Exon and junction microarrays detect widespread mouse strain- and sex-bias expression differences

Abstract

BackgroundStudies have shown that genetic and sex differences strongly influence gene expression in mice. Given the diversity and complexity of transcripts produced by alternative splicing, we sought to use microarrays to establish the extent of variation found in mouse strains and genders. Here, we surveyed the effect of strain and sex on liver gene and exon expression using male and female mice from three different inbred strains.Results71 liver RNA samples from three mouse strains – DBA/2J, C57BL/6J and C3H/HeJ – were profiled using a custom-designed microarray monitoring exon and exon-junction expression of 1,020 genes representing 9,406 exons. Gene expression was calculated via two different methods, using the 3'-most exon probe ("3' gene expression profiling") and using all probes associated with the gene ("whole-transcript gene expression profiling"), while exon expression was determined using exon probes and flanking junction probes that spanned across the neighboring exons ("exon expression profiling"). Widespread strain and sex influences were detected using a two-way Analysis of Variance (ANOVA) regardless of the profiling method used. However, over 90% of the genes identified in 3' gene expression profiling or whole transcript profiling were identified in exon profiling, along with 75% and 38% more genes, respectively, showing evidence of differential isoform expression. Overall, 55% and 32% of genes, respectively, exhibited strain- and sex-bias differential gene or exon expression.ConclusionExon expression profiling identifies significantly more variation than both 3' gene expression profiling and whole-transcript gene expression profiling. A large percentage of genes that are not differentially expressed at the gene level demonstrate exon expression variation suggesting an influence of strain and sex on alternative splicing and a need to profile expression changes at sub-gene resolution.

Sex-specific and lineage-specific alternative splicing in primates

“…To make the comparison we analyzed our data in the same way. Among the 746 human-mouse orthologous genes common to the two studies, there are 232 genes in Su et al (2008) data, and 97 genes in our data, with evidence for a difference in expression level of at least one exon between sexes (Bonferronicorrected P < 0.01), with an overlap of 37 genes (a moderate enrichment over the overlap expected by chance; P » 0.07, Fisher's exact test). The smaller number of differences identified in our data may partly reflect the pooling of three different species.…”

“…We also compared our results with those of Su et al (2008), who analyzed a total of 1020 genes in mice, and tested individual Figure 3. An example of human-specific change in exon usage.…”

“…For example, Su et al (2008) studied variation in exon usage and alternative splicing in liver samples from a number of mouse strains from both sexes, by using a custom microarray designed to probe the expression levels of 25,760 exons and exonexon junctions from 1312 genes. By analyzing the exon-level data (without correcting for overall gene expression level), Su et al (2008) found that 14% of exons are differentially expressed between sexes.…”

“…For example, Su et al (2008) studied variation in exon usage and alternative splicing in liver samples from a number of mouse strains from both sexes, by using a custom microarray designed to probe the expression levels of 25,760 exons and exonexon junctions from 1312 genes. By analyzing the exon-level data (without correcting for overall gene expression level), Su et al (2008) found that 14% of exons are differentially expressed between sexes. Similarly, using computational searches for alternative splicing events, Pan et al (2005) estimated that more than 11% of human and mouse cassette alternative exons are skipped in one species but used constitutively in the other.…”

Dynamic, Sex-Differential STAT5 and BCL6 Binding to Sex-Biased, Growth Hormone-Regulated Genes in Adult Mouse Liver

“…ex differences characterize the expression of more than 1,000 genes in mouse, rat, and human liver, affecting a wide range of biological processes, including steroid and lipid metabolism, inflammation, and diseased states (11,55,62,67,69). Sex differences in pharmacokinetics and pharmacodynamics have long been recognized and are in part a consequence of the sex-biased expression of cytochrome P450 (CYP) and other drug-metabolizing enzymes (19,50,52,63,68).…”