Genome-wide binding (ChIP-Seq) of histone-like protein (HstA) of Haloferax volcanii

Diverse studies including protemoics, genome-wide binding, and transcriptional profiling of the model halophile Halobacterium salinarum suggest that its putative histone protein acts not as a chromatin protein but a direct and indirect transcriptional regulator. Here, we characterise the putative histone (HstA) of another model halophile (Haloferax volcanii) with ChIP-Seq to understand its genome-wide binding, and compare it with binding patterns seen from histones, nucleoid-associated proteins, and transcription factors of Halobacterium salinarum, other archaea, and eukaryotes. Analysis of this data by visual inspection, start site occupancy profiles, DNA motif searching, and dinucleotide periodicity suggests that the binding mode of halophilic histones shares features with TFs, NAPs, and more typical archaeal/eukaryotic histones. Overall design: Examination of HstA binding in optimal conditions (rich media, 42°C, mid-exponential growth phase) using C-terminal HA-tagged HstA expressed in-trans under its native promoter.

多项涵盖蛋白质组学（proteomics）、全基因组结合分析及转录谱分析的研究，针对模式嗜盐古菌盐生盐杆菌（Halobacterium salinarum）展开，结果表明其推定组蛋白并非以染色质蛋白的形式发挥功能，而是兼具直接与间接转录调控作用。本研究通过染色质免疫共沉淀测序（ChIP-Seq）技术，对另一株模式嗜盐古菌沃氏盐盒菌（Haloferax volcanii）的推定组蛋白HstA进行表征，以解析其全基因组结合模式，并将其结合特征与盐生盐杆菌、其他古菌及真核生物的组蛋白、类核关联蛋白（nucleoid-associated proteins, NAPs）以及转录因子（transcription factors, TFs）的结合模式进行对比。通过目视检查、起始位点占据谱分析、DNA基序搜索及二核苷酸周期性分析对该数据进行解析后发现，嗜盐古菌组蛋白的结合模式与转录因子（TFs）、类核关联蛋白（NAPs）以及典型古菌/真核生物组蛋白的结合模式存在共有特征。实验整体设计：采用以自身天然启动子驱动、反式表达的C端HA标签融合HstA蛋白，对最优生长条件（丰富培养基、42℃、指数生长中期）下的HstA结合情况进行检测。