Effects of SUV39H1 and SUV420H1/H2 on Programmed Genome Rearrangement in Petromyzon marinus

The sea lamprey (Petromyzon marinus), diverged from the vertebrate lineage roughly 550 million years ago, prior to the evolution of several major morphological features such as jaws and paired fins/appendages. Lamprey therefore provides a comparative perspective that can be used to study the evolution of differences in genome regulation, including epigenetics and programmed genome rearrangement (PGR). Programmed genome rearrangement is a unique regulatory mechanism wherein specific genes are effectively turned off by completely eliminating their sequences from the genome. Through PGR, lamprey delete approximately 20% of their genome from all somatic cells, with these specific sequences being only retained by germline cells. The mechanisms of PGR have yet to be fully understood; however, we hypothesized that two genes (SUV420H1/2 and SUV39H1) might be involved in the process. The gene SUV420H1/2 encodes a methyltransferase that trimethylates Histone 4 at Lysine 20, a site important for recruitment of factors necessary for DNA damage response and DNA repair, which could plausibly be involved in the elimination of DNA during PGR. The gene SUV39H1 transcribes a methyltransferase that is responsible for catalyzing di- and tri-methylation of Histone 3 at Lysine 9, a significant marker for heterochromatic DNA. Due to its function, it is suspected that PGR levels might decrease in CRISPR-mediated knockouts because the embryos will be lacking a marker for chromatin packaging and deletion. Results from light-sheet microscopy demonstrated that both SUV420H1/2 and SUV39H1 significantly affect levels of PGR. These results indicate that additional genes within the suppressor of variegation family should be further investigated for potential contributions to PGR. These genes were further analyzed through immunohistochemistry, fluorescence in situ hybridization (FISH), and RNA sequencing to more directly observe the effects of knockouts on histone methylation and further precisely characterize impacts on PGR