一般调控因子对 ISW1a 复合物的核小体滑动活性产生不同影响

IF 4.3 2区 生物学 Q1 BIOLOGY Biological Research Pub Date : 2024-05-04 DOI:10.1186/s40659-024-00500-6
Andrea Oyarzún-Cisterna, Cristián Gidi, Fernanda Raiqueo, Roberto Amigo, Camila Rivas, Marcela Torrejón, José L. Gutiérrez
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引用次数: 0

摘要

染色质动态与转录调控等需要访问 DNA 的过程密切相关。参与基因调控区染色质动态的因子包括一般调控因子(GRFs)。这些因子有助于建立和维持核糖体缺失区(NDR)。这些区域通过组蛋白沉积和核小体滑动由核小体填充,后者由包括 ISW1a 在内的多种 ATP 依赖性染色质重塑复合物催化。据观察,GRFs 可作为阻止核小体滑向 NDRs 的屏障。然而,目前还不清楚不同 GRFs 阻碍滑动活动的相对能力。有鉴于此,我们对主要的 GRFs 进行了比较分析,重点分析它们调节 ISW1a 介导的核小体滑动的能力。在核小体重塑实验中测试的 GRFs 中,Rap1 是唯一能够阻碍 ISW1a 活性的因子。这种作用要求 Rap1 的同源序列位于连接体上,而连接体在核小体重塑过程中成为入口 DNA。此外,在八聚体转移试验中,Rap1 还能阻碍核小体的组装。同时,与测试的其他 GRF 相比,Rap1 对其目标序列的亲和力最高,停留时间最长。同样,通过对公开的全基因组数据进行生物信息学分析,我们发现体内核小体占据率和组蛋白沉积与 Rap1 对基因组中靶序列的亲和力成反比。我们的研究结果表明,DNA结合亲和力、停留时间和相对于核小体核心的特定翻译位置是GRFs的关键特征,它们在核小体滑动和组装中发挥着重要作用。
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General regulatory factors exert differential effects on nucleosome sliding activity of the ISW1a complex
Chromatin dynamics is deeply involved in processes that require access to DNA, such as transcriptional regulation. Among the factors involved in chromatin dynamics at gene regulatory regions are general regulatory factors (GRFs). These factors contribute to establishment and maintenance of nucleosome-depleted regions (NDRs). These regions are populated by nucleosomes through histone deposition and nucleosome sliding, the latter catalyzed by a number of ATP-dependent chromatin remodeling complexes, including ISW1a. It has been observed that GRFs can act as barriers against nucleosome sliding towards NDRs. However, the relative ability of the different GRFs to hinder sliding activity is currently unknown. Considering this, we performed a comparative analysis for the main GRFs, with focus in their ability to modulate nucleosome sliding mediated by ISW1a. Among the GRFs tested in nucleosome remodeling assays, Rap1 was the only factor displaying the ability to hinder the activity of ISW1a. This effect requires location of the Rap1 cognate sequence on linker that becomes entry DNA in the nucleosome remodeling process. In addition, Rap1 was able to hinder nucleosome assembly in octamer transfer assays. Concurrently, Rap1 displayed the highest affinity for and longest dwell time from its target sequence, compared to the other GRFs tested. Consistently, through bioinformatics analyses of publicly available genome-wide data, we found that nucleosome occupancy and histone deposition in vivo are inversely correlated with the affinity of Rap1 for its target sequences in the genome. Our findings point to DNA binding affinity, residence time and location at particular translational positions relative to the nucleosome core as the key features of GRFs underlying their roles played in nucleosome sliding and assembly.
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来源期刊
Biological Research
Biological Research 生物-生物学
CiteScore
10.10
自引率
0.00%
发文量
33
审稿时长
>12 weeks
期刊介绍: Biological Research is an open access, peer-reviewed journal that encompasses diverse fields of experimental biology, such as biochemistry, bioinformatics, biotechnology, cell biology, cancer, chemical biology, developmental biology, evolutionary biology, genetics, genomics, immunology, marine biology, microbiology, molecular biology, neuroscience, plant biology, physiology, stem cell research, structural biology and systems biology.
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