Genome-wide chromatin accessibility landscape and dynamics of transcription factor networks during ovule and fiber development in cotton
-
Published:2023-07-31
Issue:1
Volume:21
Page:
-
ISSN:1741-7007
-
Container-title:BMC Biology
-
language:en
-
Short-container-title:BMC Biol
Author:
Bao Yu, Wei Yangyang, Liu Yuling, Gao Jingjing, Cheng Shuang, Liu Guanqing, You Qi, Liu Peng, Lu Quanwei, Li Pengtao, Zhang Shulin, Hu Nan, Han Yangshuo, Liu Shuo, Wu Yuechao, Yang Qingqing, Li Zhaoguo, Ao Guowei, Liu Fang, Wang Kunbo, Jiang Jiming, Zhang TaoORCID, Zhang Wenli, Peng Renhai
Abstract
AbstractBackgroundThe development of cotton fiber is regulated by the orchestrated binding of regulatory proteins tocis-regulatory elements associated with developmental genes. Thecis–transregulatory dynamics occurred throughout the course of cotton fiber development are elusive. Here we generated genome-wide high-resolution DNase I hypersensitive sites (DHSs) maps to understand the regulatory mechanisms of cotton ovule and fiber development.ResultsWe generated DNase I hypersensitive site (DHS) profiles from cotton ovules at 0 and 3 days post anthesis (DPA) and fibers at 8, 12, 15, and 18 DPA. We obtained a total of 1185 million reads and identified a total of 199,351 DHSs through ~ 30% unique mapping reads. It should be noted that more than half of DNase-seq reads mapped multiple genome locations and were not analyzed in order to achieve a high specificity of peak profile and to avoid bias from repetitive genomic regions. Distinct chromatin accessibilities were observed in the ovules (0 and 3 DPA) compared to the fiber elongation stages (8, 12, 15, and 18 DPA). Besides, the chromatin accessibility during ovules was particularly elevated in genomic regions enriched with transposable elements (TEs) and genes in TE-enriched regions were involved in ovule cell division. We analyzedcis-regulatory modules and revealed the influence of hormones on fiber development from the regulatory divergence of transcription factor (TF) motifs. Finally, we constructed a reliable regulatory network of TFs related to ovule and fiber development based on chromatin accessibility and gene co-expression network. From this network, we discovered a novel TF, WRKY46, which may shape fiber development by regulating the lignin content.ConclusionsOur results not only reveal the contribution of TEs in fiber development, but also predict and validate the TFs related to fiber development, which will benefit the research of cotton fiber molecular breeding.
Funder
National Natural Science Foundation of China Central Plains Science and Technology Innovation Leader Project Program for Innovative Research Team (in Science and Technology) in University of Henan Province Postgraduate Improvement Project of Henan Province Tianshan Innovation team program of the Xinjiang Uygur Autonomous Region State Key Laboratory of Cotton Biology Open Fund Postdoctoral Fund of Anyang Institute of Technology Fund of Priority Academic Program Development of Jiangsu Higher Education Institutions
Publisher
Springer Science and Business Media LLC
Subject
Cell Biology,Developmental Biology,Plant Science,General Agricultural and Biological Sciences,General Biochemistry, Genetics and Molecular Biology,Physiology,Ecology, Evolution, Behavior and Systematics,Structural Biology,Biotechnology
Reference119 articles.
1. Liuning Y, Morse RH. Chromatin opening and transactivator potentiation by RAP1 in saccharomyces cerevisiae. Mol Cell Biol. 1999;19:5279–88. 2. Wu C, Wong YC, Elgin SCR. The chromatin structure of specific genes: II. Disruption of chromatin structure during gene activity. Cell. 1979;16:807–14. 3. He HH, Meyer CA, Chen MW, Jordan VC, Brown M, Liu XS. Differential DNase I hypersensitivity reveals factor-dependent chromatin dynamics. Genome Res. 2012;22:1015–25. 4. John S, Sabo PJ, Thurman RE, Sung M-H, Biddie SC, Johnson TA, et al. Chromatin accessibility pre-determines glucocorticoid receptor binding patterns. Nat Genet. 2011;43:264–8. 5. Inoue K, Imai Y. Identification of novel transcription factors in osteoclast differentiation using genome-wide analysis of open chromatin determined by DNase-seq. J Bone Miner Res. 2014;29:1823–32.
Cited by
1 articles.
订阅此论文施引文献
订阅此论文施引文献,注册后可以免费订阅5篇论文的施引文献,订阅后可以查看论文全部施引文献
|
|