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Transposable elements orchestrate subgenome-convergent and -divergent transcription in common wheat

The success of common wheat as a global staple crop was largely attributed to its genomic diversity and redundancy due to the merge of different genomes, giving rise to the major question how subgenome-divergent and -convergent transcription is mediated and harmonized in a single cell. Here, we crea...

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Autores principales: Zhang, Yuyun, Li, Zijuan, Liu, Jinyi, Zhang, Yu’e, Ye, Luhuan, Peng, Yuan, Wang, Haoyu, Diao, Huishan, Ma, Yu, Wang, Meiyue, Xie, Yilin, Tang, Tengfei, Zhuang, Yili, Teng, Wan, Tong, Yiping, Zhang, Wenli, Lang, Zhaobo, Xue, Yongbiao, Zhang, Yijing
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Nature Publishing Group UK 2022
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9663577/
https://www.ncbi.nlm.nih.gov/pubmed/36376315
http://dx.doi.org/10.1038/s41467-022-34290-w
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author Zhang, Yuyun
Li, Zijuan
Liu, Jinyi
Zhang, Yu’e
Ye, Luhuan
Peng, Yuan
Wang, Haoyu
Diao, Huishan
Ma, Yu
Wang, Meiyue
Xie, Yilin
Tang, Tengfei
Zhuang, Yili
Teng, Wan
Tong, Yiping
Zhang, Wenli
Lang, Zhaobo
Xue, Yongbiao
Zhang, Yijing
author_facet Zhang, Yuyun
Li, Zijuan
Liu, Jinyi
Zhang, Yu’e
Ye, Luhuan
Peng, Yuan
Wang, Haoyu
Diao, Huishan
Ma, Yu
Wang, Meiyue
Xie, Yilin
Tang, Tengfei
Zhuang, Yili
Teng, Wan
Tong, Yiping
Zhang, Wenli
Lang, Zhaobo
Xue, Yongbiao
Zhang, Yijing
author_sort Zhang, Yuyun
collection PubMed
description The success of common wheat as a global staple crop was largely attributed to its genomic diversity and redundancy due to the merge of different genomes, giving rise to the major question how subgenome-divergent and -convergent transcription is mediated and harmonized in a single cell. Here, we create a catalog of genome-wide transcription factor-binding sites (TFBSs) to assemble a common wheat regulatory network on an unprecedented scale. A significant proportion of subgenome-divergent TFBSs are derived from differential expansions of particular transposable elements (TEs) in diploid progenitors, which contribute to subgenome-divergent transcription. Whereas subgenome-convergent transcription is associated with balanced TF binding at loci derived from TE expansions before diploid divergence. These TFBSs have retained in parallel during evolution of each diploid, despite extensive unbalanced turnover of the flanking TEs. Thus, the differential evolutionary selection of paleo- and neo-TEs contribute to subgenome-convergent and -divergent regulation in common wheat, highlighting the influence of TE repertory plasticity on transcriptional plasticity in polyploid.
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spelling pubmed-96635772022-11-15 Transposable elements orchestrate subgenome-convergent and -divergent transcription in common wheat Zhang, Yuyun Li, Zijuan Liu, Jinyi Zhang, Yu’e Ye, Luhuan Peng, Yuan Wang, Haoyu Diao, Huishan Ma, Yu Wang, Meiyue Xie, Yilin Tang, Tengfei Zhuang, Yili Teng, Wan Tong, Yiping Zhang, Wenli Lang, Zhaobo Xue, Yongbiao Zhang, Yijing Nat Commun Article The success of common wheat as a global staple crop was largely attributed to its genomic diversity and redundancy due to the merge of different genomes, giving rise to the major question how subgenome-divergent and -convergent transcription is mediated and harmonized in a single cell. Here, we create a catalog of genome-wide transcription factor-binding sites (TFBSs) to assemble a common wheat regulatory network on an unprecedented scale. A significant proportion of subgenome-divergent TFBSs are derived from differential expansions of particular transposable elements (TEs) in diploid progenitors, which contribute to subgenome-divergent transcription. Whereas subgenome-convergent transcription is associated with balanced TF binding at loci derived from TE expansions before diploid divergence. These TFBSs have retained in parallel during evolution of each diploid, despite extensive unbalanced turnover of the flanking TEs. Thus, the differential evolutionary selection of paleo- and neo-TEs contribute to subgenome-convergent and -divergent regulation in common wheat, highlighting the influence of TE repertory plasticity on transcriptional plasticity in polyploid. Nature Publishing Group UK 2022-11-14 /pmc/articles/PMC9663577/ /pubmed/36376315 http://dx.doi.org/10.1038/s41467-022-34290-w Text en © The Author(s) 2022, corrected publication 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 license, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons license, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons license 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 license, visit http://creativecommons.org/licenses/by/4.0/ (https://creativecommons.org/licenses/by/4.0/) .
spellingShingle Article
Zhang, Yuyun
Li, Zijuan
Liu, Jinyi
Zhang, Yu’e
Ye, Luhuan
Peng, Yuan
Wang, Haoyu
Diao, Huishan
Ma, Yu
Wang, Meiyue
Xie, Yilin
Tang, Tengfei
Zhuang, Yili
Teng, Wan
Tong, Yiping
Zhang, Wenli
Lang, Zhaobo
Xue, Yongbiao
Zhang, Yijing
Transposable elements orchestrate subgenome-convergent and -divergent transcription in common wheat
title Transposable elements orchestrate subgenome-convergent and -divergent transcription in common wheat
title_full Transposable elements orchestrate subgenome-convergent and -divergent transcription in common wheat
title_fullStr Transposable elements orchestrate subgenome-convergent and -divergent transcription in common wheat
title_full_unstemmed Transposable elements orchestrate subgenome-convergent and -divergent transcription in common wheat
title_short Transposable elements orchestrate subgenome-convergent and -divergent transcription in common wheat
title_sort transposable elements orchestrate subgenome-convergent and -divergent transcription in common wheat
topic Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9663577/
https://www.ncbi.nlm.nih.gov/pubmed/36376315
http://dx.doi.org/10.1038/s41467-022-34290-w
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