Maintenance of genome integrity is essential. In the parasitic nematode Ascaris, programmed DNA elimination removes specific DNA sequences from the genome during early development in somatic cells (4-16 cell stage), leaving the germline genome intact. We found that ~13% of the genome is eliminated during DNA elimination. The eliminated DNA consists of repetitive and unique sequences, including ~1000 genes (5% of all genes). The same DNA is eliminated independently in five different pre-somatic cells that give rise to different cell lineages. The eliminated genes are primarily expressed in the germline, suggesting that DNA elimination in Ascaris is an irreversible mechanism for silencing a subset of germline-expressed genes in somatic tissues. We identified ~40 sites where chromosome breaks occur and are healed by telomere addition. We sequenced the genomes of a related horse parasitic nematode Parascaris, that also undergoes DNA elimination, to determine how conserved DNA elimination is in nematodes. The DNA breaks, eliminated genes, and the expression pattern of the eliminated genes are largely conserved between Ascaris and Parascaris indicating that DNA elimination is a specific, conserved and highly regulated process. We further show that Ascaris has holocentric chromosomes in the germline. Prior to DNA elimination in the four-cell embryo, CENP-A, the epigenetic mark of centromeres, is signi?cantly diminished in chromosome regions that will be lost. This leads to the absence of kinetochores and microtubule attachment sites necessary for chromosome segregation, resulting in loss of these chromosome regions during mitosis. These data suggest that CENP-A localization contributes to the identi?cation of regions to be retained and lost playing a regulatory and mechanistic role in DNA elimination. Finally, we identified two worm specific Argonautes (WAGO) associated with condensed chromosomes during DNA elimination. One WAGO preferentially associates with retained DNA only during a DNA elimination mitosis. The other WAGO is enriched on DNA that will be eliminated. Thus, these WAGOs, their associated small RNAs and/or proteins may play a role in nematode DNA elimination. Supported by NIH Grants AI049558 and AI114054 to RED.

Affiliation:
- Biochemistry and Molecular Genetics, University of Colorado School of Medicine, Aurora, CO