Abera Bosenu, Dinka Hunduma, Dadi Hailu, Abera Habtamu
Department of Applied Biology, School of Applied Natural Science, Adama Science and Technology University, Adama, Ethiopia.
Bio and Emerging Technology Institute, Addis Ababa, Ethiopia.
Int J Genomics. 2025 May 26;2025:5574292. doi: 10.1155/ijog/5574292. eCollection 2025.
This study investigates the promoter region and regulatory elements of chicken insulin-like growth factor (IGF) and vasoactive intestinal polypeptide (VIP) genes associated with reproductive traits. Several in silico tools, such as Neural Network Promoter Prediction (NNPP), Multiple Expectation maximizations for Motif Elicitation (MEME-Suite), GC-Profiles, microsatellite prediction (MISA-web), CLC Genomics, Multiple Association Network Integration Algorithm (GeneMANIA), and Gene Ontology for Motifs (GOMO), were used to characterize the promoter regions and regulatory elements of IGF and VIP genes. The in silico analysis showed that the highest promoter prediction scores (1.0) for TSS were obtained for three gene sequences (IGFP4, VIP, and VIPR1), while the lowest promoter prediction score (0.8) was obtained for IGF1. The present analysis revealed that the best common motif, Motif II, resembles three major transcription factor families: zinc finger family, homeobox transcription factor family, and high-mobility group factor family, accounting for about 79.17%. This study found that 62.5% of the candidate transcription factors have interaction with the Wnt signalling pathway to regulate transcription. Key regulatory elements identified in this study, such as CPEB1, MAFB, SOX15, TCF7L2, TCF3, and TCF7, play critical roles in activating and repressing transcription, with significant implications for embryonic and nervous system development. In the current study, very rich CpG islands were identified in the gene body and promoter regions of IGF and VIP genes. Generally, in silico analysis of gene promoter regions and regulatory elements in IGF and VIP genes can be helpful for comprehending regulatory networks and gene expression patterns in promoter regions, which will guide new experimental studies in gene expression assays.
本研究调查了与生殖性状相关的鸡胰岛素样生长因子（IGF）和血管活性肠多肽（VIP）基因的启动子区域及调控元件。使用了多种计算机分析工具，如神经网络启动子预测（NNPP）、基序引出的多重期望最大化（MEME-Suite）、GC分布图、微卫星预测（MISA-web）、CLC基因组学、多重关联网络整合算法（GeneMANIA）以及基序基因本体（GOMO），来表征IGF和VIP基因的启动子区域及调控元件。计算机分析表明，三个基因序列（IGFP4、VIP和VIPR1）的转录起始位点（TSS）启动子预测得分最高（1.0），而IGF1的启动子预测得分最低（0.8）。目前的分析显示，最佳共有基序Motif II类似于三个主要转录因子家族：锌指家族、同源框转录因子家族和高迁移率族因子家族，占比约79.17%。本研究发现，62.5%的候选转录因子与Wnt信号通路相互作用以调控转录。本研究中鉴定出的关键调控元件，如CPEB1、MAFB、SOX15、TCF7L2、TCF3和TCF7，在激活和抑制转录中起关键作用，对胚胎和神经系统发育具有重要意义。在当前研究中，在IGF和VIP基因的基因体和启动子区域鉴定出了非常丰富的CpG岛。一般来说，对IGF和VIP基因启动子区域及调控元件进行计算机分析有助于理解启动子区域的调控网络和基因表达模式，这将为基因表达测定的新实验研究提供指导。
