Comparative genomic analysis and epigenetic profiling of the <i>Drosophila melanogaster</i> B chromosome

Supernumerary B chromosomes have been identified in hundreds of species across many different taxa, each with their own evolutionary history, unique sequence composition, and epigenetic profile. In this study, we generated a detailed repetitive sequence and epigenetic landscape of the B chromosomes in Drosophila melanogaster. By comparing the repetitive DNA content of stocks with (+B) and without (0B) B chromosomes, we found 9 satellite DNA (satDNA) sequences that were enriched in the +B genome, 3 of which were cytogenetically confirmed to be on the B chromosomes. Our satDNA analysis also led to the discovery of 3 novel satDNA repeats that are not on the B chromosomes and have not been described previously (Sat-307, Sat-597, and Sat-228). Analysis of transposable elements (TEs) revealed that although TEs comprise similar proportions of the 0B and +B genomes, the centromeric transposon G2/Jockey is modestly enriched in the +B genome, consistent with the high number of centromeres present in the +B genome. We also immunostained both male somatic and germline tissues to gain insight into the epigenetic state of the B chromosomes and found the presence of heterochromatin-associated histone modifications (H3K9me1, H3K9me2), a lack of acetylation (H4K5ac), and the absence of RNA polymerase II in the B chromosome nuclear territory, suggesting the B chromosomes have a reduced level of transcription. Together, our work further defines the genetic composition of the D. melanogaster B chromosome and establishes its epigenetic profile, which will provide a foundation for future work investigating changes to repetitive DNA over time and how a transcriptionally repressed chromosome influences chromatin maintenance in the genome.