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


RESULTS
71 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.


CONCLUSIONS
Exon 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.
Molecular and Cellular Biology Program, University of Washington, Seattle, WA 98195, USA. wan-lin_su@merck.com
Wan-Lin
WL
Su
Barmak
B
Modrek
Debraj
D
GuhaThakurta
Stephen
S
Edwards
Jyoti K
JK
Shah
Amit V
AV
Kulkarni
Archie
A
Russell
Eric E
EE
Schadt
Jason M
JM
Johnson
John C
JC
Castle
D000818:Animals; D005091:Exons / Q000235:genetics*; D005260:Female; D020869:Gene Expression Profiling; D014644:Genetic Variation; D008099:Liver / Q000378:metabolism; D008297:Male; D051379:Mice / Q000145:classification* / Q000235:genetics*; D008809:Mice, Inbred C3H; D008810:Mice, Inbred C57BL; D008811:Mice, Inbred DBA; D020411:Oligonucleotide Array Sequence Analysis; D020641:Polymorphism, Single Nucleotide; D012326:RNA Splicing / Q000235:genetics; D012727:Sex Characteristics