Numt-Mediated Double-Strand Break Repair Mitigates Deletions during Primate Genome Evolution

Abstract

Non-homologous end joining (NHEJ) is the major mechanism of double-strand break repair (DSBR) in mammalian cells. NHEJ has traditionally been inferred from experimental systems involving induced double strand breaks (DSBs). Whether or not the spectrum of repair events observed in experimental NHEJ reflects the repair of natural breaks by NHEJ during chromosomal evolution is an unresolved issue. In primate phylogeny, nuclear DNA sequences of mitochondrial origin, numts, are inserted into naturally occurring chromosomal breaks via NHEJ. Thus, numt integration sites harbor evidence for the mechanisms that act on the genome over evolutionary timescales. We have identified 35 and 55 lineage-specific numts in the human and chimpanzee genomes, respectively, using the rhesus monkey genome as an outgroup. One hundred and fifty two numt-chromosome fusion points were classified based on their repair patterns. Repair involving microhomology and repair leading to nucleotide additions were detected. These repair patterns are within the experimentally determined spectrum of classical NHEJ, suggesting that information from experimental systems is representative of broader genetic loci and end configurations. However, in incompatible DSBR events, small deletions always occur, whereas in 54% of numt integration events examined, no deletions were detected. Numts show a statistically significant reduction in deletion frequency, even in comparison to DSBR involving filler DNA. Therefore, numts show a unique mechanism of integration via NHEJ. Since the deletion frequency during numt insertion is low, native overhangs of chromosome breaks are preserved, allowing us to determine that 24% of the analyzed breaks are cohesive with overhangs of up to 11 bases. These data represent, to the best of our knowledge, the most comprehensive description of the structure of naturally occurring DSBs. We suggest a model in which the sealing of DSBs by numts, and probably by other filler DNA, prevents nuclear processing of DSBs that could result in deleterious repair.

Directed networks reveal genomic barriers and DNA repair bypasses to lateral gene transfer among prokaryotes

“…During religation, exogenous DNA may be captured in the chromosome, leading to insertion of DNA into the genome. In eukaryotes, DNA inserted into the genome by NHEJ during evolution may include foreign DNA fragments such as mitochondrial DNA, transposable elements, and viral DNA (Moore and Haber 1996;Ricchetti et al 1999;Lin and Waldman 2001a;Lin and Waldman 2001b;Nakai et al 2003;Hazkani-Covo and Covo 2008). The classical eukaryotic NHEJ machinery includes the KU70/80 heterodimer (KU), XRCC4, Ligase IV, and DNA-PKcs proteins (Bassing and Alt 2004;Lieber et al 2004).…”

Analysis of plastid and mitochondrial DNA insertions in the nucleus (NUPTs and NUMTs) of six plant species: size, relative age and chromosomal localization

“…It was suggested that the insertion mechanism involves double-strand break repair via NHEJ (Hazkani-Covo and Covo, 2008). The availability of whole-genome sequences of more species has enabled a more detailed study of genomic structure of NUPTs and NUMTs.…”

Symbiogenesis, gradualism, and mitochondrial energy in eukaryote origin

“…No mutation, no evolution, regardless of population size. Gene transfers from endosymbiotic organelles to their host are a mechanism of mutation that is both specific to symbiogenesis and specific to the eukaryotic lineage (124,125,126). Eukaryotes are genetic chimaeras, with more bacterial genes than archaeal genes (127,128,129,130), and gene transfers from mitochondria and chloroplasts continue to permeate eukaryotic chromosomes via known mechanisms -non homologous end joining (126) -that can be observed in the laboratory (131).…”

“…Gene transfers from the mitochondrial symbiont to host chromosomes were important at eukaryote origin (41). Given what we have learned about the abundance of plastid and mitochondrial DNA in eukaryotic genome sequences (124,125,126,132,133), that set of propositions would seem far less controversial than it did 20 years ago, one would think.…”

“…At any rate, the 580 kb of recently acquired mitochondrial DNA in our own human nuclear genome (126,133) in addition to the complete 660 kb mitochondrial genome on chromosome 2 of Arabidopsis and the 130 kb complete plastid genome on chromosome 10 of rice (136) are best explained by accepting the proposition that gene transfers from mitochondria and plastids to the nucleus really do occur during evolution (137).…”