Binding of PtoRAP2.12 to demethylated and accessible chromatin regions in the PtoGntK promoter stimulates growth of poplar

IF 8.3 1区生物学 Q1 PLANT SCIENCES

New Phytologist Pub Date : 2024-11-01 DOI:10.1111/nph.20228

Yuling He, Jiaxuan Zhou, Chenfei Lv, Jinhan Zhang, Leishi Zhong, Donghai Zhang, Peng Li, Liang Xiao, Mingyang Quan, Dan Wang, Deqiang Zhang, Qingzhang Du

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引用次数: 0

Abstract

DNA methylation is an essential epigenetic modification for gene regulation in plant growth and development. However, the precise mechanisms of DNA methylation remain poorly understood, especially in woody plants.
We employed whole-genome bisulfite sequencing (WGBS), assays for transposase-accessible chromatin using sequencing (ATAC-seq), and RNA-Seq to investigate epigenetic regulatory relationships in Populus tomentosa treated with DNA methylation inhibitor 5-azacitidine. Expression-quantitative trait methylation analysis (eQTM), epigenome-wide association study (EWAS), and joint linkage-linkage disequilibrium mapping were used to explore the epigenetic regulatory genes, and using CRISPR/Cas9 to identify the role of candidate genes.
Plant developmental abnormalities occurred when DNA methylation levels were substantially reduced. DNA methylation regulated 112 expressed genes via chromatin accessibility, of which 61 genes were significantly influenced by DNA methylation variation at the population level. One DNA methylation-regulated gene, PtoGntK, was located in a major quantitative trait locus (QTL) for poplar growth. Overexpression and CRISPR/Cas9 of PtoGntK revealed it affected poplar height and stem diameter. The PtoRAP2.12 was found to bind to the demethylated accessible region in the PtoGntK promoter, thereby promoting growth in poplar.
This study identified key genes with epigenetic regulation for plant growth and provides insights into epigenetic regulation mechanisms in woody plants.

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PtoRAP2.12 与 PtoGntK 启动子中去甲基化和可访问的染色质区域结合可刺激杨树生长

DNA 甲基化是植物生长发育过程中基因调控的重要表观遗传修饰。我们采用全基因组亚硫酸氢盐测序（WGBS）、转座酶可接触染色质测序（ATAC-seq）和 RNA-Seq 等方法，研究了用 DNA 甲基化抑制剂 5-azacitidine 处理的毛白杨（Populus tomentosa）的表观遗传调控关系。利用表达-定量性状甲基化分析（eQTM）、表观遗传组关联研究（EWAS）和联合连锁不平衡图谱探索表观遗传调控基因，并利用CRISPR/Cas9鉴定候选基因的作用。DNA甲基化通过染色质可及性调控了112个表达基因，其中61个基因在群体水平上受到DNA甲基化变异的显著影响。一个受DNA甲基化调控的基因PtoGntK位于杨树生长的一个主要数量性状基因座（QTL）上。PtoGntK的过表达和CRISPR/Cas9发现它会影响杨树的高度和茎直径。该研究发现了对植物生长具有表观遗传调控作用的关键基因，为木本植物的表观遗传调控机制提供了新的见解。

本文章由计算机程序翻译，如有差异，请以英文原文为准。

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来源期刊

New Phytologist 生物-植物科学

自引率

5.30%

发文量

728

期刊介绍： New Phytologist is an international electronic journal published 24 times a year. It is owned by the New Phytologist Foundation, a non-profit-making charitable organization dedicated to promoting plant science. The journal publishes excellent, novel, rigorous, and timely research and scholarship in plant science and its applications. The articles cover topics in five sections: Physiology & Development, Environment, Interaction, Evolution, and Transformative Plant Biotechnology. These sections encompass intracellular processes, global environmental change, and encourage cross-disciplinary approaches. The journal recognizes the use of techniques from molecular and cell biology, functional genomics, modeling, and system-based approaches in plant science. Abstracting and Indexing Information for New Phytologist includes Academic Search, AgBiotech News & Information, Agroforestry Abstracts, Biochemistry & Biophysics Citation Index, Botanical Pesticides, CAB Abstracts®, Environment Index, Global Health, and Plant Breeding Abstracts, and others.