Chow Chi-Nga, Tseng Kuan-Chieh, Hou Ping-Fu, Wu Nai-Yun, Lee Tzong-Yi, Chang Wen-Chi
Institute of Tropical Plant Sciences and Microbiology, College of Biosciences and Biotechnology, National Cheng Kung University, Tainan 70101, Taiwan.
Department of Life Sciences, College of Biosciences and Biotechnology, National Cheng Kung University, Tainan 70101, Taiwan.
Comput Struct Biotechnol J. 2022 Sep 5;20:4910-4920. doi: 10.1016/j.csbj.2022.08.058. eCollection 2022.
regulatory elements of promoters are essential for gene regulation by transcription factors (TFs). However, the regulatory roles of nonpromoter regions, TFs, and epigenetic marks remain poorly understood in plants. In this study, we characterized the regulatory regions of 53 TFs and 19 histone marks in 328 chromatin immunoprecipitation (ChIP-seq) datasets from . The genome-wide maps indicated that both promoters and regions around the transcription termination sites of protein-coding genes recruit the most TFs. The maps also revealed a diverse of histone combinations. The analysis suggested that exons play critical roles in the regulation of non-coding genes. Additionally, comparative analysis between heat-stress-responsive and nonresponsive genes indicated that the genes with distinct functions also exhibited substantial differences in -regulatory regions, histone regulation, and topologically associating domain (TAD) boundary organization. By integrating multiple high-throughput sequencing datasets, this study generated regulatory models for protein-coding genes, non-coding genes, and TAD boundaries to explain the complexity of transcriptional regulation.
启动子的调控元件对于转录因子（TFs）的基因调控至关重要。然而，在植物中，非启动子区域、转录因子和表观遗传标记的调控作用仍知之甚少。在本研究中，我们对来自328个染色质免疫沉淀（ChIP-seq）数据集的53个转录因子和19个组蛋白标记的调控区域进行了表征。全基因组图谱表明，蛋白质编码基因的启动子和转录终止位点周围区域招募的转录因子最多。这些图谱还揭示了多种组蛋白组合。分析表明，外显子在非编码基因的调控中起关键作用。此外，热应激响应基因和无响应基因之间的比较分析表明，具有不同功能的基因在调控区域、组蛋白调控和拓扑相关结构域（TAD）边界组织方面也存在显著差异。通过整合多个高通量测序数据集，本研究生成了蛋白质编码基因、非编码基因和TAD边界的调控模型，以解释转录调控的复杂性。
