In Silico Analysis of Promoter Regions and Regulatory Elements of IGF and VIP Genes Associated with Reproductive Traits in Chicken

Strategic Insights -

Research from the Department of Applied Biology has investigated the promoter region and regulatory elements of chicken insulin-like growth factor (IGF) and vasoactive intestinal polypeptide (VIP) genes associated with reproductive traits. The study employed several in silico tools to characterize the promoter regions and regulatory elements of IGF and VIP genes, revealing key regulatory elements involved in activating and repressing transcription. The analysis demonstrated the significance of in silico analysis in understanding regulatory networks and gene expression patterns, guiding new experimental studies in gene expression assays.

Key Takeaways:

  • The study used several in silico tools, including Neural Network Promoter Prediction (NNPP), Multiple Expectation maximizations for Motif Elicitation (MEME-Suite), and Gene Ontology for Motifs (GOMO), 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%.
  • The 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.
  • The in silico analysis was found to be helpful for comprehending regulatory networks and gene expression patterns in promoter regions, guiding new experimental studies in gene expression assays.

Statistics:

  • 62.5% of candidate transcription factors have interaction with the Wnt signalling pathway to regulate transcription.
  • 79.17% of 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.
  • 3 gene sequences (IGFP4, VIP, and VIPR1) obtained the highest promoter prediction scores (1.0) for TSS.
  • 1 gene sequence (IGF1) obtained the lowest promoter prediction score (0.8).

Sources:

  • Promoter Region and Regulatory Elements of IGF and VIP Genes Associated With Reproductive Traits in Chicken. International Journal of Genomics, 2025,2025. (International Journal of Genomics - https://www.hindawi.com/journals/ijg/)
  • Department of Applied Biology
  • Bosenu Abera, Department of Applied Biology
  • International Journal of Genomics, published by Wiley
  • https://doi-org.sdpl.idm.oclc.org/10.1155/ijog/5574292
  • Life Science Weekly, June 17, 2025; p 3450