PUBLICATION
The role of genomic data in the discovery, annotation and evolutionary interpretation of the interferon-lambda family
- Authors
- Fox, B.A., Sheppard, P.O., and O'Hara, P.J.
- ID
- ZDB-PUB-090324-18
- Date
- 2009
- Source
- PLoS One 4(3): e4933 (Journal)
- Registered Authors
- Keywords
- Genetic interference, Interferons, Cytokines, Mammalian genomics, Genetic loci, Pseudogenes, Structural genomics, Evolutionary genetics
- MeSH Terms
-
- Animals
- Base Sequence
- Evolution, Molecular*
- Exons
- Genomics*
- Humans
- Interleukins/classification
- Interleukins/genetics*
- Introns
- Molecular Sequence Data
- Phylogeny
- Sequence Analysis, DNA
- PubMed
- 19300512 Full text @ PLoS One
Citation
Fox, B.A., Sheppard, P.O., and O'Hara, P.J. (2009) The role of genomic data in the discovery, annotation and evolutionary interpretation of the interferon-lambda family. PLoS One. 4(3):e4933.
Abstract
BACKGROUND: Type-I interferons, type-II interferons, and the IL-10 family are helical cytokines with similar three-dimensional folds. However, their homologous relationship is difficult to detect on the basis of sequence alone. We have previously described the discovery of the human type-III interferons (IFN lambda-1, -2, -3 or IL-29, IL-28A, IL-28B), which required a combination of manual and computational techniques applied to predicted protein sequences. PRINCIPAL FINDINGS: Here we describe how the use of gene structure analysis and comparative genomics enabled a more extensive understanding of these genes early in the discovery process. More recently, additional mammalian genome sequences have shown that there are between one and potentially nine copies of interferon lambda genes in each genome, and that several species have single exon versions of the interferon lambda gene. SIGNIFICANCE: The variable number of single exon type-I interferons in mammals, along with recently identified genes in zebrafish homologous to interferons allows a story of interferon evolution to be proposed. This model suggests that the gene duplications and single exon retrotransposons of mammalian type-III interferons are positively selected for within a genome. These characteristics are also shared with the fish interferons and could be responsible for the generation of the IL10 family and also the single exon type-I interferons.
Genes / Markers
Expression
Phenotype
Mutations / Transgenics
Human Disease / Model
Sequence Targeting Reagents
Fish
Orthology
Engineered Foreign Genes
Mapping