JGM, Animals, Cell Line, Chromatin, Data Interpretation, Statistical, Genetic Techniques, Humans, Mice, Sequence Analysis, DNA
Curr Protoc 2021 Aug; 1(8):e174
Chromatin Interaction Analysis Using Paired-End Tag Sequencing (ChIA-PET) is an established method to map protein-mediated chromatin interactions. A limitation, however, is that it requires a hundred million cells per experiment, which hampers its broad application in biomedical research, particularly in studies in which it is impractical to obtain a large number of cells from rare samples. To reduce the required input cell number while retaining high data quality, we developed an in situ ChIA-PET protocol, which requires as few as 1 million cells. Here, we describe detailed step-by-step procedures for performing in situ ChIA-PET from cultured cells, including both an experimental protocol for sample preparation and data generation and a computational protocol for data processing and visualization using the ChIA-PIPE pipeline. As the protocol significantly simplifies the experimental procedure, reduces ligation noise, and decreases the required input of cells compared to previous versions of ChIA-PET protocols, it can be applied to generate high-resolution chromatin contact maps mediated by various protein factors for a wide range of human and mouse primary cells. © 2021 The Authors. Current Protocols published by Wiley Periodicals LLC. Basic Protocol 1: Sample preparation and data generation Support Protocol: Bridge linker preparation Basic Protocol 2: Data processing and visualization.
Wang, Ping; Feng, Yuliang; Zhu, Kun; Chai, Haoxi; Chang, Ya-Ting; Yang, Xiaofei; Liu, Xiyuan; Shen, Chen; Gega, Eva; Lee, Byoungkoo; Kim, Minji; Ruan, Xiaoan; and Ruan, Yijun, "In situ Chromatin Interaction Analysis Using Paired-End Tag Sequencing." (2021). Faculty Research 2021. 185.