Cargando…

Genome-wide chromatin accessibility landscape and dynamics of transcription factor networks during ovule and fiber development in cotton

BACKGROUND: The development of cotton fiber is regulated by the orchestrated binding of regulatory proteins to cis-regulatory elements associated with developmental genes. The cis–trans regulatory dynamics occurred throughout the course of cotton fiber development are elusive. Here we generated geno...

Descripción completa

Detalles Bibliográficos
Autores principales: 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, Tao, Zhang, Wenli, Peng, Renhai
Formato: Online Artículo Texto
Lenguaje:English
Publicado: BioMed Central 2023
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10391996/
https://www.ncbi.nlm.nih.gov/pubmed/37525156
http://dx.doi.org/10.1186/s12915-023-01665-4
_version_ 1785082849598111744
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, Tao
Zhang, Wenli
Peng, Renhai
author_facet 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, Tao
Zhang, Wenli
Peng, Renhai
author_sort Bao, Yu
collection PubMed
description BACKGROUND: The development of cotton fiber is regulated by the orchestrated binding of regulatory proteins to cis-regulatory elements associated with developmental genes. The cis–trans regulatory 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. RESULTS: We 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 analyzed cis-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. CONCLUSIONS: Our 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. SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s12915-023-01665-4.
format Online
Article
Text
id pubmed-10391996
institution National Center for Biotechnology Information
language English
publishDate 2023
publisher BioMed Central
record_format MEDLINE/PubMed
spelling pubmed-103919962023-08-02 Genome-wide chromatin accessibility landscape and dynamics of transcription factor networks during ovule and fiber development in cotton 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, Tao Zhang, Wenli Peng, Renhai BMC Biol Research Article BACKGROUND: The development of cotton fiber is regulated by the orchestrated binding of regulatory proteins to cis-regulatory elements associated with developmental genes. The cis–trans regulatory 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. RESULTS: We 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 analyzed cis-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. CONCLUSIONS: Our 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. SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s12915-023-01665-4. BioMed Central 2023-07-31 /pmc/articles/PMC10391996/ /pubmed/37525156 http://dx.doi.org/10.1186/s12915-023-01665-4 Text en © The Author(s) 2023 https://creativecommons.org/licenses/by/4.0/Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons licence, and indicate if changes were made. The images or other third party material in this article are included in the article's Creative Commons licence, unless indicated otherwise in a credit line to the material. If material is not included in the article's Creative Commons licence and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this licence, visit http://creativecommons.org/licenses/by/4.0/ (https://creativecommons.org/licenses/by/4.0/) . The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/ (https://creativecommons.org/publicdomain/zero/1.0/) ) applies to the data made available in this article, unless otherwise stated in a credit line to the data.
spellingShingle Research Article
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, Tao
Zhang, Wenli
Peng, Renhai
Genome-wide chromatin accessibility landscape and dynamics of transcription factor networks during ovule and fiber development in cotton
title Genome-wide chromatin accessibility landscape and dynamics of transcription factor networks during ovule and fiber development in cotton
title_full Genome-wide chromatin accessibility landscape and dynamics of transcription factor networks during ovule and fiber development in cotton
title_fullStr Genome-wide chromatin accessibility landscape and dynamics of transcription factor networks during ovule and fiber development in cotton
title_full_unstemmed Genome-wide chromatin accessibility landscape and dynamics of transcription factor networks during ovule and fiber development in cotton
title_short Genome-wide chromatin accessibility landscape and dynamics of transcription factor networks during ovule and fiber development in cotton
title_sort genome-wide chromatin accessibility landscape and dynamics of transcription factor networks during ovule and fiber development in cotton
topic Research Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10391996/
https://www.ncbi.nlm.nih.gov/pubmed/37525156
http://dx.doi.org/10.1186/s12915-023-01665-4
work_keys_str_mv AT baoyu genomewidechromatinaccessibilitylandscapeanddynamicsoftranscriptionfactornetworksduringovuleandfiberdevelopmentincotton
AT weiyangyang genomewidechromatinaccessibilitylandscapeanddynamicsoftranscriptionfactornetworksduringovuleandfiberdevelopmentincotton
AT liuyuling genomewidechromatinaccessibilitylandscapeanddynamicsoftranscriptionfactornetworksduringovuleandfiberdevelopmentincotton
AT gaojingjing genomewidechromatinaccessibilitylandscapeanddynamicsoftranscriptionfactornetworksduringovuleandfiberdevelopmentincotton
AT chengshuang genomewidechromatinaccessibilitylandscapeanddynamicsoftranscriptionfactornetworksduringovuleandfiberdevelopmentincotton
AT liuguanqing genomewidechromatinaccessibilitylandscapeanddynamicsoftranscriptionfactornetworksduringovuleandfiberdevelopmentincotton
AT youqi genomewidechromatinaccessibilitylandscapeanddynamicsoftranscriptionfactornetworksduringovuleandfiberdevelopmentincotton
AT liupeng genomewidechromatinaccessibilitylandscapeanddynamicsoftranscriptionfactornetworksduringovuleandfiberdevelopmentincotton
AT luquanwei genomewidechromatinaccessibilitylandscapeanddynamicsoftranscriptionfactornetworksduringovuleandfiberdevelopmentincotton
AT lipengtao genomewidechromatinaccessibilitylandscapeanddynamicsoftranscriptionfactornetworksduringovuleandfiberdevelopmentincotton
AT zhangshulin genomewidechromatinaccessibilitylandscapeanddynamicsoftranscriptionfactornetworksduringovuleandfiberdevelopmentincotton
AT hunan genomewidechromatinaccessibilitylandscapeanddynamicsoftranscriptionfactornetworksduringovuleandfiberdevelopmentincotton
AT hanyangshuo genomewidechromatinaccessibilitylandscapeanddynamicsoftranscriptionfactornetworksduringovuleandfiberdevelopmentincotton
AT liushuo genomewidechromatinaccessibilitylandscapeanddynamicsoftranscriptionfactornetworksduringovuleandfiberdevelopmentincotton
AT wuyuechao genomewidechromatinaccessibilitylandscapeanddynamicsoftranscriptionfactornetworksduringovuleandfiberdevelopmentincotton
AT yangqingqing genomewidechromatinaccessibilitylandscapeanddynamicsoftranscriptionfactornetworksduringovuleandfiberdevelopmentincotton
AT lizhaoguo genomewidechromatinaccessibilitylandscapeanddynamicsoftranscriptionfactornetworksduringovuleandfiberdevelopmentincotton
AT aoguowei genomewidechromatinaccessibilitylandscapeanddynamicsoftranscriptionfactornetworksduringovuleandfiberdevelopmentincotton
AT liufang genomewidechromatinaccessibilitylandscapeanddynamicsoftranscriptionfactornetworksduringovuleandfiberdevelopmentincotton
AT wangkunbo genomewidechromatinaccessibilitylandscapeanddynamicsoftranscriptionfactornetworksduringovuleandfiberdevelopmentincotton
AT jiangjiming genomewidechromatinaccessibilitylandscapeanddynamicsoftranscriptionfactornetworksduringovuleandfiberdevelopmentincotton
AT zhangtao genomewidechromatinaccessibilitylandscapeanddynamicsoftranscriptionfactornetworksduringovuleandfiberdevelopmentincotton
AT zhangwenli genomewidechromatinaccessibilitylandscapeanddynamicsoftranscriptionfactornetworksduringovuleandfiberdevelopmentincotton
AT pengrenhai genomewidechromatinaccessibilitylandscapeanddynamicsoftranscriptionfactornetworksduringovuleandfiberdevelopmentincotton