This article is part of the supplement: APBioNet – Fifth International Conference on Bioinformatics (InCoB2006)

Open Access Proceedings

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

Manisha Brahmachary12, Christian Schönbach34*, Liang Yang5, Enli Huang1, Sin Lam Tan16, Rajesh Chowdhary1, SPT Krishnan1, Chin-Yo Lin7, David A Hume8, Chikatoshi Kai9, Jun Kawai109, Piero Carninci109, Yoshihide Hayashizaki109 and Vladimir B Bajic6*

Author Affiliations

1 Knowledge Extraction Laboratory, Institute for Infocomm Research, 21 Heng Mui Keng Terrace, Singapore 119613, Singapore

2 Department of Biochemistry, Faculty of Medicine, National University of Singapore, 8 Medical Drive, Singapore 117597, Singapore

3 Immunoinformatics Research Team, Advanced Genome Information Technology Group, RIKEN Genomic Sciences Center (GSC), RIKEN Yokohama Institute, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa, 230-0045, Japan

4 Division of Genomics and Genetics, School of Biological Sciences, Nanyang Technological University, Singapore 637551, Singapore

5 Department of Obstetrics and Gynecology, National University Hospital, National University of Singapore, 5 Lower Kent Ridge Road, Singapore 119074, Singapore

6 University of the Western Cape, South African National Bioinformatics Institute (SANBI), Private Bag X17, Bellville 7535, South Africa

7 Brigham Young University, Department of Microbiology and Molecular Biology, 753 WIDB, Provo, UT 84602, USA

8 ARC Special Research Centre for Functional and Applied Genomics, Institute for Molecular Bioscience, The University of Queensland, Brisbane, Queensland 4072, Australia

9 Genome Exploration Research Group (Genome Network Project Core Group), RIKEN Genomic Sciences Center (GSC), RIKEN Yokohama Institute, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa, 230-0045, Japan

10 Genome Science Laboratory, Discovery Research Institute, RIKEN Wako Institute, 2-1 Hirosawa, Wako, Saitama, 351-0198, Japan

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BMC Bioinformatics 2006, 7(Suppl 5):S8  doi:10.1186/1471-2105-7-S5-S8

Published: 18 December 2006



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.


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 motifs analyzed, we found that three represent potentially novel TF-binding motifs enriched in promoters of AMPcgs, while the other four motifs appear to be species-specific.


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.