Department of Biology, Faculty of Education and Integrated Arts and Sciences, Waseda University, 2-2 Wakamatsu-cho, Shinjuku-ku, Tokyo, 162-8480, Japan.
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.
Curr Genet. 2018 Aug;64(4):945-958. doi: 10.1007/s00294-018-0815-y. Epub 2018 Feb 27.
Inverted repeat (IR) sequences are DNA sequences that read the same from 5' to 3' in each strand. Some IRs can form cruciforms under the stress of negative supercoiling, and these IRs are widely found in genomes. However, their biological significance remains unclear. The aim of the current study is to explore this issue further. We constructed the first Escherichia coli genome-wide comprehensive map of IRs with cruciform-forming potential. Based on the map, we performed detailed and quantitative analyses. Here, we report that IRs with cruciform-forming potential are statistically enriched in the following five regions: the adjacent regions downstream of the stop codon-coding sites (referred to as the stop codons), on and around the positions corresponding to mRNA ends (referred to as the gene ends), ~ 20 to ~45 bp upstream of the start codon-coding sites (referred to as the start codons) within the 5'-UTR (untranslated region), ~ 25 to ~ 60 bp downstream of the start codons, and promoter regions. For the adjacent regions downstream of the stop codons and on and around the gene ends, most of the IRs with a repeat unit length of ≥ 8 bp and a spacer size of ≤ 8 bp were parts of the intrinsic terminators, regardless of the location, and presumably used for Rho-independent transcription termination. In contrast, fewer IRs were present in the small region preceding the start codons. In E. coli, IRs with cruciform-forming potential are actively placed or excluded in the regulatory regions for the initiation and termination of transcription and translation, indicating their deep involvement or influence in these processes.
反向重复（IR）序列是指在每条链上从 5' 到 3' 读相同的 DNA 序列。一些 IR 可以在负超螺旋的压力下形成十字形结构，这些 IR 在基因组中广泛存在。然而，它们的生物学意义尚不清楚。本研究旨在进一步探讨这个问题。我们构建了第一个具有十字形形成潜力的大肠杆菌全基因组综合 IR 图谱。基于该图谱，我们进行了详细和定量的分析。在这里，我们报告称，具有十字形形成潜力的 IR 在以下五个区域中呈统计学富集：终止密码子编码位点（称为终止密码子）下游的相邻区域、mRNA 末端（称为基因末端）附近和周围、5'UTR（非翻译区）内起始密码子编码位点上游的20 至45bp（称为起始密码子）、25 至60bp 下游的起始密码子和启动子区域。对于终止密码子下游和基因末端附近的相邻区域，大多数重复单元长度≥8bp 且间隔大小≤8bp 的 IR 是内在终止子的一部分，无论位置如何，并且可能用于 Rho 非依赖性转录终止。相比之下，在起始密码子之前的小区域中存在的 IR 较少。在大肠杆菌中，具有十字形形成潜力的 IR 被积极地放置或排除在转录和翻译起始和终止的调节区域中，表明它们在这些过程中深度参与或影响。
