Abedini Davar, Rashidi Monfared Sajad
Department of Biotechnology, Faculty of Agriculture, Tarbiat Modares University, Tehran, Iran.
Mol Biol Rep. 2018 Jun;45(3):335-345. doi: 10.1007/s11033-018-4166-z. Epub 2018 Mar 17.
A primary mechanism for controlling the development of multicellular organisms is transcriptional regulation, which carried out by transcription factors (TFs) that recognize and bind to their binding sites on promoter region. The distance from translation start site, order, orientation, and spacing between cis elements are key factors in the concentration of active nuclear TFs and transcriptional regulation of target genes. In this study, overrepresented motifs in cold and pathogenesis responsive genes were scanned via Gibbs sampling method, this method is based on detection of overrepresented motifs by means of a stochastic optimization strategy that searches for all possible sets of short DNA segments. Then, identified motifs were checked by TRANSFAC, PLACE and Soft Berry databases in order to identify putative TFs which, interact to the motifs. Several cis/trans regulatory elements were found using these databases. Moreover, cross-talk between cold and pathogenesis responsive genes were confirmed. Statistical analysis was used to determine distribution of identified motifs on promoter region. In addition, co-regulation analysis results, illustrated genes in pathogenesis responsive module are divided into two main groups. Also, promoter region was crunched to six subareas in order to draw the pattern of distribution of motifs in promoter subareas. The result showed the majority of motifs are concentrated on 700 nucleotides upstream of the translational start site (ATG). In contrast, this result isn't true in another group. In other words, there was no difference between total and compartmentalized regions in cold responsive genes.
控制多细胞生物发育的主要机制是转录调控，这是由转录因子（TFs）来执行的，转录因子能够识别并结合到启动子区域的结合位点上。顺式元件与翻译起始位点之间的距离、顺序、方向以及间隔，是影响活性核转录因子浓度和靶基因转录调控的关键因素。在本研究中，通过吉布斯采样法扫描了冷响应基因和病程相关基因中出现频率过高的基序，该方法基于一种随机优化策略来检测出现频率过高的基序，该策略会搜索所有可能的短DNA片段集合。然后，利用TRANSFAC、PLACE和Soft Berry数据库对鉴定出的基序进行检查，以识别与这些基序相互作用的推定转录因子。使用这些数据库发现了几个顺式/反式调控元件。此外，还证实了冷响应基因和病程相关基因之间的相互作用。采用统计分析来确定鉴定出的基序在启动子区域的分布。此外，共调控分析结果表明，病程相关模块中的基因分为两个主要组。同时，将启动子区域划分为六个子区域，以绘制基序在启动子子区域的分布模式。结果表明，大多数基序集中在翻译起始位点（ATG）上游700个核苷酸处。相比之下，另一组的情况并非如此。换句话说，冷响应基因的总区域和分区区域之间没有差异。
