3D genome architecture coordinates trans and cis regulation of differentially expressed ear and tassel genes in maize.

Sun, Yonghao, Dong, Liang, Zhang, Ying, Lin, Da, Xu, Weize, Ke, Changxiong, Han, Linqian, Deng, Lulu, Li, Guoliang, Jackson, David, Li, Xingwang, Yang, Fang (June 2020) 3D genome architecture coordinates trans and cis regulation of differentially expressed ear and tassel genes in maize. Genome Biology, 21 (1). p. 143. ISSN 1474-760X

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Abstract

BACKGROUND: Maize ears and tassels are two separate types of inflorescence which are initiated by similar developmental processes but gradually develop distinct architectures. However, coordinated trans and cis regulation of differentially expressed genes determining ear and tassel architecture within the 3D genome context is largely unknown. RESULTS: We identify 56,055 and 52,633 open chromatin regions (OCRs) in developing maize ear and tassel primordia using ATAC-seq and characterize combinatorial epigenome features around these OCRs using ChIP-seq, Bisulfite-seq, and RNA-seq datasets. Our integrative analysis of coordinated epigenetic modification and transcription factor binding to OCRs highlights the cis and trans regulation of differentially expressed genes in ear and tassel controlling inflorescence architecture. We further systematically map chromatin interactions at high-resolution in corresponding tissues using in situ digestion-ligation-only Hi-C (DLO Hi-C). The extensive chromatin loops connecting OCRs and genes provide a 3D view on cis- and trans-regulatory modules responsible for ear- and tassel-specific gene expression. We find that intergenic SNPs tend to locate in distal OCRs, and our chromatin interaction maps provide a potential mechanism for trait-associated intergenic SNPs that may contribute to phenotypic variation by influencing target gene expression through chromatin loops. CONCLUSIONS: Our comprehensive epigenome annotations and 3D genome maps serve as valuable resource and provide a deep understanding of the complex regulatory mechanisms of genes underlying developmental and morphological diversities between maize ear and tassel.

Item Type:	Paper
Subjects:	bioinformatics bioinformatics > genomics and proteomics > genetics & nucleic acid processing > DNA, RNA structure, function, modification bioinformatics > genomics and proteomics > genetics & nucleic acid processing bioinformatics > genomics and proteomics organism description > plant > maize bioinformatics > genomics and proteomics > genetics & nucleic acid processing > DNA, RNA structure, function, modification > genes, structure and function > gene expression bioinformatics > genomics and proteomics > genetics & nucleic acid processing > DNA, RNA structure, function, modification > genes, structure and function > gene regulation bioinformatics > genomics and proteomics > genetics & nucleic acid processing > DNA, RNA structure, function, modification > genes, structure and function > gene regulation bioinformatics > genomics and proteomics > genetics & nucleic acid processing > DNA, RNA structure, function, modification > genes, structure and function organs, tissues, organelles, cell types and functions > tissues types and functions > inflorescence organs, tissues, organelles, cell types and functions bioinformatics > genomics and proteomics > genetics & nucleic acid processing > DNA, RNA structure, function, modification > single nucleotide polymorphism organs, tissues, organelles, cell types and functions > tissues types and functions
CSHL Authors:	Jackson, David P.
Communities:	CSHL labs > Jackson lab
SWORD Depositor:	CSHL Elements
Depositing User:	CSHL Elements
Date:	16 June 2020
Date Deposited:	06 May 2021 15:06
Last Modified:	01 Feb 2024 18:51
PMCID:	PMC7296987
URI:	https://repository.cshl.edu/id/eprint/40002

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