Assessing MHC class I diversity in dairy cattle populations

The gene dense major histocompatibility complex (MHC) region, present in all jawed vertebrates, encodes molecules involved in self-non-self discrimination and the binding and presentation of antigenic peptides to T cells during the adaptive immune response. Variation in MHC genes is thought to be driven largely by pathogen-mediated selection, with diversity at MHC loci believed to benefit populations by allowing responses to rapidly evolving disease pathogens. However, in economically important dairy cattle, there are concerns that intensive selection for production and fitness traits may override natural selection. It had been hypothesised that these focussed dairy breeding practices may lead to a reduction in MHC diversity and leave cattle populations susceptible to new disease pathogens. The purpose of this study was to estimate current levels of MHC class I diversity in the UK Holstein-Friesian dairy cattle population, primarily through the assessment of diversity in bull populations with genetic input into the UK herd. In a sample of Canadian Holstein bulls, levels of class I allelic diversity were low given the size of the population sampled, but no significant loss of diversity over a twenty year period of selection was detected. Simulations of gene flow implicated trait selection as an influential force shaping diversity in the Canadian Holstein bull population. Haplotypes detected at high frequency were often negatively associated with selection traits indicating the action of heterozygote advantage. A SNP-based assay has been designed to facilitate rapid detection of common haplotypes and thus enable breeders to make more efficient selective breeding decisions whilst also maintaining MHC diversity in cattle populations. Investigations of class I diversity were expanded to incorporate the British Friesian bull population which were shown to have a markedly different pattern of class I diversity to that observed in the Canadian Holstein sample. A number of novel allele sequences and haplotypes were detected in the British Friesian bulls, the characterisation of which has contributed to our knowledge of the mechanisms driving diversity in the cattle class I region. MHC class I typing data from two bull populations and statistical analysis of trait associations with MHC haplotypes provides a comprehensive picture of MHC class I diversity in the wider UK herd and the selective forces integral to shaping diversity

Deficiency of the zinc finger protein ZFP106 causes motor and sensory neurodegeneration

Acknowledgements We are indebted to Jim Humphries, JennyCorrigan, LizDarley, Elizabeth Joynson, Natalie Walters, Sara Wells and the whole necropsy, histology, genotyping and MLC ward 6 teams at MRC Harwell for excellent technical assistance. We thank the staff of the WTSI Illumina Bespoke Team for the RNA-seq data, the Sanger Mouse Genetics Project for the initial mouse characterization and Dr David Adams for critical reading of the manuscript. We also thank KOMP for the mouse embryonic stem cells carrying the knockout first promoter-less allele (tm1a(KOMP)Wtsi) within Zfp016. Conflict of Interest statement. None declared. Funding This work was funded by the UK Medical Research Council (MRC) to A.A.-A. and a Motor Neurone Disease Association (MNDA) project grant to A.A.-A. and EMCF. D.L.H.B. is a Wellcome Trust Senior Clinical Scientist Fellow and P.F. is a MRC/MNDA Lady Edith Wolfson Clinician Scientist Fellow. Funding to pay the Open Access publication charges for this article was provided by the MRC grant number: MC_UP_A390_1106.Peer reviewedPublisher PD

Aneuploidy screening of embryonic stem cell clones by metaphase karyotyping and droplet digital polymerase chain reaction

DNA input in ddPCR reaction. The figure shows copy number of Chr 8 (crosses) and Y (squares) measured by ddPCR with various input quantities of genomic DNA template. Vertical bars are Standard Errors. The experiment demonstrates linearity across the range of concentrations relevant to the DNA preparations assayed. This is a key point for the robustness of the screen, as gDNA preparations are challenging to standardize due to the disparity of growth rates between ES cell clones. (PDF 26 kb

Mice with endogenous TDP-43 mutations exhibit gain of splicing function and characteristics of amyotrophic lateral sclerosis

TDP-43 (encoded by the gene TARDBP) is an RNA binding protein central to the pathogenesis of amyotrophic lateral sclerosis (ALS). However, how TARDBP mutations trigger pathogenesis remains unknown. Here, we use novel mouse mutants carrying point mutations in endogenous Tardbp to dissect TDP-43 function at physiological levels both in vitro and in vivo Interestingly, we find that mutations within the C-terminal domain of TDP-43 lead to a gain of splicing function. Using two different strains, we are able to separate TDP-43 loss- and gain-of-function effects. TDP-43 gain-of-function effects in these mice reveal a novel category of splicing events controlled by TDP-43, referred to as "skiptic" exons, in which skipping of constitutive exons causes changes in gene expression. In vivo, this gain-of-function mutation in endogenous Tardbp causes an adult-onset neuromuscular phenotype accompanied by motor neuron loss and neurodegenerative changes. Furthermore, we have validated the splicing gain-of-function and skiptic exons in ALS patient-derived cells. Our findings provide a novel pathogenic mechanism and highlight how TDP-43 gain of function and loss of function affect RNA processing differently, suggesting they may act at different disease stages

A large scale hearing loss screen reveals an extensive unexplored genetic landscape for auditory dysfunction

The developmental and physiological complexity of the auditory system is likely reflected in the underlying set of genes involved in auditory function. In humans, over 150 non-syndromic loci have been identified, and there are more than 400 human genetic syndromes with a hearing loss component. Over 100 non-syndromic hearing loss genes have been identified in mouse and human, but we remain ignorant of the full extent of the genetic landscape involved in auditory dysfunction. As part of the International Mouse Phenotyping Consortium, we undertook a hearing loss screen in a cohort of 3006 mouse knockout strains. In total, we identify 67 candidate hearing loss genes. We detect known hearing loss genes, but the vast majority, 52, of the candidate genes were novel. Our analysis reveals a large and unexplored genetic landscape involved with auditory function

Helios is a key transcriptional regulator of outer hair cell maturation

The sensory cells that are responsible for hearing include the cochlear inner hair cells (IHCs) and outer hair cells (OHCs), with the OHCs being necessary for sound sensitivity and tuning1. Both cell types are thought to arise from common progenitors; however, our understanding of the factors that control the fate of IHCs and OHCs remains limited. Here we identify Ikzf2 (which encodes Helios) as an essential transcription factor in mice that is required for OHC functional maturation and hearing. Helios is expressed in postnatal mouse OHCs, and in the cello mouse model a point mutation in Ikzf2 causes early-onset sensorineural hearing loss. Ikzf2cello/cello OHCs have greatly reduced prestin-dependent electromotile activity, a hallmark of OHC functional maturation, and show reduced levels of crucial OHC-expressed genes such as Slc26a5 (which encodes prestin) and Ocm. Moreover, we show that ectopic expression of Ikzf2 in IHCs: induces the expression of OHC-specific genes; reduces the expression of canonical IHC genes; and confers electromotility to IHCs, demonstrating that Ikzf2 can partially shift the IHC transcriptome towards an OHC-like identity