Global screening and extended nomenclature for 230 aphidicolin-inducible fragile sites, including 61 yet unreported ones

Abstract

Abstract. Since the first description of human fragile sites (FS) more than 40 years ago, a variety of substances were reported to induce chromosomal breaks at non-random, breakage-prone regions. According to information available from human genome browsers aphidicolin, an inhibitor of DNA replication induces 77 of 88 known common FS. However, in the literature additional FS are reported, which are also, at least in part, inducible by aphidicolin. To the best of our knowledge, here we present the first and largest ever done systematic, whole genome-directed and comprehensive screening for aphidicolin-inducible breakage-prone regions. The study was performed on stimulated peripheral blood lymphocytes of 3 unrelated healthy individuals. Twenty-five thousand metaphase spreads were analyzed and overall 22,537 FS located in 230 different loci were recorded. Sixtyone of those FS were never observed before and 52 were already previously reported but not included in genome browsers and yet verified. Interestingly, aphidicolin was able to induce all types of rare and common FS, suggesting that these breakage-prone regions are less dependent on the inducing chemicals than originally supposed. Overall, we provide the first comprehensive genome wide map for FS and studied possible correlations of chromosome length and GTG-banding level with FS-frequency. To handle FS better in future, an extension of the already existing alphabetical nomenclature for FS on single chromosomes is suggested.

Locus-specific transcription silencing at the FHIT gene suppresses replication stress-induced copy number variant formation and associated replication delay

“…We further analyzed APH-induced CFS gaps and breaks at FHIT and NLGN1 in the WT and mutant GM11713 clones. FRA3B and FRA3O correspond to the FHIT and NLGN1 gene loci, respectively ( 61 ). Locus-specific FISH probes were used to facilitate the CFS analysis ( Supplementary Figure S6 ).…”

How unfinished business from S-phase affects mitosis and beyond

“…Exposure to aphidicolin is thought to exacerbate intrinsic problems that already exist at these regions due to late/delayed DNA replication. Up to 230 aphidicolin‐induced fragile sites have been described so far in human cells (Mrasek et al , 2010), though only a subset of these appear to be expressed in any given cell type (Letessier et al , 2011). Two types of these fragile sites have been characterized, termed as ‘rare’ and ‘common’.…”

CRISPR-Cas9-mediated genome engineering exaggerates genomic deletion at 10q23.31 including thePTENgene locus mimicking cancer profiles

“…Although the precise mechanism that initiated the PAPSS2-PTEN locus deletion remains unclear, our findings indicated mechanistic similarities linked to genome fragility. Genome-wide screening identified hundreds of fragile sites leading to DNA breaks initiated upon cell treatment with DNA replication inhibitors (60,61). Among them, the PAPSS2-PTEN locus resided in the rare fragile site FRA10A (10q23.3).…”