Genome variation and conserved regulation identify genomic regions responsible for strain specific phenotypes in rat
Abstract Background 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 r...
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doaj-2209976f9c5a4ce4bc564472b75720b32020-11-24T22:52:28ZengBMCBMC Genomics1471-21642017-12-0118111810.1186/s12864-017-4351-9Genome variation and conserved regulation identify genomic regions responsible for strain specific phenotypes in ratDavid Martín-Gálvez0Denis Dunoyer de Segonzac1Man Chun John Ma2Anne E. Kwitek3David Thybert4Paul Flicek5European Molecular Biology Laboratory, European Bioinformatics InstituteEuropean Molecular Biology Laboratory, European Bioinformatics InstituteDepartment of Pharmacology, University of IowaDepartment of Pharmacology, University of IowaEuropean Molecular Biology Laboratory, European Bioinformatics InstituteEuropean Molecular Biology Laboratory, European Bioinformatics InstituteAbstract Background 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. Results 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. Conclusions 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.http://link.springer.com/article/10.1186/s12864-017-4351-9Metabolic syndromeGenome regulationEvolution |
collection |
DOAJ |
language |
English |
format |
Article |
sources |
DOAJ |
author |
David Martín-Gálvez Denis Dunoyer de Segonzac Man Chun John Ma Anne E. Kwitek David Thybert Paul Flicek |
spellingShingle |
David Martín-Gálvez Denis Dunoyer de Segonzac Man Chun John Ma Anne E. Kwitek David Thybert Paul Flicek Genome variation and conserved regulation identify genomic regions responsible for strain specific phenotypes in rat BMC Genomics Metabolic syndrome Genome regulation Evolution |
author_facet |
David Martín-Gálvez Denis Dunoyer de Segonzac Man Chun John Ma Anne E. Kwitek David Thybert Paul Flicek |
author_sort |
David Martín-Gálvez |
title |
Genome variation and conserved regulation identify genomic regions responsible for strain specific phenotypes in rat |
title_short |
Genome variation and conserved regulation identify genomic regions responsible for strain specific phenotypes in rat |
title_full |
Genome variation and conserved regulation identify genomic regions responsible for strain specific phenotypes in rat |
title_fullStr |
Genome variation and conserved regulation identify genomic regions responsible for strain specific phenotypes in rat |
title_full_unstemmed |
Genome variation and conserved regulation identify genomic regions responsible for strain specific phenotypes in rat |
title_sort |
genome variation and conserved regulation identify genomic regions responsible for strain specific phenotypes in rat |
publisher |
BMC |
series |
BMC Genomics |
issn |
1471-2164 |
publishDate |
2017-12-01 |
description |
Abstract Background 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. Results 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. Conclusions 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. |
topic |
Metabolic syndrome Genome regulation Evolution |
url |
http://link.springer.com/article/10.1186/s12864-017-4351-9 |
work_keys_str_mv |
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