Document Type

Article

Publication Date

8-2021

Publication Title

Curr Protoc

Keywords

JGM, Animals, Cell Line, Chromatin, Data Interpretation, Statistical, Genetic Techniques, Humans, Mice, Sequence Analysis, DNA

JAX Source

Curr Protoc 2021 Aug; 1(8):e174

Volume

1

Issue

8

First Page

174

Last Page

174

ISSN

2691-1299

PMID

34351700

DOI

https://doi.org/10.1002/cpz1.174

Abstract

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.

Comments

This is an open access article under the terms of the Creative Commons Attribution-NonCommercial-NoDerivs License.

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