PDF(Pubmed)
Abstract：
BACKGROUND: 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.
RESULTS: 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.
CONCLUSIONS: 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.
RESULTS: 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.
CONCLUSIONS: 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.
摘要：
背景：染色质动力学与需要获取DNA的过程密切相关，如转录调控。在基因调节区的染色质动力学中涉及的因子是一般调节因子(GRF)。这些因素有助于核小体耗尽区(NDR)的建立和维持。这些区域通过组蛋白沉积和核小体滑动被核小体填充，后者由许多ATP依赖性染色质重塑复合物催化，包括ISW1a。已经观察到，GRF可以充当核小体向NDR滑动的屏障。然而,目前尚不清楚不同GRF阻碍滑动活动的相对能力。
结果：考虑到这一点，我们对主要的GRF进行了比较分析，重点在于它们调节ISW1a介导的核小体滑动的能力。在核小体重塑试验中测试的GRF中，Rap1是唯一显示出阻碍ISW1a活性的因素。这种效应需要Rap1同源序列在连接子上的位置，该连接子在核小体重塑过程中成为进入DNA。此外,Rap1能够阻碍八聚体转移测定中的核小体组装。同时,Rap1对其靶序列显示出最高的亲和力和最长的停留时间，与其他测试的GRF相比。始终如一，通过对公开的全基因组数据的生物信息学分析，我们发现体内核小体占有率和组蛋白沉积与Rap1对其基因组靶序列的亲和力呈负相关。
结论：我们的发现指向DNA结合亲和力，相对于核小体核心的特定翻译位置的停留时间和位置是GRF在核小体滑动和组装中发挥作用的关键特征。
结果：考虑到这一点，我们对主要的GRF进行了比较分析，重点在于它们调节ISW1a介导的核小体滑动的能力。在核小体重塑试验中测试的GRF中，Rap1是唯一显示出阻碍ISW1a活性的因素。这种效应需要Rap1同源序列在连接子上的位置，该连接子在核小体重塑过程中成为进入DNA。此外,Rap1能够阻碍八聚体转移测定中的核小体组装。同时,Rap1对其靶序列显示出最高的亲和力和最长的停留时间，与其他测试的GRF相比。始终如一，通过对公开的全基因组数据的生物信息学分析，我们发现体内核小体占有率和组蛋白沉积与Rap1对其基因组靶序列的亲和力呈负相关。
结论：我们的发现指向DNA结合亲和力，相对于核小体核心的特定翻译位置的停留时间和位置是GRF在核小体滑动和组装中发挥作用的关键特征。
