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• W3034765448 abstract "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." @default.
• W3034765448 created "2020-06-19" @default.
• W3034765448 creator A5018445732 @default.
• W3034765448 creator A5018573028 @default.
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• W3034765448 creator A5054577004 @default.
• W3034765448 creator A5059548120 @default.
• W3034765448 creator A5069317995 @default.
• W3034765448 creator A5076986736 @default.
• W3034765448 creator A5080196425 @default.
• W3034765448 creator A5083514664 @default.
• W3034765448 creator A5083848380 @default.
• W3034765448 creator A5086818276 @default.
• W3034765448 date "2020-06-16" @default.
• W3034765448 modified "2023-10-11" @default.
• W3034765448 title "3D genome architecture coordinates trans and cis regulation of differentially expressed ear and tassel genes in maize" @default.
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