Program > Browse abstracts by speaker > Despot-Slade Evelin

Repetitive DNA constitutes a substantial portion of eukaryotic genomes, but is often absent from genome assemblies because its repetitive nature causes difficulties during assembly process. With the development of long-read sequencing, these regions are becoming increasingly accessible for in-depth research. Despite advances in genomics, the epigenetic regulation of repetitive DNA remains largely unexplored. In our study, we investigated the intricate landscape of transposable elements (TEs) and satellite DNA (satDNA) and their influence on neighboring regions in the insect model organism Tribolium castaneum. First, we utilized nanopore sequencing unique ability to detect methylated DNA bases to study epigenetic modifications of repetitive DNA. To further decipher epigenetic regulation, we explored mechanisms at the protein level by performing ChIP-seq experiments and targeting various active and repressive histone marks corroborated by immunostaining with different histone antibodies. Additionally, to investigate the presence of non-coding RNAs with regulatory function we performed small RNA sequencing experiments. Surprisingly, our results show the absence of 5-methylcytosine and extremely low levels of N6-methyladenine modifications, indicating that these epigenetic markers probably do not affect biological processes in the genome of T. castaneum. In contrast, histone modifications analyses indicate a possible regulatory role of these modifications in epigenetic control of TEs and satDNA. Transcriptional analysis showed developmentally regulated patterns and differentially expressed repetitive DNA. Furthermore, small RNA examination indicated a preferred sequence length originating from the most conserved part of the repetitive elements highlighting the possibility of underlying regulatory mechanisms. Our comprehensive study has provided novel insights into epigenetic mechanisms of repetitive DNA regulation in T. castaneum, laying the foundation for future investigations into their impact on gene regulation and overall genome dynamics.