核小体密度染色质免疫沉淀测序（Nucleosome Density ChIP-Seq）鉴定出与微球菌核酸酶（MNase）可及性相关的不同染色质修饰特征。

Nucleosome Density ChIP-Seq Identifies Distinct Chromatin Modification Signatures Associated with MNase Accessibility.

作者信息

Lorzadeh Alireza, Bilenky Misha, Hammond Colin, Knapp David J H F, Li Luolan, Miller Paul H, Carles Annaick, Heravi-Moussavi Alireza, Gakkhar Sitanshu, Moksa Michelle, Eaves Connie J, Hirst Martin

机构信息

Department of Microbiology and Immunology, Michael Smith Laboratories Centre for High-Throughput Biology, University of British Columbia, Vancouver, BC V6T 1Z4, Canada.

Canada's Michael Smith Genome Science Center, BC Cancer Agency Vancouver, BC V5Z 4S6, Canada.

出版信息

Cell Rep. 2016 Nov 15;17(8):2112-2124. doi: 10.1016/j.celrep.2016.10.055.

DOI:10.1016/j.celrep.2016.10.055

PMID:27851972

Abstract

Nucleosome position, density, and post-translational modification are widely accepted components of mechanisms regulating DNA transcription but still incompletely understood. We present a modified native ChIP-seq method combined with an analytical framework that allows MNase accessibility to be integrated with histone modification profiles. Application of this methodology to the primitive (CD34+) subset of normal human cord blood cells enabled genomic regions enriched in one versus two nucleosomes marked by histone 3 lysine 4 trimethylation (H3K4me3) and/or histone 3 lysine 27 trimethylation (H3K27me3) to be associated with their transcriptional and DNA methylation states. From this analysis, we defined four classes of promoter-specific profiles and demonstrated that a majority of bivalent marked promoters are heterogeneously marked at a single-cell level in this primitive cell type. Interestingly, extension of this approach to human embryonic stem cells revealed an altered relationship between chromatin modification state and nucleosome content at promoters, suggesting developmental stage-specific organization of histone methylation states.

摘要

核小体定位、密度和翻译后修饰是调节DNA转录机制中被广泛认可的组成部分，但仍未被完全理解。我们提出了一种改进的天然染色质免疫沉淀测序（ChIP-seq）方法，并结合了一个分析框架，该框架能够将微球菌核酸酶（MNase）可及性与组蛋白修饰谱整合起来。将这种方法应用于正常人脐带血细胞的原始（CD34+）亚群，使得富含一个或两个由组蛋白3赖氨酸4三甲基化（H3K4me3）和/或组蛋白3赖氨酸27三甲基化（H3K27me3）标记的核小体的基因组区域能够与其转录和DNA甲基化状态相关联。通过该分析，我们定义了四类启动子特异性图谱，并证明在这种原始细胞类型中，大多数双价标记启动子在单细胞水平上是异质性标记的。有趣的是，将这种方法扩展到人类胚胎干细胞后发现，启动子处染色质修饰状态与核小体含量之间的关系发生了改变，这表明组蛋白甲基化状态存在发育阶段特异性组织。