Programmed chromosome fragmentation in ciliated protozoa: multiple means to chromosome ends

Abstract

SUMMARY Ciliated protozoa undergo large-scale developmental rearrangement of their somatic genomes when forming a new transcriptionally active macronucleus during conjugation. This process includes the fragmentation of chromosomes derived from the germline, coupled with the efficient healing of the broken ends by de novo telomere addition. Here, we review what is known of developmental chromosome fragmentation in ciliates that have been well-studied at the molecular level ( Tetrahymena , Paramecium , Euplotes , Stylonychia , and Oxytricha ). These organisms differ substantially in the fidelity and precision of their fragmentation systems, as well as in the presence or absence of well-defined sequence elements that direct excision, suggesting that chromosome fragmentation systems have evolved multiple times and/or have been significantly altered during ciliate evolution. We propose a two-stage model for the evolution of the current ciliate systems, with both stages involving repetitive or transposable elements in the genome. The ancestral form of chromosome fragmentation is proposed to have been derived from the ciliate small RNA/chromatin modification process that removes transposons and other repetitive elements from the macronuclear genome during development. The evolution of this ancestral system is suggested to have potentiated its replacement in some ciliate lineages by subsequent fragmentation systems derived from mobile genetic elements.

End resection and telomere healing of DNA double-strand breaks during nematode programmed DNA elimination

“…In contrast, in Paramecium, microheterogeneity (500-800 bp) and macroheterogeneity (several kbs) are observed for telomere addition (12), similar to the canonical CBRs and alternative CBRs observed in Ascaris and Parascaris. Telomerase is responsible for telomere addition in ciliates (12). We identified a single telomerase gene in Ascaris and O. tipulae, and its expression is elevated in both species during PDE (20,24,25,30), suggesting the telomerase is likely responsible for telomere addition during PDE.…”

“…This differs from the telomere addition in O. tipulae, where telomeres are added directly to the break site (20). In contrast, in Paramecium, microheterogeneity (500-800 bp) and macroheterogeneity (several kbs) are observed for telomere addition (12), similar to the canonical CBRs and alternative CBRs observed in Ascaris and Parascaris. Telomerase is responsible for telomere addition in ciliates (12).…”

“…The motif-based and the sequence-independent DSBs in nematodes are reminiscent of PDE in ciliates, where in some species (Tetrahymena and Euplotes), specific motifs are used to generate the DSBs (71)(72)(73), while in others (Paramecium) the break sites appear to be sequence-independent (12). Interestingly, in Tetrahymena, the initial DSB ends are trimmed by a variable distance of 4-30 bp, leading to heterogeneity in the telomere addition sites despite using a motif-based mechanism (74).…”

“…Loss of entire chromosome(s) occurs in some arthropods, birds, lampreys, hagfish, and mammals. In the second mechanism, chromosomes are broken, and specific fragments are reproducibly retained or lost (10,12). Chromosome fragmentation requires the generation of DNA double-strand breaks (DSBs) and their subsequent healing.…”

“…The majority of the DSBs are generated during the excision of internal eliminated sequences (IESs) by domesticated transposases, followed by the fusion of broken ends through non-homologous end joining (NHEJ) mediated repair (5)(6)(7). The second form of DSBs occurs during chromosome fragmentation at the chromosome breakage sequences (12). This process is coupled with de novo telomere addition using telomerase (17,18).…”