Imprinting in Adult Female D. melanogaster

Genomic imprinting occurs when one allele in a diploid organism is epigenetically modified such that its expression differs based on the sex of the parent that transmitted the allele. In D. melanogaster, imprinting exists, but its impact on transcript abundance genome-wide is unclear. Here, we search for imprinted genes in D. melanogaster using RNA-seq to compare allele-specific expression between pools of 7-10 day old adult female progeny from reciprocal crosses. 119 genes with allelic expression patterns consistent with imprinting were identified and showed significant clustering within the genome. Surprisingly, additional analysis of several of these genes showed that imprinting-like expression was caused by something other than imprinting in every case. Specifically, genomic heterogeneity and high levels of intrinsic noise were responsible for differences in relative allelic expression observed for putatively imprinted genes. Consequently, our data show no convincing evidence for imprinting of D. melanogaster genes in their native genomic locations.