Chromatin spatial organization of wild type and mutant peanuts reveals high-resolution genomic architecture and interaction alterations

Abstract Background Three-dimensional (3D) chromatin organization provides a critical foundation to investigate gene expression regulation and cellular homeostasis. Results Here, we present the first 3D genome architecture maps in wild type and mutant allotetraploid peanut lines, which illustrate A/...

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Autores principales:	Xingguo Zhang, Manish K. Pandey, Jianping Wang, Kunkun Zhao, Xingli Ma, Zhongfeng Li, Kai Zhao, Fangping Gong, Baozhu Guo, Rajeev K. Varshney, Dongmei Yin
Formato:	article
Lenguaje:	EN
Publicado:	BMC 2021
Materias:	Peanut 3D structure Hi-C ATAC-seq Gene expression Gene regulation Biology (General) QH301-705.5 Genetics QH426-470
Acceso en línea:	https://doaj.org/article/819c2afb5f334da78f8db67e6364007d
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spelling	oai:doaj.org-article:819c2afb5f334da78f8db67e6364007d2021-11-21T12:41:58ZChromatin spatial organization of wild type and mutant peanuts reveals high-resolution genomic architecture and interaction alterations10.1186/s13059-021-02520-x1474-760Xhttps://doaj.org/article/819c2afb5f334da78f8db67e6364007d2021-11-01T00:00:00Zhttps://doi.org/10.1186/s13059-021-02520-xhttps://doaj.org/toc/1474-760XAbstract Background Three-dimensional (3D) chromatin organization provides a critical foundation to investigate gene expression regulation and cellular homeostasis. Results Here, we present the first 3D genome architecture maps in wild type and mutant allotetraploid peanut lines, which illustrate A/B compartments, topologically associated domains (TADs), and widespread chromatin interactions. Most peanut chromosomal arms (52.3%) have active regions (A compartments) with relatively high gene density and high transcriptional levels. About 2.0% of chromosomal regions switch from inactive to active (B-to-A) in the mutant line, harboring 58 differentially expressed genes enriched in flavonoid biosynthesis and circadian rhythm functions. The mutant peanut line shows a higher number of genome-wide cis-interactions than its wild-type. The present study reveals a new TAD in the mutant line that generates different chromatin loops and harbors a specific upstream AP2EREBP-binding motif which might upregulate the expression of the GA2ox gene and decrease active gibberellin (GA) content, presumably making the mutant plant dwarf. Conclusions Our findings will shed new light on the relationship between 3D chromatin architecture and transcriptional regulation in plants.Xingguo ZhangManish K. PandeyJianping WangKunkun ZhaoXingli MaZhongfeng LiKai ZhaoFangping GongBaozhu GuoRajeev K. VarshneyDongmei YinBMCarticlePeanut3D structureHi-CATAC-seqGene expressionGene regulationBiology (General)QH301-705.5GeneticsQH426-470ENGenome Biology, Vol 22, Iss 1, Pp 1-21 (2021)
institution	DOAJ
collection	DOAJ
language	EN
topic	Peanut 3D structure Hi-C ATAC-seq Gene expression Gene regulation Biology (General) QH301-705.5 Genetics QH426-470
spellingShingle	Peanut 3D structure Hi-C ATAC-seq Gene expression Gene regulation Biology (General) QH301-705.5 Genetics QH426-470 Xingguo Zhang Manish K. Pandey Jianping Wang Kunkun Zhao Xingli Ma Zhongfeng Li Kai Zhao Fangping Gong Baozhu Guo Rajeev K. Varshney Dongmei Yin Chromatin spatial organization of wild type and mutant peanuts reveals high-resolution genomic architecture and interaction alterations
description	Abstract Background Three-dimensional (3D) chromatin organization provides a critical foundation to investigate gene expression regulation and cellular homeostasis. Results Here, we present the first 3D genome architecture maps in wild type and mutant allotetraploid peanut lines, which illustrate A/B compartments, topologically associated domains (TADs), and widespread chromatin interactions. Most peanut chromosomal arms (52.3%) have active regions (A compartments) with relatively high gene density and high transcriptional levels. About 2.0% of chromosomal regions switch from inactive to active (B-to-A) in the mutant line, harboring 58 differentially expressed genes enriched in flavonoid biosynthesis and circadian rhythm functions. The mutant peanut line shows a higher number of genome-wide cis-interactions than its wild-type. The present study reveals a new TAD in the mutant line that generates different chromatin loops and harbors a specific upstream AP2EREBP-binding motif which might upregulate the expression of the GA2ox gene and decrease active gibberellin (GA) content, presumably making the mutant plant dwarf. Conclusions Our findings will shed new light on the relationship between 3D chromatin architecture and transcriptional regulation in plants.
format	article
author	Xingguo Zhang Manish K. Pandey Jianping Wang Kunkun Zhao Xingli Ma Zhongfeng Li Kai Zhao Fangping Gong Baozhu Guo Rajeev K. Varshney Dongmei Yin
author_facet	Xingguo Zhang Manish K. Pandey Jianping Wang Kunkun Zhao Xingli Ma Zhongfeng Li Kai Zhao Fangping Gong Baozhu Guo Rajeev K. Varshney Dongmei Yin
author_sort	Xingguo Zhang
title	Chromatin spatial organization of wild type and mutant peanuts reveals high-resolution genomic architecture and interaction alterations
title_short	Chromatin spatial organization of wild type and mutant peanuts reveals high-resolution genomic architecture and interaction alterations
title_full	Chromatin spatial organization of wild type and mutant peanuts reveals high-resolution genomic architecture and interaction alterations
title_fullStr	Chromatin spatial organization of wild type and mutant peanuts reveals high-resolution genomic architecture and interaction alterations
title_full_unstemmed	Chromatin spatial organization of wild type and mutant peanuts reveals high-resolution genomic architecture and interaction alterations
title_sort	chromatin spatial organization of wild type and mutant peanuts reveals high-resolution genomic architecture and interaction alterations
publisher	BMC
publishDate	2021
url	https://doaj.org/article/819c2afb5f334da78f8db67e6364007d
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Chromatin spatial organization of wild type and mutant peanuts reveals high-resolution genomic architecture and interaction alterations

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