Polymorphisms in Ly6 genes in Msq1 encoding susceptibility to mouse adenovirus type 1

Abstract

Strain-specific differences in susceptibility to mouse adenovirus type 1 (MAV-1) are linked to the quantitative trait locus Msq1 on mouse chromosome 15. This region contains 14 Ly6 or Ly6-related genes, many of which are known to be expressed on the surface of immune cells, suggesting a possible role in host defense. We analyzed these genes for polymorphisms between MAV-1-susceptible and MAV-1-resistant inbred mouse strains. Sequencing of cDNAs identified 12 coding-region polymorphisms in 2010109I03Rik, Ly6e, Ly6a, Ly6c1, and Ly6c2, six of which were nonsynonymous and five of which were previously unlisted in dbSNP Build 132. We also clarified sequence discrepancies in GenBank for the coding regions of I830127L07Rik and Ly6g. Additionally, Southern blotting revealed size polymorphisms within the DNA regions of Ly6e, Ly6a, and Ly6g. Collectively, these genetic variations have implications for the structure, function, and/or expression of Ly6 and Ly6-related genes that may contribute to the observed strain-specific differences in susceptibility to MAV-1.

Figure 1. Msq1 map

Polymorphism data from this study are displayed on the gene map of the Msq1 portion of the Ly6 region of Chr 15, based on NCBI Build 37/mm9. Boxes indicate Ly6 or Ly6-related genes. Arrowheads denote the direction of transcription of the gene along the chromosome (forward or reverse strand).

Figure 2. I830127L07Rik protein alignments

RIKEN BMM sequence is from a bone marrow macrophage-derived cDNA clone of I830127L07Rik (NCBI Accession AK153212.1). GNOMON is a predicted amino acid sequence for I830127L07Rik from a computer-based prediction using GNOMON analysis of the C57BL/6J genome (NCBI Accession XM_001477102.1). Thymus-Derived represents the putative amino acid sequence of the I830127L07Rik transcript that we amplified from the thymus of an SJL/J mouse. Asterisks (*) denote the ten conserved cysteine residues of the LY6/uPAR domain. DNASTAR Lasergene MegAlign was used to perform this ClustalW alignment. Dashes denote absent amino acids. Periods indicate a stop codon.

Figure 3. Genomic Size Polymorphisms

Southern blotting was used to analyze size differences in genes in the Msq1 interval among mouse strains at the genomic level. (A) Annotations from UCSC Genome Browser, RefSeq, and Ensembl were assembled to create diagrams of the restriction fragments containing the appropriate Ly6 or Ly6-related gene. Black boxes indicate exons. Ly6e, Ly6i, and Ly6h have multiple spliced forms; the longest splice variant is depicted. Nucleotide positions of flanking restriction sites for the enzymes shown to the right are indicated below each line diagram (NCBI Build 37/mm9, Chr 15). (B) Radiolabeled probes were produced from cDNA-derived PCR products by Klenow extension for the Ly6 and Ly6-related genes indicated above each Southern blot. DNA size markers are indicated on the left of each blot. Arrowheads indicate bands of interest. B = BALB/cJ, S = SJL/J, C = C57BL/6J, and 1 = 129S6SvEv/Tac, F1 = tail-derived CSJL/J (BALB/cJ × SJL/J), F1* = brain-derived CSJL/J (BALB/cJ × SJL/J), (−) = negative control, (+) = positive control.