Comprehensive Chromosome End Remodeling during Programmed DNA Elimination

• Published in: Current biology 2020-09, Vol.30 (17), p.3397-3413.e4
• Main Authors: Wang, Jianbin, Veronezi, Giovana M.B., Kang, Yuanyuan, Zagoskin, Maxim, O’Toole, Eileen T., Davis, Richard E.
• Format: Article
• Language: English
• Subjects: Animals; Ascaris; Ascaris suum - genetics; chromosome end remodeling; Chromosome Mapping; DNA, Helminth - genetics; Female; genome assembly; Genome, Helminth; Helminth Proteins - genetics; Hi-C; histones; Male; micronuclei; mitosis; nematode; PacBio; programmed DNA elimination; Repetitive Sequences, Nucleic Acid; Sex Chromosomes - genetics; subtelomeric breaks; Telomere - genetics; telomere healing; tomography; ultrastructure
• ISSN: 0960-9822; 1879-0445
• DOI: 10.1016/j.cub.2020.06.058

Germline and somatic genomes are in general the same in a multicellular organism. However, 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 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 these repeats, breaks regions, and eliminated genes remained unknown. We used PacBio long-read 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. 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 Ascaris DNA elimination and show that eliminated DNA is incorporated into 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 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. [Display omitted] •Genome analysis enables a comprehensive chromosome view of nematode DNA elimination•All chromosome ends undergo subtelomeric DNA breaks and de novo telomere addition•All chromosome regions eliminated contain germline expressed genes•Eliminated DNA is sequestered into micronuclei and then cytoplasmic autophagosomes Comprehensive genome analysis of DNA elimination in the nematode Ascaris by Wang et al. provides a chromosome view of DNA elimination demonstrating all chromosome ends undergo subtelomeric DNA breaks, loss of distal sequences, and de novo telomere healing. The eliminated DNA is incorporated into micronuclei that become cytoplasmic autophagosomes.