Cloning of genetically tagged chromosome break sequences reveals new fragile sites at 6p21 and 13q22

Fechter, Anne; Buettel, Isabel; Kuehnel, Elisabeth; Schwab, Manfred; Savelyeva, Larissa

doi:10.1002/ijc.22564

Cited by 20 publications

(14 citation statements)

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“…3). Additionally, 52 identified and in parts mapped FS were already published, but not included in the current genome browser versions (13,14,15,16,17,19,23,34). Most of these sites were confirmed in this study which underlines their eligibility to be appreciated as FS.…”

Section: ------------------------------------------------------------supporting

confidence: 51%

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

Weise¹

2010

Int J Oncol

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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.

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Section: ------------------------------------------------------------supporting

confidence: 51%

“…Additionally, differences in the observable FS-frequency within different individuals are well known (11,12). Besides these 88 official, database-annotated common FS others were observed and reported, including six recently reported new sites, particularly FRA4F (13), FRA7K (14), FRA6H (15), FRA9G (16), FRA13E (15) and FRA18C (17).…”

Section: Introductionmentioning

confidence: 94%

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

Weise¹

2010

Int J Oncol

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“…Recently, four novel common fragile sites, FRA4F (Rozier et al, 2004), FRA7K (Helmrich et al, 2007), FRA6H, and FRA13E (Fechter et al, 2007b), which are not recorded in the GDB Human Genome Database, have been identified. In the present study, we report the precise genomic localization of another novel aphidicolin-inducible common fragile site, FRA9G, spanning an 300 kb region at 9p22.2.…”

Section: Discussionmentioning

confidence: 98%

“…However, the exact number of common fragile sites appears to be even larger than those identified by classical cytogenetic analysis. This is documented by the fact that application of high resolution mapping approaches revealed four new common fragile sites in the human genome, FRA4F (Rozier et al, 2004), FRA7K (Helmrich et al, 2007), FRA6H, and FRA13E (Fechter et al, 2007b). Breaks at individual common fragile sites have been found to scatter over large genomic region encompassing hundreds to thousands of kilobases.…”

Section: Introductionmentioning

confidence: 95%

Novel aphidicolin‐inducible common fragile site FRA9G maps to 9p22.2, within the C9orf39 gene

Sawińska

Schmitt

Sagulenko

et al. 2007

Genes Chromosomes & Cancer

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Common fragile sites represent a component of normal chromosome structure that form gaps and breaks on metaphase chromosomes after partial inhibition of DNA synthesis. In humans, cytogenetic locations of 89 common fragile sites are listed in the Genome Database; however, the exact number of fragile sites remains unknown. The application of high resolution mapping approaches continues to reveal new common fragile sites in the human genome. Here, we identified a novel aphidicolin-inducible common fragile site FRA9G, which maps to chromosomal band 9p22.2. We have characterized the structure of the fragile DNA sequence that extends over a genomic region of approximately 300 kb within the C9orf39 (chromosome 9 open reading frame 39) gene. Analysis of incidence in healthy individuals showed that FRA9G is commonly expressed in the population. Heterozygous BRCA2 mutation carriers exhibit an almost sevenfold increase of FRA9G expression compared to an unrelated control population group. Identification of a novel aphidicolin-inducible common fragile site at 9p22 may have implications for understanding the mechanism of genetic instability in tumorigenesis and other genetic disorders.

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“…Chromosome breakage at CFSs can lead to translocations and gross chromosome terminal deletions after APH treatment in somatic cell hybrid systems in which there is no negative selection for loss of genes distal to the CFS (8,9). CFSs are also preferred sites of integration for transfected DNA in cells pretreated with APH (10)(11)(12) and have been implicated in breakage leading to intrachromosomal gene amplification events in cultured CHO cells (13).…”

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confidence: 99%

Replication stress induces tumor-like microdeletions in FHIT /FRA3B

Durkin

Ragland

Arlt

et al. 2008

Proc. Natl. Acad. Sci. U.S.A.

112

109

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Common fragile sites (CFSs) are loci that preferentially exhibit metaphase chromosome gaps and breaks after partial inhibition of DNA synthesis. The fragile site FRA3B, which lies within the FHIT tumorsuppressor gene, is a site of frequent heterozygous and homozygous deletions in many cancer cells and precancerous lesions. The great majority of FHIT and other CFS-associated gene rearrangements in tumors are submicroscopic, intralocus deletions of hundreds of kilobases that often result in inactivation of associated genes. Although CFS instability leads to chromosome gaps and breaks and translocations, there has been no direct evidence showing that CFS instability or replication stress can generate large submicroscopic deletions of the type seen in cancer cells. Here, we have produced FHIT/FRA3B deletions closely resembling those in tumors by exposing humanmouse chromosome 3 somatic hybrid cells to aphidicolin-mediated replication stress. Clonal cell populations were analyzed for deletions by using PCR, array comparative genomic hybridization (aCGH), and FISH. Thirteen percent to 23% of clones exhibited submicroscopic FHIT deletions spanning Ϸ200 -600 kb within FRA3B. Chromosomes with FRA3B deletions exhibited significantly decreased fragility of this locus, with a 2-to 12-fold reduction in metaphase gaps and breaks compared with controls. Sequence analysis showed no regions of homology at breakpoints and suggests involvement of NHEJ in generating the deletions. Our results demonstrate that replication stress induces a remarkably high frequency of tumor-like microdeletions that reduce fragility at a CFS in cultured cells and suggests that similar conditions during tumor formation lead to intralocus deletion and inactivation of genes at CFSs and perhaps elsewhere in the genome.fragile site ͉ genome instability ͉ replication stress C ommon fragile sites (CFSs) are regions of the genome that are particularly susceptible to forming gaps and breaks on metaphase chromosomes under conditions of replication stress induced by certain inhibitors of DNA synthesis, particularly the polymeraseinhibiting drug, aphidicolin (APH) (1, 2). The ATR-dependent DNA damage checkpoint has been shown to be centrally involved in maintenance of CFS stability, leading to the model that CFS lesions result from stalled replication at these sites (3-6).In addition to cytogenetic ''expression'' of CFS gaps and breaks on metaphase chromosomes, CFSs exhibit a number of additional characteristics of unstable DNA in cultured cells. After induction with APH, the majority of CFS breaks display sister chromatid exchanges (SCEs) (7). Chromosome breakage at CFSs can lead to translocations and gross chromosome terminal deletions after APH treatment in somatic cell hybrid systems in which there is no negative selection for loss of genes distal to the CFS (8, 9). CFSs are also preferred sites of integration for transfected DNA in cells pretreated with APH (10-12) and have been implicated in breakage leading to intrachromosomal gene amplification events in ...

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Cloning of genetically tagged chromosome break sequences reveals new fragile sites at 6p21 and 13q22

Cited by 20 publications

References 64 publications

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

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

Novel aphidicolin‐inducible common fragile site FRA9G maps to 9p22.2, within the C9orf39 gene

Replication stress induces tumor-like microdeletions in FHIT /FRA3B

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