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. 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. 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.

中文翻译：

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3D基因组架构协调玉米中差异表达的穗和雄穗基因的反式和顺式调控


玉米穗和雄穗是两种不同类型的花序，它们由相似的发育过程启动，但逐渐形成不同的结构。然而，在 3D 基因组背景下决定穗和雄穗结构的差异表达基因的协调反式和顺式调节在很大程度上是未知的。我们使用 ATAC-seq 识别了玉米穗和雄穗原基发育过程中的 56,055 和 52,633 个开放染色质区域 (OCR)，并使用 ChIP-seq、Bisulfite-seq 和 RNA-seq 数据集表征了这些 OCR 周围的组合表观基因组特征。我们对协调表观遗传修饰和转录因子与 OCR 结合的综合分析强调了穗和雄穗控制花序结构中差异表达基因的顺式和反式调节。我们进一步使用原位消化连接 Hi-C (DLO Hi-C) 以高分辨率系统地绘制相应组织中染色质相互作用的图谱。连接 OCR 和基因的广泛染色质环提供了负责穗和雄穗特异性基因表达的顺式和反式调节模块的 3D 视图。我们发现基因间 SNP 往往位于远端 OCR，并且我们的染色质相互作用图谱为性状相关的基因间 SNP 提供了潜在机制，可能通过染色质环影响靶基因表达而导致表型变异。我们全面的表观基因组注释和 3D 基因组图谱是宝贵的资源，有助于深入了解玉米穗和雄穗发育和形态多样性背后的基因复杂调控机制。