Chinese Bulletin of Botany ›› 2021, Vol. 56 ›› Issue (6): 664-675.DOI: 10.11983/CBB21115

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Chromatin Accessibility and the Gene Expression Regulation in Plants

Zhanjie Li1, Yuan Qin1,2,*()   

  1. 1Fujian Provincial Key Laboratory of Haixia Applied Plant System Biology, Key Laboratory of Genetics, Breeding and Multiple Utilization of Crops, Ministry of Education, College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou 350002, China
    2College of Life Science, Fujian Agriculture and Forestry University, Fuzhou 350002, China
  • Received:2021-07-12 Accepted:2021-10-12 Online:2021-11-01 Published:2021-11-12
  • Contact: Yuan Qin

Abstract: The topological organization of nucleosomes across the genome is non-uniform. While densely arranged within constitutive heterochromatin, histones are depleted at regulatory loci. Chromatin accessibility is the degree to which nuclear macromolecules are able to physically contact with regulatory DNA. Following the development of next-generation sequencing technology, a variety of quantitative methods, including DNase-seq, ATAC-seq, MNase-seq and NOMe-seq, have been developed to measure genome-wide chromatin accessibility easily and efficiently. In this review, we first introduced the technical principles of the four principal methods for measuring chromatin accessibility. And then we summarized the critical biophysical determinants of chromatin accessibility, including nucleosome occupancy, histone modification and TFs combination. Finally, we described recent advances of chromatin regulation during development and stress responses in plants. Our goal is to provide a reference for researches about genome-wide chromatin accessibility mapping, identification of cis-regulatory elements, and the dissection of epigenetic and genetic regulatory networks.

Key words: chromatin accessibility, histone modification, DNase-seq, ATAC-seq, regulatory elements