Genome variation and conserved regulation identify genomic regions responsible for strain specific phenotypes in rat

The genomes of laboratory rat strains are characterised by a mosaic haplotype structure caused by their unique breeding history. These mosaic haplotypes have been recently mapped by extensive sequencing of key strains. Comparison of genomic variation between two closely related rat strains with different phenotypes has been proposed as an effective strategy for the discovery of candidate strain-specific regions involved in phenotypic differences. We developed a method to prioritise strain-specific haplotypes by integrating genomic variation and genomic regulatory data predicted to be involved in specific phenotypes. Specifically, we aimed to identify genomic regions associated with Metabolic Syndrome (MetS), a disorder of energy utilization and storage affecting several organ systems. We compared two Lyon rat strains, Lyon Hypertensive (LH) which is susceptible to MetS, and Lyon Low pressure (LL), which is susceptible to obesity as an intermediate MetS phenotype, with a third strain (Lyon Normotensive, LN) that is resistant to both MetS and obesity. Applying a novel metric, we ranked the identified strain-specific haplotypes using evolutionary conservation of the occupancy three liver-specific transcription factors (HNF4A, CEBPA, and FOXA1) in five rodents including rat. Consideration of regulatory information effectively identified regions with liver-associated genes and rat orthologues of human GWAS variants related to obesity and metabolic traits. We attempted to find possible causative variants and compared them with the candidate genes proposed by previous studies. In strain-specific regions with conserved regulation, we found a significant enrichment for published evidence to obesity—one of the metabolic symptoms shown by the Lyon strains—amongst the genes assigned to promoters with strain-specific variation. Our results show that the use of functional regulatory conservation is a potentially effective approach to select strain-specific genomic regions associated with phenotypic differences among Lyon rats and could be extended to other systems.

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Author Martín-Gálvez, David
Last Updated November 20, 2019, 16:44 (UTC)
Created August 1, 2019, 10:29 (UTC)
Article Host Type publisher
Article Is Open Access true
Article License Type cc-by
Article Version Type publishedVersion
Citation Report https://scite.ai/reports/10.1186/s12864-017-4351-9
DOI 10.1186/s12864-017-4351-9
Date Last Updated 2019-06-08T23:16:07.661121
Evidence open (via page says license)
Funder code(s) European Commission (HEALTH-F4-2010-241504); Wellcome Trust (WT108749/Z/15/Z); National Institutes of Health (R01 HL089895, R21 DK089417); National Institutes of Health (R01 HL089895, R21 DK089417)
Journal Is Open Access true
Open Access Status gold
PDF URL https://bmcgenomics.biomedcentral.com/track/pdf/10.1186/s12864-017-4351-9
Publisher URL https://doi.org/10.1186/s12864-017-4351-9