Functional Analyses of Histone Methyltransferases in Sea Lamprey Embryos Undergoing Programmed DNA Elimination

During early embryogenesis, the sea lamprey (Petromyzon marinus) undergoes a dramatic form of genome reprogramming wherein specific chromosomes are selectively eliminated from somatic progenitor cells. These programmatic elimination events effectively silence all genes on these chromosomes in all somatic cells. Previous studies in lamprey and other eliminating species have shown that epigenetic silencing marks are enriched on germline-specific chromosomes during programmed elimination. These silencing marks include the histone marks H3K9me3 and H4K20me3, which are respectively deposited by KMT1A/SUV39 and KMT5/SUV420 methyltransferases. To test whether lamprey homologs of these methyltransferases contribute to deposition of silencing marks on eliminated (micronucleated) chromatin and whether these marks contribute to the highly coordinated process of DNA elimination in sea lamprey, we used Cas9 gene editing, lightsheet imaging and RNA sequencing to investigate their potential roles in DNA elimination and more generally during early development. Analysis of knockout embryos for four histone methyltransferases show that these genes contribute to the deposition of repressive histone marks on elimination micronuclei, but are not essential for programmed DNA elimination per se. Analysis of later embryogenic stages suggests that these marks may contribute to interim silencing of germline-specific chromosomes, and reveals major impacts on post-blastula survival and development.