Comprehensive Chromosome End Remodeling During Programmed DNA Elimination

Abstract

Germline and somatic genomes are typically the same in a multicellular organism. However, in some organisms including the parasitic nematode Ascaris, programmed DNA elimination leads to a reduced somatic genome compared to germline cells. Previous work on the parasitic nematode Ascaris demonstrated that programmed DNA elimination encompasses high fidelity chromosomal breaks at specific genome locations and loss of specific genome sequences including a major tandem repeat of 120 bp and ~1,000 germline-expressed genes. However, the precise chromosomal locations of the 120 bp repeats, the breaks regions, and the eliminated genes remained unknown. Here, we used PacBio longread sequencing and chromosome conformation capture (Hi-C) to obtain fully assembled chromosomes of Ascaris germline and somatic genomes, enabling a complete chromosomal view of DNA elimination.Surprisingly, we found that all 24 germline chromosomes undergo comprehensive chromosome end remodeling with DNA breaks in their subtelomeric regions and loss of distal sequences including the telomeres at both chromosome ends. All new Ascaris somatic chromosome ends are recapped by de novo telomere healing. We provide an ultrastructural analysis of DNA elimination and show that Ascaris eliminated DNA is incorporated into many double membrane-bound structures, similar to micronuclei, during telophase of a DNA elimination mitosis. These micronuclei undergo dynamic changes including loss of active histone marks and localize to the cytoplasm following daughter nuclei formation and cytokinesis where they form autophagosomes. Comparative analysis of nematode chromosomes suggests that germline chromosome fusions occurred forming Ascaris sex chromosomes that become independent chromosomes following DNA elimination breaks in somatic cells. These studies provide the first chromosomal view and define novel features and functions of metazoan programmed DNA elimination.

Delete and survive: strategies of programmed genetic material elimination in eukaryotes

“…2). In nematodes, following DNA breaks chromosomal fragment ends are healed with de novo telomere addition (Müller & Tobler, 2000; Wang et al ., 2020) (Fig. 2B).…”

Nematode Small RNA Pathways in the Absence of piRNAs

“…For AGO-clade Ascaris Argonautes, the miRNA Argonautes (AsALG-1 and AsALG-6) are expressed in both the male and female germline, early development, and larvae but are present at much lower levels in somatic tissues including the muscle, intestine, and carcass. AsALG-6 is eliminated during Ascaris programmed DNA elimination [66][67][68]. The 26G-RNA Argonaute, AsALG-4, is highly and predominantly expressed in the male germline and highest during meiosis.…”

“…Ascaris chromosomes exhibit a relatively uniform distribution of genes [67] (Figure S4). However, repetitive sequences and mobile elements are biased toward DNA that is eliminated during programmed DNA elimination [66][67][68].…”

“…Ascaris chromosomes exhibit a relatively uniform distribution of genes [67] (Figure S4). However, repetitive sequences and mobile elements are biased toward DNA that is eliminated during programmed DNA elimination [66][67][68]. These eliminated sequences are at the ends of all germline chromosome (including 50-100 kb of subtelomeric repeat sequence that precedes the telomeres) and in the middle of a few chromosomes.…”

“…These genes can be categorized into two broad groups based on their expression profiles. One group includes genes expressed throughout male germline development (M1-M7; 4,363 genes) whereas the other group are genes specifically expressed during meiosis (M5-M7; 1,163 genes, of which 232 are eliminated by programmed DNA elimination in early development [66][67][68]). Figure 6A shows an example of these two groups as neighboring genes on chromosome 1.…”