Elsevier

Genomics

Volume 84, Issue 2, August 2004, Pages 331-345
Genomics

Characterization of the type I interferon locus and identification of novel genes

https://doi.org/10.1016/j.ygeno.2004.03.003Get rights and content

Abstract

The human type I interferon (IFN) genes are clustered on human chromosome 9p21 and the mouse genes are located in the region of conserved synteny on mouse chromosome 4. We have identified two novel mouse Ifna genes (Ifna12, Ifna13) and Ifnl2 (IFN-like 2, a homologue of Limitin/IFN-like 1). Another type I IFN gene was designated Ifne1. Mouse Ifne1 was expressed in ovaries and uterus but not in tissues of hematopoietic origin. IFN-ε1 has general structural characteristics of a type I IFN. These studies represent the first detailed annotation of the mouse type I IFN locus, and the products of these novel genes may have important functions in reproduction and host defense.

Section snippets

Annotation of the type I interferon genomic locus

To obtain a more complete annotation of the genes and potential transcriptional units in the mouse type I Ifn gene cluster, ∼430 kb of mouse genomic DNA located on MMU chromosome 4 at 42.6 cM (Fig. 1A) was analyzed in detail using the NIX suite of programs. Mouse Ifn genes, including Ifna1, Ifna2, Ifna3 (IfnaA), Ifna4, Ifna5, Ifna6, Ifna7, Ifna8 (IfnaB), Ifna9, Ifna10 (Ifna6-T), Ifna11, and Ifnb (IFN-β), were identified; these genes were subsequently confirmed by BLASTN and BLASTX analysis and

Discussion

The characterization of gene clusters has provided important insights into the physiological and pathological functions of related genes. Functionally related genes are often clustered together: see, for example, the major histocompatibility genes [34], the antimicrobial β-defensin genes [35], the class II cytokine receptor genes [36], and the genes encoding cytokines, such as interleukins 4, 13, and 5. This may give efficiency for coregulation, for example, via locus control regions [23].

Analysis of the type I IFN locus

Approximately 300 kb of mouse genomic DNA from contig GA_x5J8B7W6GG0 (encompassing the centromeric end of the type I Ifn locus) and ∼120 kb of mouse genomic DNA from contig GA_x5J8B7W6711 (encompassing the 3′ end of the type I Ifn locus on MMU chromosome 4) was obtained from Celera (www.celera.com>). Whenever possible, ambiguous bases in these data were identified by comparison with Contig NW_000209 from NCBI (www.ncbi.nlm.nih.gov>). Approximately 150 kb of human genomic DNA from contig NT_023974.11

Acknowledgements

Xiang-ming Liu (Center for Functional Genomics and Human Disease) and Mireille Lahoud (Walter and Eliza Hall Institute, Parkville, Australia) are thanked for their generous gifts of cDNA. This is Research Paper 005 from SUBIT.

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    Sequence data from this article have been deposited with the GenBank Data Library under Accession Nos. AY190044AY190047.

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