Genome-wide maps of HMGD1 and H1-bound nucleosomes.. Drosophila melanogaster

Chromatin architectural proteins interact with nucleosomes to modulate chromatin accessibility and higher-order chromatin structure. While these proteins are almost certainly important for gene regulation they have been studied far less than the core histone proteins. Here we describe the genomic distributions and functional roles of two chromatin architectural proteins: histone H1 and the high mobility group protein HMGD1, in Drosophila S2 cells. Using ChIP-seq, biochemical and gene specific approaches, we find that HMGD1 binds to highly accessible regulatory chromatin and active promoters. In contrast, H1 is primarily associated with heterochromatic regions marked with repressive histone marks. However, the ratio of HMGD1 to H1 is better correlated with chromatin accessibility, gene expression and nucleosome spacing variation than either protein alone suggesting a competitive mechanism between these proteins. Indeed, we show that HMGD1 and H1 compensate each other’s absence by binding reciprocally to chromatin resulting in changes to nucleosome repeat length and distinct gene expression patterns. Collectively our data suggest that dynamic and mutually exclusive binding of H1 and HMGD1 to nucleosomes and linker sequences may control the fluid chromatin structure that is required for transcriptional regulation. This study thus provides a framework to further study the interplay between chromatin architectural proteins and epigenetics in gene regulation. Overall design: ChIP-seq of HMGD1 and Histone H1 bound nucleosomes as well as MNase-seq of total nucleosome in Drosophila S2 cells

染色质结构蛋白（Chromatin architectural proteins）与核小体（nucleosomes）相互作用，可调控染色质可及性（chromatin accessibility）及高阶染色质结构（higher-order chromatin structure）。尽管这类蛋白无疑对基因调控（gene regulation）至关重要，但相较于核心组蛋白（core histone proteins），相关研究仍较为匮乏。本研究针对果蝇S2细胞（Drosophila S2 cells）中的两种染色质结构蛋白——组蛋白H1（histone H1）与高迁移率族蛋白HMGD1（high mobility group protein HMGD1），阐述其基因组分布特征与功能角色。本研究借助染色质免疫共沉淀测序（ChIP-seq）、生物化学与基因特异性分析技术，发现HMGD1可结合于高度开放的调控性染色质与活跃启动子区域。与之相反，H1主要定位于带有抑制性组蛋白修饰标记的异染色质区域。然而，相较于单独的任一蛋白，HMGD1与H1的比值与染色质可及性、基因表达及核小体间距变异的相关性更强，提示二者间存在竞争性结合机制。进一步实验证实，HMGD1与H1可通过相互置换结合染色质，彼此弥补对方的缺失，进而改变核小体重复长度并催生独特的基因表达谱。综合本研究数据可见，H1与HMGD1以动态互斥的方式结合核小体及连接序列，或可调控转录调控过程所需的动态染色质结构。本研究为进一步探究基因调控中染色质结构蛋白与表观遗传学（epigenetics）的相互作用提供了研究框架。实验设计概要：针对果蝇S2细胞中结合HMGD1与组蛋白H1的核小体进行染色质免疫共沉淀测序（ChIP-seq），并对总核小体进行微球菌核酸酶测序（MNase-seq）。