Major in Integrative Bioscience and Biomedical Engineering, Graduate School of Science and Engineering, Waseda University, 2-2 Wakamatsu-cho, Shinjuku-ku, Tokyo 162-8480, Japan.
Department of Biology, Faculty of Education and Integrated Arts and Sciences, Waseda University, 2-2 Wakamatsu-cho, Shinjuku-ku, Tokyo 162-8480, Japan.
J Biochem. 2024 Mar 25;175(4):395-404. doi: 10.1093/jb/mvad111.
Numerous noncoding (nc)RNAs have been identified. Similar to the transcription of protein-coding (mRNA) genes, long noncoding (lnc)RNA genes and most of micro (mi)RNA genes are transcribed by RNA polymerase II (Pol II). In the transcription of mRNA genes, core promoters play an indispensable role; they support the assembly of the preinitiation complex (PIC). However, the structural and/or physical properties of the core promoters of lncRNA and miRNA genes remain largely unexplored, in contrast with those of mRNA genes. Using the core promoters of human genes, we analyzed the repertoire and population ratios of residing core promoter elements (CPEs) and calculated the following five DNA physical properties (DPPs): duplex DNA free energy, base stacking energy, protein-induced deformability, rigidity and stabilizing energy of Z-DNA. Here, we show that their CPE and DPP profiles are similar to those of mRNA gene promoters. Importantly, the core promoters of these three classes of genes have two highly distinctive sites in their DPP profiles around the TSS and position -27. Similar characteristics in DPPs are also found in the 5'-flanking regions of tRNA genes, indicating their common essential roles in transcription initiation over the kingdom of RNA polymerases.
已经鉴定出许多非编码 (nc)RNA。与蛋白质编码 (mRNA) 基因的转录相似，长非编码 (lnc)RNA 基因和大多数 micro (mi)RNA 基因由 RNA 聚合酶 II (Pol II) 转录。在 mRNA 基因的转录中，核心启动子起着不可或缺的作用；它们支持起始前复合物 (PIC) 的组装。然而，与 mRNA 基因相比，lncRNA 和 miRNA 基因的核心启动子的结构和/或物理特性在很大程度上仍未得到探索。使用人类基因的核心启动子，我们分析了核心启动子元件 (CPE) 的种类和群体比例，并计算了以下五个 DNA 物理特性 (DPP)：双链 DNA 自由能、碱基堆积能、蛋白诱导的可变形性、刚性和 Z-DNA 的稳定能。在这里，我们表明它们的 CPE 和 DPP 图谱与 mRNA 基因启动子的图谱相似。重要的是，这三类基因的核心启动子在 TSS 和 -27 位置周围的 DPP 图谱中具有两个高度独特的位点。tRNA 基因 5'侧翼区也存在 DPP 相似的特征，表明它们在 RNA 聚合酶王国的转录起始中具有共同的基本作用。
