Computational promoter analysis of mouse, rat and human antimicrobial peptide-coding genes

Brahmachary, M., Schonbach, C., Yang, L., Huang, E. L., Tan, S. L., Chowdhary, R., Krishnan, S. P. T., Lin, C. Y., Hume, D. A., Kai, C., Kawai, J., Carninci, P., Hayashizaki, Y. and Bajic, V. B. (2006) Computational promoter analysis of mouse, rat and human antimicrobial peptide-coding genes. Bmc Bioinformatics, 7 Supp. 5: Article number S8. doi:10.1186/1471-2105-7-S5-S8

Author Brahmachary, M.
Schonbach, C.
Yang, L.
Huang, E. L.
Tan, S. L.
Chowdhary, R.
Krishnan, S. P. T.
Lin, C. Y.
Hume, D. A.
Kai, C.
Kawai, J.
Carninci, P.
Hayashizaki, Y.
Bajic, V. B.
Title Computational promoter analysis of mouse, rat and human antimicrobial peptide-coding genes
Journal name Bmc Bioinformatics   Check publisher's open access policy
ISSN 1471-2105
Publication date 2006
Sub-type Article (original research)
DOI 10.1186/1471-2105-7-S5-S8
Open Access Status DOI
Volume 7
Issue Supp. 5
Start page Article number S8
Total pages 14
Place of publication London, United Kingdom
Publisher Biomed Central Ltd
Language eng
Subject 270201 Gene Expression
360100 Political Science
Abstract Background: Mammalian antimicrobial peptides (AMPs) are effectors of the innate immune response. A multitude of signals coming from pathways of mammalian pathogen/pattern recognition receptors and other proteins affect the expression of AMP-coding genes (AMPcgs). For many AMPcgs the promoter elements and transcription factors that control their tissue cell-specific expression have yet to be fully identified and characterized. Results: Based upon the RIKEN full-length cDNA and public sequence data derived from human, mouse and rat, we identified 178 candidate AMP transcripts derived from 61 genes belonging to 29 AMP families. However, only for 31 mouse genes belonging to 22 AMP families we were able to determine true orthologous relationships with 30 human and 15 rat sequences. We screened the promoter regions of AMPcgs in the three species for motifs by an ab initio motif finding method and analyzed the derived promoter characteristics. Promoter models were developed for alpha-defensins, penk and zap AMP families. The results suggest a core set of transcription factors (TFs) that regulate the transcription of AMPcg families in mouse, rat and human. The three most frequent core TFs groups include liver, nervous system-specific and nuclear hormone receptors (NHRs). Out of 440 novel TF-binding motifs enriched in promoters of AMPcgs, while the other four motifs appear to be species-specific. Conclusion: Our large-scale computational analysis of promoters of 22 families of AMPcgs across three mammalian species suggests that their key transcriptional regulators are likely to be TFs of the liver-, nervous system-specific and NHR groups. The computationally inferred promoter elements and potential TF binding motifs provide a rich resource for targeted experimental validation of TF binding and signaling studies that aim at the regulation of mouse, rat or human AMPcgs.
Keyword Biochemical Research Methods
Biotechnology & Applied Microbiology
Proenkephalin Gene
Q-Index Code C1
Q-Index Status Provisional Code
Institutional Status UQ

Document type: Journal Article
Sub-type: Article (original research)
Collection: Institute for Molecular Bioscience - Publications
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Citation counts: TR Web of Science Citation Count  Cited 18 times in Thomson Reuters Web of Science Article | Citations
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Created: Wed, 19 Sep 2007, 17:12:09 EST