high-resolution protein architecture of the budding yeast genome

Author: Matthew J. Rossi, Prashant K. Kuntala, William K. M. Lai, Naomi Yamada, Nitika Badjatia, Chitvan Mittal, Guray Kuzu, Kylie Bocklund, Nina P. Farrell, Thomas R. Blanda, Joshua D. Mairose, Ann V. Basting, Katelyn S. Mistretta, David J. Rocco, Emily S. Perkinson, Gretta D. Kellogg, Shaun Mahony, B. Franklin Pugh

Issue&Volume: 2021-03-10

Abstract: The genome-wide architecture of chromatin-associated proteins that maintains chromosome integrity and gene regulation is not well defined. Here we use chromatin immunoprecipitation, exonuclease digestion and DNA sequencing (ChIP–exo/seq)1,2 to define this architecture in Saccharomyces cerevisiae. We identify 21 meta-assemblages consisting of roughly 400 different proteins that are related to DNA replication, centromeres, subtelomeres, transposons and transcription by RNA polymerase (Pol) I, II and III. Replication proteins engulf a nucleosome, centromeres lack a nucleosome, and repressive proteins encompass three nucleosomes at subtelomeric X-elements. We find that most promoters associated with Pol II evolved to lack a regulatory region, having only a core promoter. These constitutive promoters comprise a short nucleosome-free region (NFR) adjacent to a +1 nucleosome, which together bind the transcription-initiation factor TFIID to form a preinitiation complex. Positioned insulators protect core promoters from upstream events. A small fraction of promoters evolved an architecture for inducibility, whereby sequence-specific transcription factors (ssTFs) create a nucleosome-depleted region (NDR) that is distinct from an NFR. We describe structural interactions among ssTFs, their cognate cofactors and the genome. These interactions include the nucleosomal and transcriptional regulators RPD3-L, SAGA, NuA4, Tup1, Mediator and SWI–SNF. Surprisingly, we do not detect interactions between ssTFs and TFIID, suggesting that such interactions do not stably occur. Our model for gene induction involves ssTFs, cofactors and general factors such as TBP and TFIIB, but not TFIID. By contrast, constitutive transcription involves TFIID but not ssTFs engaged with their cofactors. From this, we define a highly integrated network of gene regulation by ssTFs.

DOI: 10.1038/s41586-021-03314-8

Source: https://www.nature.com/articles/s41586-021-03314-8

Nature:《自然》,创刊于1869年。隶属于施普林格·自然出版集团,最新IF:43.07
官方网址:http://www.nature.com/
投稿链接:http://www.nature.com/authors/submit_manuscript.html


本期文章:《自然》:Online/在线发表

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