Journal article
Genomics-based approaches to gene discovery in innate immunity
Immunological reviews, Vol.190(1), pp.137-145
12/2002
DOI: 10.1034/j.1600-065x.2002.19010.x
PMID: 12493011
Abstract
The completion of draft sequences of the human and mouse genomes offers many opportunities for gene discovery in the field of immunology through the application of the methods of computational genomics. One arm of the innate immune system includes the antimicrobial peptides that protect multicellular organisms from a diverse spectrum of microorganisms. The beta-defensins comprise an important family of mammalian antimicrobial peptides. To better define the beta-defensin gene family, we developed an approach to search genomic databases for conserved motifs present in the beta-defensin family using HMMER, a computational search tool based on hidden Markov models (HMMs), in combination with the basic local alignment search tool. The approach was first used to identify candidate second-exon coding regions, and later applied to finding associated first exons. This strategy discovered 28 new human and 43 new mouse beta-defensin genes in five syntenic chromosomal regions. Within each syntenic cluster, the gene sequences and organization were similar, suggesting that each cluster pair arose from a common ancestor and was retained because of conserved functions. These findings demonstrate an important proof-of-principle for a genome-wide search strategy to identify genes with conserved structural motifs. Such an approach may be readily adopted to address other questions of relevance to immunology.
Details
- Title: Subtitle
- Genomics-based approaches to gene discovery in innate immunity
- Creators
- ToddE Scheetz - Department of Pediatrics, The University of Iowa, Iowa City, IA 52242, USAJennifer A BartlettJesse D WaltersBrian C SchutteThomas L CasavantPaul B McCray Jr
- Resource Type
- Journal article
- Publication Details
- Immunological reviews, Vol.190(1), pp.137-145
- Publisher
- England
- DOI
- 10.1034/j.1600-065x.2002.19010.x
- PMID
- 12493011
- ISSN
- 0105-2896
- eISSN
- 1600-065X
- Grant note
- CA85188 / NCI NIH HHS P30-HD27748 / NICHD NIH HHS HL-61234 / NHLBI NIH HHS
- Language
- English
- Date published
- 12/2002
- Academic Unit
- Roy J. Carver Department of Biomedical Engineering; Electrical and Computer Engineering; Microbiology and Immunology; Pulmonary Medicine; Stead Family Department of Pediatrics; Internal Medicine; Ophthalmology and Visual Sciences
- Record Identifier
- 9983980049102771
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