Epigenome profiling reveals distinctive regulatory features and cis-regulatory elements in pepper

文献类型： 外文期刊

第一作者： Yang, Hongji

作者： Yang, Hongji;Yu, Guorong;Lv, Zhidong;Li, Tonghui;Fu, Ying;Zhu, Zhangsheng;He, Hang;Qin, Guochen;Xue, Yan;Li, Tonghui;Wang, Xi;Liu, Feng;Liu, Feng;Guo, Guangjun;Wang, Ming;Zhong, Zhenhui

作者机构：

关键词： Epigenome; Pepper (Capsicum spp.); Cis-regulatory element; Promoter; Enhancer; Proteome; Development; Heat stress; Disease; Transcriptional regulation

期刊名称：GENOME BIOLOGY （ 影响因子：9.4； 五年影响因子：16.3 ）

ISSN： 1474-760X

年卷期： 2025 年 26 卷 1 期

页码：

收录情况： SCI

摘要： BackgroundPepper (Capsicum annuum) is one of the earliest and most widely cultivated vegetable crops worldwide. While the large and complex genome of pepper severely hampered the understanding of its functional genome, it also indicates a rich yet unexplored reservoir of regulatory elements (REs). In fact, variations in the REs represent a major driving force in evolution and domestication in both plants and animals. However, identification of the REs remains difficult especially for plants with complex genomes.ResultsHere, we present a comprehensive epigenomic landscape of Capsicum annuum, Zhangshugang (ST-8), including chromatin accessibility, histone modifications, DNA methylation, and transcriptome. We also develop comparative crosslinked immunoprecipitation mass spectrometry to reveal the proteome associated with certain chromatin features. Through integrated analysis of these epigenetic features, we profile promoters and enhancers involved in development, heat stress and cucumber mosaic virus challenges. We generate stress responsive expression networks composed of potential transcription activators and their target genes. Through population genetics analysis, we demonstrate that some regulatory elements show lower nucleotide diversity compare to other genomic regions during evolution.ConclusionsWe demonstrate that variations in the REs may contribute to more diversified and agronomically desired phenotypes. Our study provides a foundation not only for studying gene regulation, but also for targeted genetic and epigenetic manipulation for pepper improvement.

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