Transcription of a centromere-enriched retroelement and local retention of its RNA are significant features of the CENP-A chromatin landscape

Abstract

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 similarly 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.