Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

Transcription profiling of mouse CD4 cells isolated from an ENU induced mutant Sanroque vs. wildtype

ABSTRACT: Male C57BL/6 mice were treated with ENU to generate single base substitutions, the variant genome sequences were breed to homozygosity in inbreeding pedigrees, and screened for antinuclear autoantibodies (ANA). The sanroque pedigree contained multiple progeny with ANA of mixed homogeneous nuclear and cytoplasmic immunofluorescence pattern by 12 weeks of age, due to an autosomal recessive gene variant. Comparison of the gene expression profile of CD4 cells from Sanroque to wild type was performed.

ORGANISM(S): Mus musculus

SUBMITTER: Teresa Lambe

PROVIDER: E-GEOD-2376 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Publications

A RING-type ubiquitin ligase family member required to repress follicular helper T cells and autoimmunity.

Vinuesa Carola G CG Cook Matthew C MC Angelucci Constanza C Athanasopoulos Vicki V Rui Lixin L Hill Kim M KM Yu Di D Domaschenz Heather H Whittle Belinda B Lambe Teresa T Roberts Ian S IS Copley Richard R RR Bell John I JI Cornall Richard J RJ Goodnow Christopher C CC

Nature 20050501 7041

Despite the sequencing of the human and mouse genomes, few genetic mechanisms for protecting against autoimmune disease are currently known. Here we systematically screen the mouse genome for autoimmune regulators to isolate a mouse strain, sanroque, with severe autoimmune disease resulting from a single recessive defect in a previously unknown mechanism for repressing antibody responses to self. The sanroque mutation acts within mature T cells to cause formation of excessive numbers of follicul ...[more]

PMID: 15917799

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Project description:The Lundehund is an old dog breed with remarkable anatomical features including polydactyly in all four limbs and extraordinary flexibility of the spine. We genotyped 28 Lundehund using the canine Illumina high density beadchip to estimate the effective population size (Ne) and inbreeding coefficients as well as to identify potential regions of positive selection. The decay of linkage disequilibrium was slow with r2=0.95 in 50 kb distance. The last 7-200 generations ago, Ne was at 10-13. An increase of Ne was noted in the very recent generations with a peak value of 19 for Ne at generation 4. The FROH estimated for 50-, 65- and 358-SNP windows were 0.87, 087 and 0.81, respectively. The most likely estimates for FROH after removing identical-by-state segments due to linkage disequilibria were at 0.80-0.81. The extreme loss of heterozygosity has been accumulated through continued inbreeding over 200 generations within a probably closed population with a small effective population size. The mean inbreeding coefficient based on pedigree data for the last 11 generations (FPed=0.10) was strongly biased downwards due to the unknown coancestry of the founders in this pedigree data. The long-range haplotype test identified regions with genes involved in processes of immunity, olfaction, woundhealing and neuronal development as potential targets of selection. The genes QSOX2, BMPR1B and PRRX2 as well as MYOM1 are candidates for selection on the Lundehund characteristics small body size, increased number of digits per paw and extraordinary mobility, respectively. The objectives of the present study were to genotype 28 Lundehund using the canine Illumina high density beadchip (Illumina, San Diego, CA, USA) to estimate the effective population size (Ne) from data on linkage disequilibria (LD). We identified runs of homozygosity (ROH) as regions with a local loss of genetic variation. Inbreeding coefficients were calculated on the basis of pedigree data (FPed) and genotype information (FROH, FIS) to compare the results of these different methods for this population. We applied the long-range haplotype test to search for potential selective sweeps.

Dataset Information

Transcription profiling of mouse CD4 cells isolated from an ENU induced mutant Sanroque vs. wildtype

Publications

A RING-type ubiquitin ligase family member required to repress follicular helper T cells and autoimmunity.

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