title: Extensive variation between tissues in allele specific expression in an outbred mammal.
abstract: BACKGROUND
  Allele specific gene expression (ASE), with the paternal allele more expressed than the maternal allele or vice versa, appears to be a common phenomenon in humans and mice. In other species the extent of ASE is unknown, and even in humans and mice there are several outstanding questions. These include; to what extent is ASE tissue specific? how often does the direction of allele expression imbalance reverse between tissues? how often is only one of the two alleles expressed? is there a genome wide bias towards expression of the paternal or maternal allele; and finally do genes that are nearby on a chromosome share the same direction of ASE? Here we use gene expression data (RNASeq) from 18 tissues from a single cow to investigate each of these questions in turn, and then validate some of these findings in two tissues from 20 cows.
  
  
  RESULTS
  Between 40 and 100 million sequence reads were generated per tissue across three replicate samples for each of the eighteen tissues from the single cow (the discovery dataset). A bovine gene expression atlas was created (the first from RNASeq data), and differentially expressed genes in each tissue were identified. To analyse ASE, we had access to unambiguously phased genotypes for all heterozygous variants in the cow's whole genome sequence, where these variants were homozygous in the whole genome sequence of her sire, and as a result we were able to map reads to parental genomes, to determine SNP and genes showing ASE in each tissue. In total 25,251 heterozygous SNP within 7985 genes were tested for ASE in at least one tissue. ASE was pervasive, 89 % of genes tested had significant ASE in at least one tissue. This large proportion of genes displaying ASE was confirmed in the two tissues in a validation dataset. For individual tissues the proportion of genes showing significant ASE varied from as low as 8-16 % of those tested in thymus to as high as 71-82 % of those tested in lung. There were a number of cases where the direction of allele expression imbalance reversed between tissues. For example the gene SPTY2D1 showed almost complete paternal allele expression in kidney and thymus, and almost complete maternal allele expression in the brain caudal lobe and brain cerebellum. Mono allelic expression (MAE) was common, with 1349 of 4856 genes (28 %) tested with more than one heterozygous SNP showing MAE. Across all tissues, 54.17 % of all genes with ASE favoured the paternal allele. Genes that are closely linked on the chromosome were more likely to show higher expression of the same allele (paternal or maternal) than expected by chance. We identified several long runs of neighbouring genes that showed either paternal or maternal ASE, one example was five adjacent genes (GIMAP8, GIMAP7 copy1, GIMAP4, GIMAP7 copy 2 and GIMAP5) that showed almost exclusive paternal expression in brain caudal lobe.
  
  
  CONCLUSIONS
  Investigating the extent of ASE across 18 bovine tissues in one cow and two tissues in 20 cows demonstrated 1) ASE is pervasive in cattle, 2) the ASE is often MAE but ranges from MAE to slight overexpression of the major allele, 3) the ASE is most often tissue specific and that more than half the time displays divergent allele specific expression patterns across tissues, 4) across all genes there is a slight bias towards expression of the paternal allele and 5) genes expressing the same parental allele are clustered together more than expected by chance, and there are several runs of large numbers of genes expressing the same parental allele.
authors.affiliation: Department of Economic Development, Jobs, Transport and Resources, Agribiosciences Building, 5 Ring Rd, Bundoora, Australia. amanda.chamberlain@ecodev.vic.gov.au.|Dairy Futures Cooperative Research Centre, Agribiosciences Building, 5 Ring Rd, Bundoora, Australia. amanda.chamberlain@ecodev.vic.gov.au.
authors.forename: Amanda J
authors.initials: AJ
authors.lastname: Chamberlain
authors.affiliation: Department of Economic Development, Jobs, Transport and Resources, Agribiosciences Building, 5 Ring Rd, Bundoora, Australia. christy.vanderjagt@ecodev.vic.gov.au.|Dairy Futures Cooperative Research Centre, Agribiosciences Building, 5 Ring Rd, Bundoora, Australia. christy.vanderjagt@ecodev.vic.gov.au.
authors.forename: Christy J
authors.initials: CJ
authors.lastname: Vander Jagt
authors.affiliation: Department of Economic Development, Jobs, Transport and Resources, Agribiosciences Building, 5 Ring Rd, Bundoora, Australia. ben.hayes@ecodev.vic.gov.au.|Dairy Futures Cooperative Research Centre, Agribiosciences Building, 5 Ring Rd, Bundoora, Australia. ben.hayes@ecodev.vic.gov.au.|La Trobe University, Agribiosciences Building, 5 Ring Rd, Bundoora, Australia. ben.hayes@ecodev.vic.gov.au.
authors.forename: Benjamin J
authors.initials: BJ
authors.lastname: Hayes
authors.affiliation: Department of Economic Development, Jobs, Transport and Resources, Agribiosciences Building, 5 Ring Rd, Bundoora, Australia. majid.khansefid@ecodev.vic.gov.au.|Dairy Futures Cooperative Research Centre, Agribiosciences Building, 5 Ring Rd, Bundoora, Australia. majid.khansefid@ecodev.vic.gov.au.|Institute of Land and Food, University of Melbourne, Royal Parade, Parkville, Australia. majid.khansefid@ecodev.vic.gov.au.
authors.forename: Majid
authors.initials: M
authors.lastname: Khansefid
authors.affiliation: Department of Economic Development, Jobs, Transport and Resources, 1301 Hazeldean Rd, Ellinbank, Australia. leah.marrett@ecodev.vic.gov.au.
authors.forename: Leah C
authors.initials: LC
authors.lastname: Marett
authors.affiliation: Dairy Futures Cooperative Research Centre, Agribiosciences Building, 5 Ring Rd, Bundoora, Australia. catriona.millen@abri.une.edu.au.|Institute of Land and Food, University of Melbourne, Royal Parade, Parkville, Australia. catriona.millen@abri.une.edu.au.
authors.forename: Catriona A
authors.initials: CA
authors.lastname: Millen
authors.affiliation: Department of Economic Development, Jobs, Transport and Resources, Agribiosciences Building, 5 Ring Rd, Bundoora, Australia. thuy.nguyen@ecodev.vic.gov.au.
authors.forename: Thuy T T
authors.initials: TT
authors.lastname: Nguyen
authors.affiliation: Department of Economic Development, Jobs, Transport and Resources, Agribiosciences Building, 5 Ring Rd, Bundoora, Australia. mike.goddard@ecodev.vic.gov.au.|Institute of Land and Food, University of Melbourne, Royal Parade, Parkville, Australia. mike.goddard@ecodev.vic.gov.au.
authors.forename: Michael E
authors.initials: ME
authors.lastname: Goddard
mesh_terms: D000483:Alleles; D000818:Animals; D021461:Animals, Outbred Strains / Q000235:genetics*; D002417:Cattle; D002874:Chromosome Mapping; D005260:Female; D015870:Gene Expression; D020869:Gene Expression Profiling / Q000379:methods; D018392:Genomic Imprinting; D008168:Lung / Q000378:metabolism; D008297:Male; D009928:Organ Specificity; D020641:Polymorphism, Single Nucleotide; D017423:Sequence Analysis, RNA / Q000379:methods; D013950:Thymus Gland / Q000378:metabolism