Department of Chemistry, Seoul National University, Seoul 08826, Korea.
Plant Genomics and Breeding Institute, Seoul National University, Seoul 08826, Korea.
Nucleic Acids Res. 2023 Oct 27;51(19):10261-10277. doi: 10.1093/nar/gkad710.
Three-dimensional (3D) chromatin structure is linked to transcriptional regulation in multicellular eukaryotes including plants. Taking advantage of high-resolution Hi-C (high-throughput chromatin conformation capture), we detected a small structural unit with 3D chromatin architecture in the Arabidopsis genome, which lacks topologically associating domains, and also in the genomes of tomato, maize, and Marchantia polymorpha. The 3D folding domain unit was usually established around an individual gene and was dependent on chromatin accessibility at the transcription start site (TSS) and transcription end site (TES). We also observed larger contact domains containing two or more neighboring genes, which were dependent on accessible border regions. Binding of transcription factors to accessible TSS/TES regions formed these gene domains. We successfully simulated these Hi-C contact maps via computational modeling using chromatin accessibility as input. Our results demonstrate that gene domains establish basic 3D chromatin architecture units that likely contribute to higher-order 3D genome folding in plants.
三维（3D）染色质结构与包括植物在内的多细胞真核生物的转录调控有关。利用高分辨率 Hi-C（高通量染色质构象捕获）技术，我们在拟南芥基因组中检测到了一种缺乏拓扑关联结构域的具有 3D 染色质结构的小结构单元，在番茄、玉米和地钱的基因组中也检测到了这种结构。3D 折叠结构域单元通常围绕单个基因建立，并依赖于转录起始位点（TSS）和转录终止位点（TES）处的染色质可及性。我们还观察到了包含两个或更多相邻基因的更大的接触域，这些接触域依赖于可及的边界区域。转录因子与可及的 TSS/TES 区域的结合形成了这些基因域。我们使用染色质可及性作为输入，通过计算建模成功模拟了这些 Hi-C 接触图谱。我们的结果表明，基因域建立了基本的 3D 染色质结构单元，这些单元可能有助于植物中更高阶的 3D 基因组折叠。
