Genome-Wide Identification of Regulatory DNA Elements in Crop Plants

  • Zhanjie Li
  • Kai WangEmail author
Part of the Methods in Molecular Biology book series (MIMB, volume 2072)


cis-regulatory DNA elements (CREs) are noncoding but functional DNA sequences. The binding of regulatory proteins into CRE regions leads to chromatin high sensitive to DNase I digestion, which are termed as DNase I hypersensitive sites (DHSs). These DHSs can be efficiently detected through DNase I digestion followed by high-throughput DNA sequencing (DNase-seq). Thus, DNase-seq has become a powerful technique for DHSs mapping at whole-genome level in both plants and animals. Here we describe a DNase-seq procedure modified and developed for crop plants. These plants usually contain large amounts of repetitive sequences and complex organic constituents. With the main improvement in nuclei isolation, this method has been successfully used in mapping DHSs in cotton and sugarcane.

Key words

DNase-seq Regulatory DNA elements Open chromatin Transcription factor occupancy 



This work was supported by the National Natural Science Foundation of China (31771862), Scientific Research Foundation of the Education Department of Fujian Province (JK2017016), and Natural Science Foundation of Fujian Province (2018J01711).


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© Springer Science+Business Media, LLC, part of Springer Nature 2020

Authors and Affiliations

  1. 1.Key Laboratory of Genetics, Breeding and Multiple Utilization of Crops, Ministry of Education, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems BiologyFujian Agriculture and Forestry UniversityFuzhouChina
  2. 2.National Engineering Research Center of SugarcaneFujian Agriculture and Forestry UniversityFuzhouChina

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