Identifying misregulated genes contributing to male lethality in <i>D. melanogaster/D. simulans</i> hybrids with RNA-seq.

Identifying misregulated genes contributing to male lethality in D. melanogaster/D. simulans hybrids with RNA-seq. Kevin HC Wei, Andrew G Clark, Daniel A Barbash. Molecular Biology and Genetics, Cornell, Ithaca, NY.

Mutations in the D. melanogaster (D. mel) gene Hybrid male rescue (Hmr) suppress male larval lethality in F1 hybrids produced by D. mel females mated to D. simulans (D. sim) males. However, the function of Hmr within D. mel and the mechanism by which it induces male lethality in hybrids remains poorly understood. To investigate the role of Hmr in both D. mel and hybrid genomes during larval development, we profiled the transcriptomes of 72hr-old larvae with RNA-seq to identify genes misregulated in Hmr mutants (Hmr^- D. mel) compared to wildtype D.mel (wt D. mel), and genes differentially regulated in rescued hybrids (Hmr^- hybrid) compared to lethal hybrids (wt hybrid). In Hmr^- D.mel, we only detected 20 genes significantly misregulated; almost all of them (18) are upregulated, strongly indicating that Hmr is a repressor. Comparing between the Hmr^- and wt hybrids, we identified a large set of 473 differentially expressed genes. In contrast to the over-representation of upregulated genes in Hmr^- D. mel, fewer genes are up-regulated (154) than down-regulated (319) in Hmr^- hybrids. Additionally, of the differentially expressed autosomal genes between the hybrids, significantly more D. mel alleles are misregulated (345) than D. sim alleles (265), suggesting the D.mel genome is under greater perturbation in the wt hybrids. To characterize developmental defects contributing to hybrid lethality, we compared the expression profiles of our 72 hr-old larva to that of L2 and early L3 larva generated by the modENCODE consortium. Consistent with previous reports that hybrids are developmentally delayed, hybrids in general are more L2-like than D. mel, and wt hybrids have the most genes expressed at L2-like levels. Of the 42 genes expressed at L2-like levels only in wt hybrids, we find a striking enrichment for genes expressed in the larval central nervous system (31) and the thoracioabdominal ganglion (37), suggesting a substantial developmental lag for the nervous system of wt hybrids.