Dissecting the sources of genetic variation in regulation of gene expression within D. simulans isolates. Hosseinali Asgharian¹, Rita M Graze², Bradley J Main¹, Marta L Wayne², Alison M Morse², Lauren M McIntyre², Sergey V Nuzhdin¹. 1) Molecular and Computational Biology, University of Southern California, Los Angeles, CA; 2) Molecular Genetics and Microbiology, University of Florida, Gainesville, FL.

   Variation in cis and trans controllers of gene expression (e.g. change in DNA sequence of a promoter, or change in protein sequence or abundance of a transcription factor) can result in gene expression variation. Understanding the nature of this variation is essential to the study of phenotypic and genomic evolution. We used overall and allele-specific expression profiling in Drosophila simulans lines to estimate the prevalence of gene expression variation due to cis, trans and cis-by-trans effects. Allelic imbalance in the heterozygous F1 offspring of two isogenic lines (referred to as full heterozygotes) is due to cis effects. Differential expression of the same allele in the heterozygous F1 vs. the homozygous parental line is due to a trans effect. Introgression lines with a common reference background and a varying natural allele for a large portion of the 3rd chromosome were constructed. F1 introgression heterozygotes were made by backcrossing the introgression to the reference line. The difference in allelic imbalance for genes within the introgression region in the full heterozygotes vs. in the introgression heterozygotes reflects cis-by-trans interactions. At FDR=0.2, 60% (5454/9090) of autosomal genes in females, 49% (744/1507) of X-linked genes in females and 48% (4361/9089) of autosomal genes in males showed evidence for cis variation. In contrast, genes showing trans variation was only ~1.5% of genes in most settings, the exception being autosomal genes in females where it was 6.2% (565/9104). Cis-by-trans interactions were seen in 8.0% (77/967) and 2.7% (26/968) of genes in females and males, respectively. The connection of cis, trans and cis-by-trans variation with sex-biased expression, functional category (GO annotation) and belonging to the tentative groups of transcription factors or target genes was explored.