Content of and interactions between repetitive elements in programmatically eliminated chromosomes of the sea lamprey (Petromyzon marinus)

ABSTRACT The sea lamprey (Petromyzon marinus) is one of few vertebrate species that is known to reproducibly eliminate large fractions of its genome during normal embryonic development. In lamprey, elimination events are initiated at the 6th embryonic cleavage and result in the loss of ∼20% of an embryo’s genomic DNA from essentially all somatic cell lineages (these same sequences are retained in the germline). This germline-specific DNA is lost in the form of large fragments, including entire chromosomes, and available evidence suggests that DNA elimination acts as a permanent silencing mechanism that prevents the somatic expression of a specific subset of “germline” genes. However, reconstruction of eliminated regions has proven challenging due to the complexity of the lamprey karyotype (84 small pairs of somatic chromosomes and ∼100 pairs of germline chromosomes), the exceedingly high repeat content of the genome and even higher repeat content of eliminated fragments. We applied an integrative approach aimed at further characterization of the large-scale structure of eliminated segments, including: 1) in silico identification of germline-enriched repeats; mapping the chromosomal location of specific repetitive sequences in germline metaphases, and verification of repeat specificity to eliminated chromosomes by 3D DNA/DNA-hybridization to embryonic lagging anaphases. Our integrative approach resulted in the discovery of multiple highly abundant repetitive elements that are found exclusively on the eliminated (germline-specific) chromosomes which in turn permitted the identification of 12 individual chromosomes that are programmatically eliminated during early embryogenesis. The fidelity of germline-specific repetitive elements and their distinctive patterning in elimination anaphases are taken as evidence that these sequences might contribute to the specific targeting of chromosomes for elimination and possibly in molecular interactions that mediate their decelerated poleward movement in chromosome elimination anaphases, isolation from the primary nuclei and eventual degradation. AUTHOR SUMMARY Epigenetic silencing methods provide a means of precisely restricting gene expression while maintaining the integrity of the genomic template that encodes this information, and are employed by diverse species throughout the tree of life. Programmed genome rearrangement (PGR) represents a parallel approach that maintains genome integrity across generations but alters the genomes of cells within an organism. To better resolve elimination events that take place during PGR in the sea lamprey (one of few vertebrate species known to undergo large scale PGR) we sought to identify sequences that define specific eliminated chromosomes. Using computational predictions and cytogenetic validation, we identified six new repetitive elements that are restricted to the eliminated chromosomes and permit the identification of twelve distinct eliminated chromosomes. Analysis of these repeats in meiotic testes and in embryos sampled during the process of elimination shows that these repeats localize to specific subcellular regions, and suggest a potential role of these repetitive elements in targeting chromosomes for silencing via elimination.