Epigenetic regulation of seed-specific gene expression by DNA methylation valleys in castor bean

doi:10.1186/s12915-022-01259-6

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	Epigenetic regulation of seed-specific gene expression by DNA methylation valleys in castor bean
	Han, Bing; Wu, Di; Zhang, Yanyu; Li, De-Zhu; Xu, Wei; Liu, Aizhong
	2022
发表期刊	BMC BIOLOGY
卷号	20 期号:1 页码:57
摘要	Background: Understanding the processes governing angiosperm seed growth and development is essential both for fundamental plant biology and for agronomic purposes. Master regulators of angiosperm seed development are expressed in a seed-specific manner. However, it is unclear how this seed specificity of transcription is established. In some vertebrates, DNA methylation valleys (DMVs) are highly conserved and strongly associated with key developmental genes, but comparable studies in plants are limited to Arabidopsis and soybean. Castor bean (Ricinus communis) is a valuable model system for the study of seed biology in dicots and source of economically important castor oil. Unlike other dicots such as Arabidopsis and soybean, castor bean seeds have a relatively large and persistent endosperm throughout seed development, representing substantial structural differences in mature seeds. Here, we performed an integrated analysis of RNA-seq, whole-genome bisulfite sequencing, and ChIP-seq for various histone marks in the castor bean. Results: We present a gene expression atlas covering 16 representative tissues and identified 1162 seed-specific genes in castor bean (Ricinus communis), a valuable model for the study of seed biology in dicots. Upon whole-genome DNA methylation analyses, we detected 32,567 DMVs across five tissues, covering similar to 33% of the castor bean genome. These DMVs are highly hypomethylated during development and conserved across plant species. We found that DMVs have the potential to activate transcription, especially that of tissue-specific genes. Focusing on seed development, we found that many key developmental regulators of seed/endosperm development, including AGL61, AGL62, LEC1, LEC2, ABI3, and WRI1, were located within DMVs. ChIP-seq for five histone modifications in leaves and seeds clearly showed that the vast majority of histone modification peaks were enriched within DMVs, and their remodeling within DMVs has a critical role in the regulation of seed-specific gene expression. Importantly, further experiment analysis revealed that distal DMVs may act as cis-regulatory elements, like enhancers, to activate downstream gene expression. Conclusions: Our results point to the importance of DMVs and special distal DMVs behaving like enhancers, in the regulation of seed-specific genes, via the reprogramming of histone modifications within DMVs. Furthermore, these results provide a comprehensive understanding of the epigenetic regulator roles in seed development in castor bean and other important crops.
关键词	Seed-specific genes DNA methylation valleys Histone modifications Enhancer Castor bean RICINUS-COMMUNIS L. CENTRAL CELL ARABIDOPSIS EMBRYOGENESIS TRANSCRIPTION ENDOSPERM IDENTIFICATION ACCUMULATION PLANTS OIL
DOI	10.1186/s12915-022-01259-6
收录类别	SCI
WOS记录号	WOS:000762413400002
引用统计
文献类型	期刊论文
条目标识符	http://ir.kib.ac.cn/handle/151853/74781
专题	中国科学院昆明植物研究所
推荐引用方式 GB/T 7714	Han, Bing,Wu, Di,Zhang, Yanyu,et al. Epigenetic regulation of seed-specific gene expression by DNA methylation valleys in castor bean[J]. BMC BIOLOGY,2022,20(1):57.
APA	Han, Bing,Wu, Di,Zhang, Yanyu,Li, De-Zhu,Xu, Wei,&Liu, Aizhong.(2022).Epigenetic regulation of seed-specific gene expression by DNA methylation valleys in castor bean.BMC BIOLOGY,20(1),57.
MLA	Han, Bing,et al."Epigenetic regulation of seed-specific gene expression by DNA methylation valleys in castor bean".BMC BIOLOGY 20.1(2022):57.

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