Sequence analysis of a 212 kb defensin gene cluster on ECA 27q17.
Abstract: Defensins are a family of evolutionary ancient antimicrobial peptides consisting of three sub-families: alpha-, beta- and theta-defensins. This investigation was focused on the genomic characterization of equine beta-defensins and the investigation of the potential clustering of beta-defensin genes in the equine genome. Six genomic BAC clones were isolated from the CHORI-241 library and one of these was mapped by FISH to ECA 27q17. This location was confirmed by RH-mapping. The contiguous 212 kb sequence of this clone was determined. Sequence analysis revealed the identification of ten pseudogenes and nine genes, six of which were highly homologous to human beta-defensin DEFB4. Clustering of the beta-defensin genes was confirmed and the order of the genes on the analyzed BAC was related to the corresponding defensin cluster on HSA 8. The knowledge about the sequence and the genomic structure of the equine beta-defensin genes will improve the classification of different paralogous defensin genes and is a prerequisite for subsequent functional studies. Additionally, the first alpha-defensin-like sequence outside the groups of primates, lagomorphs and rodents (glires) was identified.
Publication Date: 2006-04-05 PubMed ID: 16723195DOI: 10.1016/j.gene.2006.03.006Google Scholar: Lookup
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- Comparative Study
- Journal Article
- Research Support
- Non-U.S. Gov't
Summary
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The research study focuses on the genomic characterization of equine beta-defensins, a type of antimicrobial peptides, and the confirmation of their clustering in the equine genome, along with the discovery of an alpha-defensin-like sequence not typically found outside of certain groups.
Research Methodology
- In this study, six genomic BAC (bacterial artificial chromosome) clones were isolated from a CHORI-241 library for analysis. This is a procedure used to create an artificial chromosome in a bacterial cell that is then used to multiply and store copies of a particular DNA sequence.
- One of these clones was subsequently mapped using Fluorescence In Situ Hybridisation (FISH). This is a technique used to visualize and map the genetic material in an individual’s cells, including specific genes or portions of genes.
- This location was then confirmed using RH (Radiation hybrid) mapping, another technique used for determining the location of genes within a genome.
- The research team then determined the sequence of a 212 kb (kilo base pairs) segment from the chosen clone.
Defensin Gene Analysis
- Sequence analysis led to identifying ten pseudogenes, that are non-functioning segments of DNA, that resemble functional genes.
- Nine functioning genes were identified, six of which were found to be very similar to the human beta-defensin DEFB4. These genes are part of our immune system that helps protect against infection.
- The analysis confirmed the clustering of the beta-defensin genes, meaning they are grouped close together on the same chromosome, in this case, the ECA 27q17.
Implication of the Findings
- The order of the genes on the analyzed BAC was found to be related to the corresponding defensin cluster on HSA 8, the eighth human chromosome.
- This research information about the sequence and genomic structure of equine beta-defensin genes can help improve the classification of different paralogous defensin genes, or genes that are derived from duplication within a genome.
- The study also sets the groundwork for future functional studies by providing essential information on the structure of these genes.
- Additionally, the study identified the presence of an alpha-defensin-like sequence in a location where it is not typically found, making it the first detected outside of primates, lagomorphs, and rodents.
Cite This Article
APA
Looft C, Paul S, Philipp U, Regenhard P, Kuiper H, Distl O, Chowdhary BP, Leeb T.
(2006).
Sequence analysis of a 212 kb defensin gene cluster on ECA 27q17.
Gene, 376(2), 192-198.
https://doi.org/10.1016/j.gene.2006.03.006 Publication
Researcher Affiliations
- Institute of Animal Breeding and Husbandry, Christian Albrecht University of Kiel, D-24098 Kiel, Germany.
MeSH Terms
- Animals
- Base Sequence
- Chromosomes, Artificial, Bacterial
- Chromosomes, Mammalian
- Codon, Terminator
- Computational Biology
- DNA, Complementary
- Databases, Genetic
- Evolution, Molecular
- Exons
- Gene Duplication
- Gene Library
- Gene Order
- Genome
- Horses / genetics
- Molecular Sequence Data
- Multigene Family
- Pseudogenes
- Radiation Hybrid Mapping
- Sequence Analysis, DNA
- alpha-Defensins / genetics
- beta-Defensins / genetics
Citations
This article has been cited 5 times.- Van Cleemput J, Poelaert KCK, Laval K, Vanderheijden N, Dhaenens M, Daled S, Boyen F, Pasmans F, Nauwynck HJ. An Alphaherpesvirus Exploits Antimicrobial β-Defensins To Initiate Respiratory Tract Infection.. J Virol 2020 Mar 31;94(8).
- Bruhn O, Grötzinger J, Cascorbi I, Jung S. Antimicrobial peptides and proteins of the horse--insights into a well-armed organism.. Vet Res 2011 Sep 2;42(1):98.
- Bruhn O, Paul S, Tetens J, Thaller G. The repertoire of equine intestinal alpha-defensins.. BMC Genomics 2009 Dec 23;10:631.
- Hollox EJ, Armour JA. Directional and balancing selection in human beta-defensins.. BMC Evol Biol 2008 Apr 16;8:113.
- Bruhn O, Regenhard P, Michalek M, Paul S, Gelhaus C, Jung S, Thaller G, Podschun R, Leippe M, Grötzinger J, Kalm E. A novel horse alpha-defensin: gene transcription, recombinant expression and characterization of the structure and function.. Biochem J 2007 Oct 15;407(2):267-76.
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