Genome Instability at Common Fragile Sites: Searching for the Cause of Their Instability

Common fragile sites (CFS) are heritable nonrandomly distributed loci on human chromosomes that exhibit an increased frequency of chromosomal breakage under conditions of replication stress. They are considered the preferential targets for high genomic instability from the earliest stages of human cancer development, and increased chromosome instability at these loci has been observed following replication stress in a subset of human genetic diseases. Despite their biological and medical relevance, the molecular basis of CFS fragility in vivo has not been fully elucidated. At present, different models have been proposed to explain how instability at CFS arises and multiple factors seem to contribute to their instability. However, all these models involve DNA replication and suggest that replication fork stalling along CFS during DNA synthesis is a very frequent event. Consistent with this, the maintenance of CFS stability relies on the ATR-dependent checkpoint, together with a number of proteins promoting the recovery of stalled replication forks. In this review, we discuss mainly the possible causes that threaten the integrity of CFS in the light of new findings, paying particular attention to the role of the S-phase checkpoint.

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Common fragile sites are characterised by faulty condensin loading after replication stress

10.1101/508713 ◽

2018 ◽

Cited By ~ 1

Author(s):

Lora Boteva ◽

Ryu-Suke Nozawa ◽

Catherine Naughton ◽

Kumiko Samejima ◽

William C Earnshaw ◽

...

Keyword(s):

Cell Cycle ◽

Dna Synthesis ◽

Chromosome Instability ◽

Replication Stress ◽

Fragile Sites ◽

Molecular Configuration ◽

Common Fragile Sites ◽

Molecular Defects ◽

Specific Manner ◽

Chromatin Folding

Cells coordinate interphase to mitosis transition but recurrent cytogenetic lesions appear at common fragile sites (CFSs) in a tissue-specific manner following replication stress, marking regions of instability in cancer. Despite such a distinct defect no model fully explains their molecular configuration. We show that CFSs are characterised by impaired chromatin folding manifested as disrupted mitotic structures visible using molecular FISH probes in the presence and absence of replication stress. Chromosome condensation assays reveal that compaction-resistant chromatin lesions persist at CFSs throughout the cell cycle and mitosis. Subsequently cytogenetic and molecular lesions arise due to faulty condensin loading at CFSs, through a defect in condensin I mediated compaction and are coincident with mitotic DNA synthesis (MIDAS). This model suggests that in conditions of exogenous replication stress, aberrant condensin loading leads to molecular defects and CFS formation, concomitantly providing an environment for MIDAS, which, if not resolved, result in chromosome instability.

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Replication Stress and Telomere Dysfunction Are Present in Cultured Human Embryonic Stem Cells

Cytogenetic and Genome Research ◽

10.1159/000441245 ◽

2015 ◽

Vol 146 (4) ◽

pp. 251-260 ◽

Cited By ~ 3

Author(s):

Christine Janson ◽

Kristine Nyhan ◽

John P. Murnane

Keyword(s):

Stem Cells ◽

Dna Damage ◽

Embryonic Stem Cells ◽

Human Embryonic Stem Cells ◽

Chromosome Instability ◽

Embryonic Stem ◽

Replication Stress ◽

Activin A ◽

Fragile Sites ◽

Telomere Dysfunction

Replication stress causes DNA damage at fragile sites in the genome. DNA damage at telomeres can initiate breakage-fusion-bridge cycles and chromosome instability, which can result in replicative senescence or tumor formation. Little is known about the extent of replication stress or telomere dysfunction in human embryonic stem cells (hESCs). hESCs are grown in culture with the expectation of being used therapeutically in humans, making it important to minimize the levels of replication stress and telomere dysfunction. Here, the hESC line UCSF4 was cultured in a defined medium with growth factor Activin A, exogenous nucleosides, or DNA polymerase inhibitor aphidicolin. We used quantitative fluorescence in situ hybridization to analyze individual telomeres for dysfunction and observed that it can be increased by aphidicolin or Activin A. In contrast, adding exogenous nucleosides relieved dysfunction, suggesting that telomere dysfunction results from replication stress. Whether these findings can be applied to other hESC lines remains to be determined. However, because the loss of telomeres can lead to chromosome instability and cancer, we conclude that hESCs grown in culture for future therapeutic purposes should be routinely checked for replication stress and telomere dysfunction.

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Oncogene-induced replication stress preferentially targets common fragile sites in preneoplastic lesions. A genome-wide study

Oncogene ◽

10.1038/sj.onc.1210989 ◽

2007 ◽

Vol 27 (23) ◽

pp. 3256-3264 ◽

Cited By ~ 112

Author(s):

P K Tsantoulis ◽

A Kotsinas ◽

P P Sfikakis ◽

K Evangelou ◽

M Sideridou ◽

...

Keyword(s):

Replication Stress ◽

Fragile Sites ◽

Preneoplastic Lesions ◽

Common Fragile Sites ◽

Genome Wide ◽

A Genome ◽

Genome Wide Study

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Oligodeoxynucleotide Binding to (CTG) · (CAG) Microsatellite Repeats Inhibits Replication Fork Stalling, Hairpin Formation, and Genome Instability

Molecular and Cellular Biology ◽

10.1128/mcb.01265-12 ◽

2012 ◽

Vol 33 (3) ◽

pp. 571-581 ◽

Cited By ~ 13

Author(s):

Guoqi Liu ◽

Xiaomi Chen ◽

Michael Leffak

Keyword(s):

Replication Fork ◽

Trinucleotide Repeat ◽

Cell Model ◽

Replication Stress ◽

Dna Hairpin ◽

Replication Fork Stalling ◽

Fork Stalling ◽

Hairpin Formation ◽

Lagging Strand

ABSTRACT(CTG)n· (CAG)ntrinucleotide repeat (TNR) expansion in the 3′ untranslated region of the dystrophia myotonica protein kinase (DMPK) gene causes myotonic dystrophy type 1. However, a direct link between TNR instability, the formation of noncanonical (CTG)n· (CAG)nstructures, and replication stress has not been demonstrated. In a human cell model, we found that (CTG)45· (CAG)45causes local replication fork stalling, DNA hairpin formation, and TNR instability. Oligodeoxynucleotides (ODNs) complementary to the (CTG)45· (CAG)45lagging-strand template eliminated DNA hairpin formation on leading- and lagging-strand templates and relieved fork stalling. Prolonged cell culture, emetine inhibition of lagging-strand synthesis, or slowing of DNA synthesis by low-dose aphidicolin induced (CTG)45· (CAG)45expansions and contractions. ODNs targeting the lagging-strand template blocked the time-dependent or emetine-induced instability but did not eliminate aphidicolin-induced instability. These results show directly that TNR replication stalling, replication stress, hairpin formation, and instability are mechanistically linkedin vivo.

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Dormant replication origin firing links replication stress to whole chromosomal instability in human cancer

10.1101/2021.10.11.463929 ◽

2021 ◽

Author(s):

Ann-Kathrin Schmidt ◽

Nicolas Boehly ◽

Xiaoxiao Zhang ◽

Benjamin O. Slusarenko ◽

Magdalena Hennecke ◽

...

Keyword(s):

Cancer Cells ◽

Chromosomal Instability ◽

Replication Origin ◽

Human Cancer ◽

Chromosome Instability ◽

Replication Stress ◽

S Phase ◽

Origin Firing ◽

Human Cancer Cells ◽

Chromosome Missegregation

Chromosomal instability (CIN) is a hallmark of cancer and comprises structural CIN (S-CIN) and whole chromosome instability (W-CIN). Replication stress (RS), a condition of slowed or stalled DNA replication during S phase, has been linked to S-CIN, whereas defects in mitosis leading to chromosome missegregation and aneuploidy can account for W-CIN. It is well established that RS can activate additional replication origin firing that is considered as a rescue mechanism to suppress chromosomal instability in the presence of RS. In contrast, we show here that an increase in replication origin firing during S phase can contribute to W-CIN in human cancer cells. Increased origin firing can be specifically triggered by overexpression of origin firing genes including GINS1 and CDC45, whose elevated expression significantly correlates with W-CIN in human cancer specimens. Moreover, endogenous mild RS present in cancer cells characterized by W-CIN or modulation of the origin firing regulating ATR-CDK1-RIF1 axis induces dormant origin firing, which is sufficient to trigger chromosome missegregation and W-CIN. Importantly, chromosome missegregation upon increased dormant origin firing is mediated by increased microtubule growth rates leading to the generation of lagging chromosomes in mitosis, a condition prevalent in chromosomally unstable cancer cells. Thus, our study identified increased or dormant replication origin firing as a hitherto unrecognized, but cancer-relevant trigger for chromosomal instability.

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Common fragile sites and human cancer

Cancer Genetics and Cytogenetics ◽

10.1016/0165-4608(88)90070-2 ◽

1988 ◽

Vol 36 (1) ◽

pp. 13-23 ◽

Cited By ~ 21

Author(s):

Patrizia Vernole ◽

Bruna Tedeschi ◽

Daniela Caporossi ◽

Benedetto Nicoletti

Keyword(s):

Human Cancer ◽

Fragile Sites ◽

Common Fragile Sites

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Replication stress induces specific enrichment of RECQ1 at common fragile sites FRA3B and FRA16D

Molecular Cancer ◽

10.1186/1476-4598-12-29 ◽

2013 ◽

Vol 12 (1) ◽

pp. 29 ◽

Cited By ~ 30

Author(s):

Xing Lu ◽

Swetha Parvathaneni ◽

Toshifumi Hara ◽

Ashish Lal ◽

Sudha Sharma

Keyword(s):

Replication Stress ◽

Fragile Sites ◽

Common Fragile Sites

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Faculty Opinions recommendation of Large transcription units unify copy number variants and common fragile sites arising under replication stress.

Faculty Opinions – Post-Publication Peer Review of the Biomedical Literature ◽

10.3410/f.725225811.793513120 ◽

2016 ◽

Author(s):

Antony Carr

Keyword(s):

Copy Number ◽

Copy Number Variants ◽

Replication Stress ◽

Fragile Sites ◽

Common Fragile Sites

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Crosstalk between CST and RPA regulates RAD51 activity during replication stress

Nature Communications ◽

10.1038/s41467-021-26624-x ◽

2021 ◽

Vol 12 (1) ◽

Author(s):

Kai-Hang Lei ◽

Han-Lin Yang ◽

Hao-Yen Chang ◽

Hsin-Yi Yeh ◽

Dinh Duc Nguyen ◽

...

Keyword(s):

Ionic Strength ◽

Replication Fork ◽

Protein A ◽

Replication Stress ◽

High Ionic Strength ◽

Close Proximity ◽

Fork Stalling ◽

Low Ionic Strength ◽

Exchange Activity

AbstractReplication stress causes replication fork stalling, resulting in an accumulation of single-stranded DNA (ssDNA). Replication protein A (RPA) and CTC1-STN1-TEN1 (CST) complex bind ssDNA and are found at stalled forks, where they regulate RAD51 recruitment and foci formation in vivo. Here, we investigate crosstalk between RPA, CST, and RAD51. We show that CST and RPA localize in close proximity in cells. Although CST stably binds to ssDNA with a high affinity at low ionic strength, the interaction becomes more dynamic and enables facilitated dissociation at high ionic strength. CST can coexist with RPA on the same ssDNA and target RAD51 to RPA-coated ssDNA. Notably, whereas RPA-coated ssDNA inhibits RAD51 activity, RAD51 can assemble a functional filament and exhibit strand-exchange activity on CST-coated ssDNA at high ionic strength. Our findings provide mechanistic insights into how CST targets and tethers RAD51 to RPA-coated ssDNA in response to replication stress.

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