Fig 1.
PDE occurs during nematode early embryogenesis.
(A) Theodor Boveri’s drawing of P. univalens DNA elimination in a two-cell embryo. Left: interphase, chromosomes in the pre-somatic cell (top) are fragmented from PDE, while the chromosomes from the germ cell (bottom) are intact. Right: anaphase, the pre-somatic cell sequesters the chromosome fragments and leaves the HET arms at the metaphase plate. Image from Wikimedia commons. (B) P. univalens and Ascaris early cell lineage during early development. Germ cells are red, pre-somatic cells are yellow and surrounded by red dots, and somatic cells are blue. PDE occurs during successive divisions in early embryogenesis. Figure adapted from [37,38]. (C) A 4-cell Ascaris embryo with 2 cells undergoing PDE. DAPI staining showing eliminated DNA (artificially colored in red for emphasis) is left at the metaphase plate (red arrow) but retained DNA is segregated to the daughter nuclei. (D) A 6-cell Ascaris embryo with 1 cell undergoing PDE. Eliminated DNA begins to degrade during late anaphase (red arrow). Eliminated DNA fragments from previous PDE events are seen scattered across the embryo. Images in (C) and (D) are from [36]. (E) DAPI and H3S10P immuno-staining of Ascaris PDE. Eliminated DNA at the metaphase plate (red arrow) is stained with an antibody against H3S10P. (F) H3S10P Immuno-EM shows double-membrane bound H3S10P-positive structures between daughter nuclei during telophase of Ascaris PDE. Daughter nuclei are circled in blue. The region containing eliminated DNA is circled in green (for comparison with (E)). Double-membrane structures positive for H3S10P are marked with an asterisk (*). (G) Inset from (F). Arrows point to double-membrane structure. (E) and (F) are adapted from [41].
Fig 2.
Genetic material lost during PDE.
(A) A linear presentation of Ascaris germline chromosomes. All chromosome ends and 12 internal regions are eliminated (shown in red). Many larger chromosomes have internally eliminated sequences which split them into smaller chromosomes in the soma. Eliminated regions containing 121-bp repeats are marked with a red *. Figure adapted from [6]. (B) FISH of 121-bp repeats and telomeric sequences. Top: anaphase in a germline embryo undergoing non-PDE mitosis, with telomeres and 121-bp repeats passing to daughter nuclei. Bottom: anaphase of a PDE mitosis showing 121-bp repeats and telomeres are left at the metaphase plate. (C) Eliminated genes are highly enriched with testis and embryo-expressed genes. Shown are changes of the proportion (in percentage, y-axis) of tissue-specific genes in retained and eliminated DNA (x-axis). (D) Conservation of eliminated genes among Ascaris, Parascaris, and Toxocara. About 36% of genes eliminated in Ascaris have their orthologous genes eliminated in Parascaris and Toxocara. These genes tend to have enriched expression in the testis. Figure adapted from [6].
Fig 3.
(A) A model of PDE process in Ascaris. See text for detailed description. (B) ATAC-seq of Ascaris shows CBRs have open chromatin during PDE (60 hours, 4-cell). (C) Ascaris telomere addition forms in 3–6-kb regions of the genome. Top: telomere addition from a single worm’s intestine (derived from 1 PDE event) shows 2 telomere addition sites. Bottom: telomere addition from a population of worms shows telomeres are randomly distributed across the CBR. (B) and (C) adapted from [40]. (D) CENP-A staining of a 4-cell embryo with 2 cells undergoing PDE. Eliminated DNA (red arrows) is not stained with CENP-A, suggesting the loss of centromeres in the eliminated DNA. Adapted from [39]. (E) A model of centromere reorganization for PDE. Left: germline division with centromeres distributed across the entire chromosome. Right: PDE mitosis with centromeres absent on eliminated regions of the genome. Adapted from [39].
Fig 4.
An evolution model of PDE in nematode chromosomes.
(A) Fusions in Ascaris sex chromosomes. Two representative sex chromosomes with distinct ancestral regions (Nigon elements; each Nigon group is shown in a different color). Eliminated DNA is at the junction of different Nigon elements. (B) Fusion and evolution of chromosomes in nematodes with PDE. Left: hypothetical ancient chromosome karyotypes before and after chromosome end remodeling and DNA elimination in Ascaris, P. univalens, and O. tipulae. Right: modern karyotypes before and after DNA elimination showing internal breaks and end-remodeling. For simplicity, a representative chromosome is shown for all chromosomes within a group that have the same pattern of elimination (terminal and/or internal). The number of chromosomes for each group is indicated above the representative chromosome. (A) and (B) are adapted from [45].