Abstract
BackgroundWe have recently identified a number of Quantitative Trait Loci (QTL) contributing to the 2-fold muscle weight difference between the LG/J and SM/J mouse strains and refined their confidence intervals. To facilitate nomination of the candidate genes responsible for these differences we examined the transcriptome of the tibialis anterior (TA) muscle of each strain by RNA-Seq.Results13,726 genes were expressed in mouse skeletal muscle. Intersection of a set of 1061 differentially expressed transcripts with a mouse muscle Bayesian Network identified a coherent set of differentially expressed genes that we term the LG/J and SM/J Regulatory Network (LSRN). The integration of the QTL, transcriptome and the network analyses identified eight key drivers of the LSRN (Kdr, Plbd1, Mgp, Fah, Prss23, 2310014F06Rik, Grtp1, Stk10) residing within five QTL regions, which were either polymorphic or differentially expressed between the two strains and are strong candidates for quantitative trait genes (QTGs) underlying muscle mass. The insight gained from network analysis including the ability to make testable predictions is illustrated by annotating the LSRN with knowledge-based signatures and showing that the SM/J state of the network corresponds to a more oxidative state. We validated this prediction by NADH tetrazolium reductase staining in the TA muscle revealing higher oxidative potential of the SM/J compared to the LG/J strain (p<0.03).ConclusionThus, integration of fine resolution QTL mapping, RNA-Seq transcriptome information and mouse muscle Bayesian Network analysis provides a novel and unbiased strategy for nomination of muscle QTGs.
Highlights
We have recently identified a number of Quantitative Trait Loci (QTL) contributing to the 2-fold muscle weight difference between the LG/J and SM/J mouse strains and refined their confidence intervals
The analyses based on three independent sources of information converged on a set of eight genes (Kdr, Plbd1, Mgp, Fah, Prss23, 2310014F06Rik, Grtp1, Stk10) as the most likely quantitative trait genes (QTGs) residing within five QTL regions
Transcriptome The present study identified 13,726 genes expressed in mouse skeletal muscle, which approximately doubles the number reported earlier in a microarray based study
Summary
We have recently identified a number of Quantitative Trait Loci (QTL) contributing to the 2-fold muscle weight difference between the LG/J and SM/J mouse strains and refined their confidence intervals. To facilitate nomination of the candidate genes responsible for these differences we examined the transcriptome of the tibialis anterior (TA) muscle of each strain by RNA-Seq. The aim of functional genomics is to understand the role of specific genes in phenotypic variation. The forward genetics approach has led to a large number of identified genomic regions, known as quantitative trait loci (QTL), influencing various phenotypes, including those for muscle weight [1,2,3,4]. It has been proposed that testing for the expression differences could identify genes underlying phenotypic differences [7] Implementation of such strategy led to several nominations of QTG’s [8,9]. Transcriptome analyses by means of a massive parallel sequencing technology, RNA-Seq, circumvents the above-mentioned limitations [11,12], it is highly replicable [13] and a very attractive research method for an unbiased identification of differentially expressed genes
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