3D genome architecture coordinates trans and cis regulation of differentially expressed ear and tassel genes in maize
3D genome architecture coordinates trans and cis regulation of differentially expressed ear and tassel genes in maize
复制标题
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
DOI：
10.1186/s13059-020-02063-7
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发表时间：
2020-06-16
期刊：
影响因子：
12.3
通讯作者：
Yang, Fang
中科院分区：
文献类型：
--
作者：
Sun, Yonghao;Dong, Liang;Yang, Fang
背景
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开始，但逐渐发展出不同的结构。然而，协调的反式和顺式调节差异表达的基因决定耳朵和雄穗结构内的3D基因组背景下，在很大程度上是未知的。
结果
我们使用ATAC-seq在发育中的玉米穗和雄穗原基中鉴定了56，055和52，633个开放染色质区域（OCR），并使用ChIP-seq，Bisulite-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。我们的综合分析协调表观遗传修饰和转录因子结合OCR突出的顺式和反式调节差异表达的基因在穗和雄穗控制花序结构。我们进一步系统地映射染色质的相互作用，在相应的组织中使用原位消化连接只有Hi-C（DLO Hi-C）的高分辨率。广泛的染色质环连接OCR和基因提供了一个三维视图的顺式和反式调控模块负责耳朵和雄穗特异性基因表达。我们发现，基因间的SNP往往位于远端的OCR，我们的染色质相互作用图谱提供了一个潜在的机制，性状相关的基因间的SNP，可能有助于表型变异，通过影响目标基因的表达，通过染色质环。
结论
我们全面的表观基因组注释和3D基因组图谱作为宝贵的资源，并提供了玉米穗和雄穗之间发育和形态差异的基因的复杂调控机制的深入理解。
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.