Cis-regulatory determinants of Y-linked gene expression variation. Timothy Sackton, Jun Zhou, Daniel Hartl. Organismic & Evol Bio, Harvard Univ, Cambridge, MA.

   Over the past five years, our lab has demonstrated that variation on the Y chromosome in Drosophila has significant effects on the expression of hundreds of autosomal and X-linked genes. This phenomenon is not solely attributable to expression of Y-linked genes, as it is observable in XXY females (where transcription from the Y is absent) suggesting that structural variation on the Y chromosome plays a role in modulating expression elsewhere in the genome. Recently, we have shown that genes that are susceptible to Y-linked regulatory variation (YRV) are significantly more likely to be located in intercalary heterochromatin and present in the nuclear periphery than expected. However, it remains unclear if the expression effects of Y-linked variation are solely driven by the genomic location of the target genes, or if cis-regulatory sequences can impact the susceptibility of a gene to YRV. In order to address this question, we measured allele-specific expression using RNA-seq in D. simulans intraspecific crosses where in all cases the genomic background is the same, but each F1 strain carries a different D. simulans Y chromosome. In this design, cis-regulatory effects can be detected if we observe genes whose expression differs between alleles in some Y chromosomal contexts but not others. This kind of allele-by-Y effect can only easily arise if a particular Y chromosome shifts the expression of one allele at a locus but not the other, presumably due to cis-regulatory sequence on only one of the two alleles. Here, we present the results of this analysis, which demonstrate the impact of cis-regulatory sequences on YRV.