Spectrum of variations in dog-1/FANCJ and mdf-1/MAD1 defective Caenorhabditis elegans strains after long-term propagation

Abstract

BackgroundWhole and partial chromosome losses or gains and structural chromosome changes are hallmarks of human tumors. Guanine-rich DNA, which has a potential to form a G-quadruplex (G4) structure, is particularly vulnerable to changes. In Caenorhabditis elegans, faithful transmission of G-rich DNA is ensured by the DOG-1/FANCJ deadbox helicase.ResultsTo identify a spectrum of mutations, after long-term propagation, we combined whole genome sequencing (WGS) and oligonucleotide array Comparative Genomic Hybridization (oaCGH) analysis of a C. elegans strain that was propagated, in the absence of DOG-1 and MDF-1/MAD1, for a total of 470 generations, with samples taken for long term storage (by freezing) in generations 170 and 270. We compared the genomes of F170 and F470 strains and identified 94 substitutions, 17 InDels, 3 duplications, and 139 deletions larger than 20 bp. These homozygous variants were predicted to impact 101 protein-coding genes. Phenotypic analysis of this strain revealed remarkable fitness recovery indicating that mutations, which have accumulated in the strain, are not only tolerated but also cooperate to achieve long-term population survival in the absence of DOG-1 and MDF-1. Furthermore, deletions larger than 20 bp were the only variants that frequently occurred in G-rich DNA. We showed that 126 of the possible 954 predicted monoG/C tracts, larger than 14 bp, were deleted in unc-46 mdf-1 such-4; dog-1 F470 (JNC170).ConclusionsHere, we identified variants that accumulated in C. elegans’ genome after long-term propagation in the absence of DOG-1 and MDF-1. We showed that DNA sequences, with G4-forming potential, are vulnerable to deletion-formation in this genetic background.Electronic supplementary materialThe online version of this article (doi:10.1186/s12864-015-1402-y) contains supplementary material, which is available to authorized users.

Systematic analysis of mutational spectra associated with DNA repair deficiency inC. elegans

“…all 11 dog-1 deficient samples, 81% of long deletions (17/21) and 78% (109/139) of shorter, 50-400 bp deletions overlapped with one of the 4291 regions in the C. elegans genome predicted to form G-quadruplex structures(Marsico et al 2019), in line with previous reports(Tarailo-Graovac et al 2015) …”

“…DOG-1, the C. elegans ortholog of the mammalian FANCJ helicase, facilitates error-free replication through DNA tertiary structures formed by Grich DNA sequences referred to as G-quadruplexes (Cheung et al 2002;Youds et al 2008;Tarailo-Graovac et al 2015). Indeed, dog-1 mutants exhibited increased mutagenesis (Fig.…”

Genetic Modifiers and Rare Mendelian Disease

“…The experimental challenge includes establishing high-throughput forward genetic screening techniques utilizing model organisms as current mutagenesis and screening techniques often take years to identify modifiers [152][153][154]. On the other hand, the computational challenge exists in identifying genetic modifiers by comprehensively analyzing all the variants from an individual genome [155,156].…”

Getting Ready for the Dance: FANCJ Irons Out DNA Wrinkles

“…Tarailo-Graovac et al investigated the incidence of chromosomal abnormalities observed in the absence of both DOG-1 and MDF-1, a component of the spindle-assemble checkpoint that operates to prevent abnormal whole chromosome gains and losses. Using a whole genomics approach, the authors showed that >20 base pair insertions/deletions were most commonly observed near the G-rich DNA in the absence of both DOG-1 and MDF-1, leading the authors to propose that only the neutral or advantageous insertions/deletions were tolerated in this genetic background after longtime propagation [ 49 ].…”