A centromere-derived retroelement RNA localizes in cis and is a core element of the transcriptional landscape of Drosophila centromeres

Centromeres are essential chromosomal landmarks that dictate the point of attachment between chromosomes and spindle microtubules during cell division. The stable transmission of the centromere site through generations is ensured by a unique chromatin containing the histone H3 variant CENP-A. Previous studies have highlighted the impact of transcription on promoting CENP-A deposition. However, the specific sequences undergoing this transcription and their contribution to centromere function in metazoan systems remain elusive. In this study, we unveil the centromeric transcriptional landscape and explore its correlation with CENP-A in D. melanogaster, currently the only in vivo model with assembled centromeres. We find that the centromere-enriched retroelement G2/Jockey-3 (hereafter referred to as Jockey-3) is a major driver of centromere transcription, producing RNAs that localize to all mitotic centromeres, with the Y centromere showing the most transcription. Taking advantage of the polymorphism of Jockey-3, we show that these RNAs remain associated with their cognate DNA sequences in cis. Using a LacI/lacO system to generate de novo centromeres, we find that Jockey-3 transcripts do not localize to ectopic sites, suggesting they are unlikely to function as non-coding RNAs with a structural role at centromeres. At de novo centromeres on the lacO array, the presence of CENP-A augments the detection of exogenous lacO-derived transcripts specifically in metaphase. We propose that Jockey-3 contributes to the epigenetic maintenance of the centromere by promoting chromatin transcription, while inserting in a region that permits its continuous transmission. Given the conservation of retroelements as centromere components across taxa, our findings have broad implications in understanding this widespread association.

The evolutionary history of Drosophila simulans Y chromosomes reveals molecular signatures of resistance to sex ratio meiotic drive

The recent evolutionary history of the Y chromosome in Drosophila simulans, a worldwide species of Afrotropical origin, is closely linked to that of X-linked meiotic drivers (Paris system). The spread of the Paris drivers in natural populations has elicited the selection of drive resistant Y chromosomes. To infer the evolutionary history of the Y chromosome in relation to the Paris drive, we sequenced 21 iso-Y lines, each carrying a Y chromosome from a different location. Among them, 13 lines carry a Y chromosome that is able to counteract the effect of the drivers. Despite their very different geographical origins, all sensitive Y's are highly similar, suggesting that they share a recent common ancestor. The resistant Y chromosomes are more divergent and segregate in four distinct clusters. The phylogeny of the Y chromosome confirms that the resistant lineage predates the emergence of Paris drive. The ancestry of the resistant lineage is further supported by the examination of Y-linked sequences in the sister species of D. simulans, D. sechellia, and D. mauritiana. We also characterized the variation in repeat content among Y chromosomes and identified multiple simple satellites associated with resistance. Altogether, the molecular polymorphism allows us to infer the demographic and evolutionary history of the Y chromosome and provides new insights on the genetic basis of resistance.