Department of Zoology, DAV University, Jalandhar, Punjab, India.
Department of Biotechnology, Panjab University, Chandigarh, India.
PLoS One. 2023 Aug 17;18(8):e0290035. doi: 10.1371/journal.pone.0290035. eCollection 2023.
The cis-regulatory data that help in transcriptional regulation is arranged into modular pieces of a few hundred base pairs called CRMs (cis-regulatory modules) and numerous binding sites for multiple transcription factors are prominent characteristics of these cis-regulatory modules. The present study was designed to localize transcription factor binding site (TFBS) clusters on twelve Anterior-posterior (A-P) genes in Tribolium castaneum and compare them to their orthologous gene enhancers in Drosophila melanogaster. Out of the twelve A-P patterning genes, six were gap genes (Kruppel, Knirps, Tailless, Hunchback, Giant, and Caudal) and six were pair rule genes (Hairy, Runt, Even-skipped, Fushi-tarazu, Paired, and Odd-skipped). The genes along with 20 kb upstream and downstream regions were scanned for TFBS clusters using the Motif Cluster Alignment Search Tool (MCAST), a bioinformatics tool that looks for set of nucleotide sequences for statistically significant clusters of non-overlapping occurrence of a given set of motifs. The motifs used in the current study were Hunchback, Caudal, Giant, Kruppel, Knirps, and Even-skipped. The results of the MCAST analysis revealed the maximum number of TFBS for Hunchback, Knirps, Caudal, and Kruppel in both D. melanogaster and T. castaneum, while Bicoid TFBS clusters were found only in D. melanogaster. The size of all the predicted TFBS clusters was less than 1kb in both insect species. These sequences revealed more transversional sites (Tv) than transitional sites (Ti) and the average Ti/Tv ratio was 0.75.
有助于转录调控的顺式调控数据被排列成几百个碱基对的模块，称为 CRMs（顺式调控模块），这些顺式调控模块的显著特征是有多个转录因子的多个结合位点。本研究旨在定位在 Tribolium castaneum 中的 12 个前后（A-P）基因上的转录因子结合位点（TFBS）簇，并将它们与其在 Drosophila melanogaster 中的同源基因增强子进行比较。在这 12 个 A-P 模式基因中，有 6 个是缺口基因（Kruppel、Knirps、Tailless、Hunchback、Giant 和 Caudal），6 个是配对规则基因（Hairy、Runt、Even-skipped、Fushi-tarazu、Paired 和 Odd-skipped）。使用 motif cluster alignment search tool（MCAST）扫描了基因及其上下游 20kb 区域的 TFBS 簇，MCAST 是一种生物信息学工具，用于查找给定 motif 集的核苷酸序列的集合，这些序列的出现是统计显著的非重叠簇。在本研究中使用的基序是 Hunchback、Caudal、Giant、Kruppel、Knirps 和 Even-skipped。MCAST 分析的结果显示，在 D. melanogaster 和 T. castaneum 中，Hunchback、Knirps、Caudal 和 Kruppel 的 TFBS 簇数量最多，而 Bicoid TFBS 簇仅在 D. melanogaster 中发现。在这两种昆虫中，所有预测的 TFBS 簇的大小都小于 1kb。这些序列显示出比转换位（Ti）更多的颠换位（Tv），平均 Ti/Tv 比为 0.75。
