Characterization of the type I interferon locus and identification of novel genes☆
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.
References (53)
- et al.
Human interferon omega (omega) binds to the alpha/beta receptor
J. Biol. Chem.
(1991) - et al.
Interferon-kappa, a novel type I interferon expressed in human keratinocytes
J. Biol. Chem.
(2001) - et al.
The interferon genes
Prog. Nucleic Acid Res. Mol. Biol.
(1986) - et al.
Type I interferons and limitin: a comparison of structures, receptors, and functions
Cytokine Growth Factor Rev.
(2001) - et al.
Trophoblast interferons
Placenta
(1999) - et al.
Interferon-delta: the first member of a novel type I interferon family
Biochimie
(1998) - et al.
Structure of the human type-I interferon gene cluster determined from a YAC clone contig
Genomics
(1994) - et al.
Isolation and characterization of a novel interferon-alpha-encoding gene, IFN-alpha 11, within a murine IFN cluster
Gene
(1991) - et al.
Drosophila kelch motif is derived from a common enzyme fold
J. Mol. Biol.
(1994) - et al.
The kelch repeat superfamily of proteins: propellers of cell function
Trends Cell. Biol.
(2000)
Structure and expression of a new murine interferon-alpha gene: MuIFN-alpha I9
Gene
Crystal structure of ovine interferon-tau at 2.1 Å resolution
Mol. Biol.
Zinc mediated dimer of human interferon-alpha 2b revealed by X-ray crystallography
Structure
NPS@: network protein sequence analysis
Trends Biochem. Sci.
Protein structure computing in the genomic era
Res. Microbiol.
The soluble murine type I interferon receptor Ifnar-2 is present in serum, is independently regulated, and has both agonistic and antagonistic properties
Blood
How cells respond to interferons
Annu. Rev. Biochem.
Interferons and their actions
Annu. Rev. Biochem.
Limitin: an interferon-like cytokine that preferentially influences B-lymphocyte precursors
Nat. Med.
Trophoblast interferon and pregnancy
Reproduction
Chromosomal localization of human leukocyte, fibroblast, and immune interferon genes by means of in situ hybridization
Proc. Natl. Acad. Sci. USA
Linkage analysis of the mouse interferon-alpha locus on chromosome 4
J. Exp. Med.
Mouse interferon alpha and beta genes are linked at the centromere proximal region of chromosome 4
J. Gen. Virol.
Subchromosomal localization of mouse IFN-alpha genes by in situ hybridization
J. Interferon Res.
Characterization of a mouse interferon gene locus. I. Isolation of a cluster of four alpha interferon genes
Nucleic Acids Res.
Structure of a murine alpha interferon pseudogene with a repetitive R-type sequence in the 3′ flanking region
Mol. Cell. Biol.
Cited by (194)
Epithelially Restricted Interferon Epsilon Protects Against Colitis
2024, Cellular and Molecular Gastroenterology and HepatologyWTAP-mediated m6A modification of IFNE is required for antiviral defense in condyloma acuminata
2023, Journal of Dermatological ScienceCytokines and microRNAs in SARS-CoV-2: What do we know?
2022, Molecular Therapy Nucleic AcidsModeling Innate Antiviral Immunity in Physiological Context
2022, Journal of Molecular Biology