A high resolution atlas of gene expression in the domestic sheep (Ovis aries)

Abstract

Sheep are a key source of meat, milk and fibre for the global livestock sector, and an important biomedical model. Global analysis of gene expression across multiple tissues has aided genome annotation and supported functional annotation of mammalian genes. We present a large-scale RNA-Seq dataset representing all the major organ systems from adult sheep and from several juvenile, neonatal and prenatal developmental time points. The Ovis aries reference genome (Oar v3.1) includes 27,504 genes (20,921 protein coding), of which 25,350 (19,921 protein coding) had detectable expression in at least one tissue in the sheep gene expression atlas dataset. Network-based cluster analysis of this dataset grouped genes according to their expression pattern. The principle of ‘guilt by association’ was used to infer the function of uncharacterised genes from their co-expression with genes of known function. We describe the overall transcriptional signatures present in the sheep gene expression atlas and assign those signatures, where possible, to specific cell populations or pathways. The findings are related to innate immunity by focusing on clusters with an immune signature, and to the advantages of cross-breeding by examining the patterns of genes exhibiting the greatest expression differences between purebred and crossbred animals. This high-resolution gene expression atlas for sheep is, to our knowledge, the largest transcriptomic dataset from any livestock species to date. It provides a resource to improve the annotation of the current reference genome for sheep, presenting a model transcriptome for ruminants and insight into gene, cell and tissue function at multiple developmental stages.Author SummarySheep are ruminant mammals kept as livestock for the production of meat, milk and wool in agricultural industries across the globe. Genetic and genomic information can be used to improve production traits such as disease resiliance. The sheep genome is however missing important information relating to gene function and many genes, which may be important for productivity, have no informative gene name. This can be remedied using RNA-Sequencing to generate a global expression profile of all protein-coding genes, across multiple organ systems and developmental stages. Clustering genes based on their expression profile across tissues and cells allows us to assign function to those genes. If for example a gene with no informative gene name is expressed in macrophages and is found within a cluster of known macrophage related genes it is likely to be involved in macrophage function and play a role in innate immunity. This information improves the quality of the reference genome and provides insight into biological processes underlying the complex traits that influence the productivity of sheep and other livestock species.

The equine mononuclear phagocyte system: The relevance of the horse as a model for understanding human innate immunity

“…In turn, this may facilitate the identification of novel therapeutic targets for both endotoxaemia and sepsis in man, an objective which has been met with limited success via the use of rodent models. Similar studies have already been performed in other large animal models such as pig and sheep 60,61,211 …”

“…In mice, macrophages are routinely generated in vitro from bone marrow progenitors for subsequent functional studies 58,59 . This approach has recently been extended to large animal species expedited by the capacity to freeze cells for future culture following recovery 21,60‐62 . We have recently published a comparative analysis of RNA‐seq data of horse BMDM and their response to lipopolysaccharide (LPS) with similar data for ruminants (sheep, goat, cow and water buffalo), pig, mouse and rat (in press).…”

“…Published studies, mainly in mice, have differed in their conclusions with respect to the existence of significant functional differences between these populations of lung macrophages 152‐156 . As bronchoalveolar lavage (BAL) is a practical and commonly used method of obtaining resident airway cells, there are several published transcriptome analyses of BAL‐derived AMs in different species, including large animals such as pigs, 157 sheep 61 and horses 22 . They are clearly distinct from other tissue macrophages, expressing many lectin‐like receptors apparently adapted to recognise, internalise and eliminate inhaled microorganisms.…”

Comprehensive Transcriptional Profiling of the Gastrointestinal Tract of Ruminants from Birth to Adulthood Reveals Strong Developmental Stage Specific Gene Expression

“…Consistent with this view, analysis of the pig gene expression atlas (Freeman et al 2012) revealed that there were a large number of genes for C-type lectins that were highly-expressed in alveolar macrophages but almost undetectable in the pig GI tract despite the high expression of known macrophage-specific transcripts (Freeman et al 2012). To determine if this was also the case in sheep we examined the expression of six C-type lectin marker genes ( CD68 , CLEC4D , CLEC4E , CLEC5A , CLEC7A and SIGLEC1 ) using the gene expression profiles for the sheep atlas dataset on BioGPS (Clark et al 2017a). In sheep, as in pig, CLEC4D , CD68 , CLEC4E and CLEC7A were all highly expressed in sheep alveolar macrophages, but barely detected in the GI tract tissues.…”

“…In mice, macrophage-specific conditional deletion of the IL10 receptor causes severe spontaneous colitis (Zigmond et al 2014) as does a full mutation of the IL10 gene (Kühn et al 1993). In the sheep atlas dataset on BioGPS, IL10 mRNA is strongly induced in macrophages by lipopolysaccharide (Clark et al 2017a). However, the induction is rapid and transient, and decays completely after 24 hr.…”