Pellegrini Matteo, Ferrari Roberto
Department of Molecular, Cell and Developmental, University of California, Los Angeles, CA, USA.
Methods Mol Biol. 2012;802:377-87. doi: 10.1007/978-1-61779-400-1_25.
The access of transcription factors and the replication machinery to DNA is regulated by the epigenetic state of chromatin. In eukaryotes, this complex layer of regulatory processes includes the direct methylation of DNA, as well as covalent modifications to histones. Using next-generation sequencers, it is now possible to obtain profiles of epigenetic modifications across a genome using chromatin immunoprecipitation followed by sequencing (ChIP-seq). This technique permits the detection of the binding of proteins to specific regions of the genome with high resolution. It can be used to determine the target sequences of transcription factors, as well as the positions of histones with specific modification of their N-terminal tails. Antibodies that selectively bind methylated DNA may also be used to determine the position of methylated cytosines. Here, we present a data analysis pipeline for processing ChIP-seq data, and discuss the limitations and idiosyncrasies of these approaches.
转录因子和复制机制对DNA的访问受染色质的表观遗传状态调控。在真核生物中，这一复杂的调控过程层包括DNA的直接甲基化以及组蛋白的共价修饰。利用新一代测序仪，现在可以通过染色质免疫沉淀测序（ChIP-seq）获得全基因组表观遗传修饰图谱。该技术能够高分辨率地检测蛋白质与基因组特定区域的结合。它可用于确定转录因子的靶序列，以及N端尾巴具有特定修饰的组蛋白的位置。选择性结合甲基化DNA的抗体也可用于确定甲基化胞嘧啶的位置。在此，我们展示了一个用于处理ChIP-seq数据的数据分析流程，并讨论了这些方法的局限性和特性。
