State Key Laboratory for Crop Genetics and Germplasm Enhancement, JiangSu Collaborative Innovation Center for Modern Crop Production (JCIC-MCP), Nanjing Agriculture University, Nanjing, Jiangsu 210095, China.
Sci Rep. 2016 Aug 25;6:32088. doi: 10.1038/srep32088.
Bidirectional gene pairs tend to be highly coregulated and function in similar biological processes in eukaryotic genomes. Structural features and functional consequences of bidirectional promoters (BDPs) have received considerable attention among diverse species. However, the underlying mechanisms responsible for the bidirectional transcription and coexpression of BDPs remain poorly understood in plants. In this study, we integrated DNase-seq, RNA-seq, ChIP-seq and MNase-seq data and investigated the effect of physical DNase I hypersensitive site (DHS) positions on the transcription of rice BDPs. We found that the physical position of a DHS relative to the TSS of bidirectional gene pairs can affect the expression of the corresponding genes: the closer a DHS is to the TSS, the higher is the expression level of the genes. Most importantly, we observed that the distribution of DHSs plays a significant role in the regulation of transcription and the coexpression of gene pairs, which are possibly mediated by orchestrating the positioning of histone marks and canonical nucleosomes around BDPs. Our results demonstrate that the combined actions of chromatin structures with DHSs, which contain functional cis-elements for interaction with transcriptional machinery, may play an important role in the regulation of the bidirectional transcription or coexpression in rice BDPs. Our findings may help to enhance the understanding of DHSs in the regulation of bidirectional gene pairs.
双向基因对往往在真核生物基因组中高度协同调控，并具有相似的生物学功能。在不同物种中，双向启动子（BDP）的结构特征和功能后果受到了相当多的关注。然而，BDP 双向转录和共表达的潜在机制在植物中仍知之甚少。在这项研究中，我们整合了 DNase-seq、RNA-seq、ChIP-seq 和 MNase-seq 数据，研究了物理 DNase I 超敏位点（DHS）位置对水稻 BDP 转录的影响。我们发现，相对于双向基因对 TSS 的 DHS 的物理位置可以影响相应基因的表达：DHS 越靠近 TSS，基因的表达水平越高。最重要的是，我们观察到 DHS 的分布在基因对的转录调控和共表达中起着重要作用，这可能是通过协调围绕 BDP 定位组蛋白标记和规范核小体来介导的。我们的结果表明，具有 DHS 的染色质结构的协同作用，其中包含与转录机制相互作用的功能顺式元件，可能在水稻 BDP 双向转录或共表达的调控中发挥重要作用。我们的发现可能有助于增强对 DHS 在双向基因对调控中的作用的理解。
