Lorzadeh Alireza, Lopez Gutierrez Rodrigo, Jackson Linda, Moksa Michelle, Hirst Martin
Department of Microbiology and Immunology, Michael Smith Laboratories Centre for High-Throughput Biology, University of British Columbia.
Department of Microbiology and Immunology, Michael Smith Laboratories Centre for High-Throughput Biology, University of British Columbia; Canada's Michael Smith Genome Science Center, BC Cancer Agency;
J Vis Exp. 2017 Dec 12(130):56085. doi: 10.3791/56085.
We present a modified native chromatin immunoprecipitation sequencing (ChIP-seq) experimental protocol compatible with a Gaussian mixture distribution based analysis methodology (nucleosome density ChIP-seq; ndChIP-seq) that enables the generation of combined measurements of micrococcal nuclease (MNase) accessibility with histone modification genome-wide. Nucleosome position and local density, and the posttranslational modification of their histone subunits, act in concert to regulate local transcription states. Combinatorial measurements of nucleosome accessibility with histone modification generated by ndChIP-seq allows for the simultaneous interrogation of these features. The ndChIP-seq methodology is applicable to small numbers of primary cells inaccessible to cross-linking based ChIP-seq protocols. Taken together, ndChIP-seq enables the measurement of histone modification in combination with local nucleosome density to obtain new insights into shared mechanisms that regulate RNA transcription within rare primary cell populations.
我们提出了一种改良的天然染色质免疫沉淀测序（ChIP-seq）实验方案，该方案与基于高斯混合分布的分析方法（核小体密度ChIP-seq；ndChIP-seq）兼容，能够在全基因组范围内生成微球菌核酸酶（MNase）可及性与组蛋白修饰的联合测量结果。核小体位置和局部密度，以及其组蛋白亚基的翻译后修饰，共同作用以调节局部转录状态。通过ndChIP-seq生成的核小体可及性与组蛋白修饰的组合测量允许同时探究这些特征。ndChIP-seq方法适用于基于交联的ChIP-seq方案无法处理的少量原代细胞。综上所述，ndChIP-seq能够结合局部核小体密度测量组蛋白修饰，从而深入了解调节稀有原代细胞群体内RNA转录的共同机制。
