Bimodal distribution of RNA expression levels in human skeletal muscle tissue

Abstract

BackgroundMany human diseases and phenotypes are related to RNA expression, levels of which are influenced by a wide spectrum of genetic and exposure-related factors. In a large genome-wide study of muscle tissue expression, we found that some genes exhibited a bimodal distribution of RNA expression, in contrast to what is usually assumed in studies of a single healthy tissue. As bimodality has classically been considered a hallmark of genetic control, we assessed the genome-wide prevalence, cause, and association of this phenomenon with diabetes-related phenotypes in skeletal muscle tissue from 225 healthy Pima Indians using exon array expression chips.ResultsTwo independent batches of microarrays were used for bimodal assessment and comparison. Of the 17,881 genes analyzed, eight (GSTM1, HLA-DRB1, ERAP2, HLA-DRB5, MAOA, ACTN3, NR4A2, and THNSL2) were found to have bimodal expression replicated in the separate batch groups, while 24 other genes had evidence of bimodality in only one group. Some bimodally expressed genes had modest associations with pre-diabetic phenotypes, of note ACTN3 with insulin resistance. Most of the other bimodal genes have been reported to be involved with various other diseases and characteristics. Association of expression with cis genetic variation in a subset of 149 individuals found all but one of the confirmed bimodal genes and nearly half of all potential ones to be highly significant expression quantitative trait loci (eQTL). The rare prevalence of these bimodally expressed genes found after controlling for batch effects was much lower than the prevalence reported in other studies. Additional validation in data from separate muscle expression studies confirmed the low prevalence of bimodality we observed.ConclusionsWe conclude that the prevalence of bimodal gene expression is quite rare in healthy muscle tissue (<0.2%), and is much lower than limited reports from other studies. The major cause of these clearly bimodal expression patterns in homogeneous tissue appears to be cis-polymorphisms, indicating that such bimodal genes are, for the most part, eQTL. The high frequency of disease associations reported with these genes gives hope that this unique feature may identify or actually be an underlying factor responsible for disease development.

Genes and the ageing muscle: a review on genetic association studies

“…Thus, future expression studies in the elderly might also help providing new insights into the genetic associations of important disease phenotypes in this population. For instance, the authors of the aforementioned study found that insulin sensitivity was higher in those individuals with the low mode of ACTN3 expression (Mason et al 2011).…”

“…Nonetheless, ideally this would require collecting skeletal muscle biopsies, which might not be easily feasible in the elderly. The relevant information that can be obtained with gene expression studies is best exemplified by a recent study on the RNA expression of 17,881 genes at the skeletal muscle level in a cohort of healthy Pima Indians (age range 18-50 years) (Mason et al 2011). Using exon array expression chips, the authors found ACTN3 to be one of the only eight genes that showed bimodal expression.…”

An integrative analysis reveals coordinated reprogramming of the epigenome and the transcriptome in human skeletal muscle after training

“…This is exemplified by THNSL2 (in the bottom left panel of Figure 4D), whose bimodal expression has been linked to a cis-eQTL in muscle tissue. 25 A c c e p t e d M a n u s c r i p t 10 For more examples, see Table S12.…”

HLA-DRB1 reduces the risk of type 2 diabetes mellitus by increased insulin secretion

“…Gene expression signals were normalised using the robust multichip average method [20] and GC correction. The parameters of the best-fitting bimodal distribution were estimated by maximum likelihood methods after transforming expression data to correct for skewness using the most appropriate Box-Cox parameter, as previously described [10,21]. Individuals were classified into high and low expression categories of HLA-DRB1 based on these parameters [10].…”

“…The expression levels of several skeletal muscle mRNA transcripts in the exon array study had a bimodal frequency distribution, and these transcripts were found to be highly significant expression quantitative trait loci (eQTL), one of which was transcribed from HLA-DRB1 [10]. The aim of the present study was to assess genetic variation at the HLA-DRB1 region and determine its possible role in gene expression and type 2 diabetes.…”