Interrogating Global Chromatin Interaction Network by High-Throughput Chromosome Conformation Capture (Hi-C) in Plants

Wenjing Wang; Longjian Niu; Chunhui Hou

doi:10.1007/978-1-0716-2253-7_5

Interrogating Global Chromatin Interaction Network by High-Throughput Chromosome Conformation Capture (Hi-C) in Plants

Methods Mol Biol. 2022:2484:55-67. doi: 10.1007/978-1-0716-2253-7_5.

Authors

Wenjing Wang^{1

2}, Longjian Niu¹, Chunhui Hou³

Affiliations

¹ Department of Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen, China.
² School of Life Science and Stake Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Hong Kong, China.
³ Department of Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen, China. houch@sustech.edu.cn.

PMID: 35461444
DOI: 10.1007/978-1-0716-2253-7_5

Abstract

High-throughput chromosome conformation capture (Hi-C) enables the global quantification of chromatin interaction frequency in eukaryotic nuclei. This method is based on in situ Hi-C, in which chromatin is cross-linked with formaldehyde, then digested with restriction enzyme. Biotin-labeled nucleotide is incorporated before the spatially adjacent DNA ends are ligated, making it possible to enrich specifically the chimeric ligation products for deep sequencing. In this chapter, we describe a modified in situ Hi-C protocol for the global chromatin interaction analysis in plants.

Keywords: 3D genome organization; Chromatin interaction; Chromosome conformation capture; High-throughput sequencing; In situ Hi-C; Plants.

Publication types

Research Support, Non-U.S. Gov't

MeSH terms

Cell Nucleus / genetics
Chromatin* / genetics
Chromosomes*
DNA
High-Throughput Nucleotide Sequencing / methods
Nucleic Acid Conformation
Plants / genetics

Substances

Chromatin
DNA