Fragile Genes That Are Frequently Altered in Cancer: Players Not Passengers

2016 ◽  
Vol 150 (3-4) ◽  
pp. 208-216 ◽  
Author(s):  
Jenna R. Karras ◽  
Morgan S. Schrock ◽  
Bahadir Batar ◽  
Kay Huebner
Keyword(s):  
Genome Instability ◽  
Fragile Site ◽  
Replication Stress ◽  
Fragile Sites ◽  
Gap Formation ◽  
A Genome ◽  
Protein Functions ◽  
Fhit Protein ◽  
The Stability ◽  
Selection Of

FHIT, located at FRA3B, is one of the most commonly deleted genes in human cancers, and loss of FHIT protein is one of the earliest events in cancer initiation. However, location of FHIT at a chromosomal fragile site, a locus prone to breakage and gap formation under even mild replication stress, has encouraged claims that FHIT loss is a passenger event in cancers. We summarize accumulated evidence that FHIT protein functions as a genome “caretaker” required to protect the stability of genomes of normal cells of most tissues from agents causing intrinsic and extrinsic DNA damage. FHIT loss leads to intracellular replication stress and subsequent genome instability, which provides an opportunistic mutational landscape in preneoplasias for selection of a variety of other cancer-driving mutations. We also review evidence showing that FHIT loss leads to enhanced activation of other common fragile sites, including the FRA16D/WWOX locus, and creates optimal single-stranded DNA substrates for the hypermutator enzyme, APOBEC3B.

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

Oncogene ◽  
2007 ◽  
Vol 27 (23) ◽  
pp. 3256-3264 ◽  
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

scholarly journals DNA synthesis by Pol η promotes fragile site stability by preventing under-replicated DNA in mitosis

2013 ◽  
Vol 201 (3) ◽  
pp. 395-408 ◽  
Author(s):  
Valérie Bergoglio ◽  
Anne-Sophie Boyer ◽  
Erin Walsh ◽  
Valeria Naim ◽  
Gaëlle Legube ◽  
...  
Keyword(s):  
Dna Synthesis ◽  
Dna Sequences ◽  
Molecular Mechanisms ◽  
Fragile Site ◽  
Fragile Sites ◽  
Nuclear Bodies ◽  
Replication Checkpoint ◽  
Genome Damage ◽  
Fork Stalling ◽  
The Stability

Human DNA polymerase η (Pol η) is best known for its role in responding to UV irradiation–induced genome damage. We have recently observed that Pol η is also required for the stability of common fragile sites (CFSs), whose rearrangements are considered a driving force of oncogenesis. Here, we explored the molecular mechanisms underlying this newly identified role. We demonstrated that Pol η accumulated at CFSs upon partial replication stress and could efficiently replicate non-B DNA sequences within CFSs. Pol η deficiency led to persistence of checkpoint-blind under-replicated CFS regions in mitosis, detectable as FANCD2-associated chromosomal sites that were transmitted to daughter cells in 53BP1-shielded nuclear bodies. Expression of a catalytically inactive mutant of Pol η increased replication fork stalling and activated the replication checkpoint. These data are consistent with the requirement of Pol η–dependent DNA synthesis during S phase at replication forks stalled in CFS regions to suppress CFS instability by preventing checkpoint-blind under-replicated DNA in mitosis.

scholarly journals MRE11-RAD50-NBS1 activates Fanconi Anemia R-loop suppression at transcription-replication conflicts

2018 ◽  
Author(s):  
Emily Yun-chia Chang ◽  
James P. Wells ◽  
Shu-Huei Tsai ◽  
Yan Coulombe ◽  
Yujia A. Chan ◽  
...  
Keyword(s):  
Dna Replication ◽  
Fanconi Anemia ◽  
Replication Fork ◽  
Genome Instability ◽  
Human Cancer ◽  
Replication Stress ◽  
Maintenance Factors ◽  
Genome Wide ◽  
A Genome ◽  
Dna Replication Stress

SUMMARYEctopic R-loop accumulation causes DNA replication stress and genome instability. To avoid these outcomes, cells possess a range of anti-R-loop mechanisms, including RNaseH that degrades the RNA moiety in R-loops. To comprehensively identify anti-R-loop mechanisms, we performed a genome-wide trigenic interaction screen in yeast lacking RNH1 and RNH201. We identified >100 genes critical for fitness in the absence of RNaseH, which were enriched for DNA replication fork maintenance factors such as RAD50. We show in yeast and human cells that R-loops accumulate during RAD50 depletion. In human cancer cell models, we find that RAD50 and its partners in the MRE11-RAD50-NBS1 complex regulate R-loop-associated DNA damage and replication stress. We show that a non-nucleolytic function of MRE11 is important for R-loop suppression via activation of PCNA-ubiquitination by RAD18 and recruiting anti-R-loop helicases in the Fanconi Anemia pathway. This work establishes a novel role for MRE11-RAD50-NBS1 in directing tolerance mechanisms of transcription-replication conflicts.

scholarly journals FANCD2 tunes the UPR preventing mitochondrial stress-­induced common fragile site instability

2019 ◽  
Author(s):  
Philippe Fernandes ◽  
Benoit Miotto ◽  
Claude Saint-Ruf ◽  
Viola Nähse ◽  
Silvia Ravera ◽  
...  
Keyword(s):  
Gene Expression ◽  
Genome Instability ◽  
Fragile Site ◽  
Transcriptional Response ◽  
Genomic Analysis ◽  
Fragile Sites ◽  
The Unfolded Protein Response ◽  
And Function ◽  
Large Genes ◽  
Genomic Regions

AbstractCommon fragile sites (CFSs) are genomic regions frequently involved in cancer-associated rearrangements. Most CFSs lie within large genes, and their instability relies on transcription- and replication-dependent mechanisms. Here, we uncover a role for the UBL5-dependent branch of the unfolded protein response pathway (UPR) in the maintenance of CFS stability. We show that genetic or pharmacological UPR activation induces CFS gene expression and concomitant relocalization of FANCD2, a master regulator of CFS stability, to CFSs. Furthermore, a genomic analysis of FANCD2 binding sites identified an enrichment for mitochondrial UPR transcriptional response elements in FANCD2 bound regions. We demonstrated that depletion of FANCD2 increases CFS gene transcription and their instability while also inducing mitochondrial dysfunction and triggering the activation of the UPR pathway. Depletion of UBL5, a mediator of the UPR, but not ATF4, reduces CFS gene expression and breakage in FANCD2-depleted cells. We thus demonstrate that FANCD2 recruitment and function at CFSs depends on transcription and UPR signaling, and in absence of transcription or UBL5, FANCD2 is dispensable for CFS stability. We propose that FANCD2 coordinates nuclear and mitochondrial activities by tuning the UPR to prevent genome instability.

scholarly journals Visualizing locus-specific sister chromatid exchange reveals differential patterns of replication stress-induced fragile site breakage

Oncogene ◽  
2019 ◽  
Vol 39 (6) ◽  
pp. 1260-1272 ◽  
Author(s):  
Irina Waisertreiger ◽  
Katherine Popovich ◽  
Maya Block ◽  
Krista R. Anderson ◽  
Jacqueline H. Barlow
Keyword(s):  
Dna Repair ◽  
Sister Chromatid ◽  
Sister Chromatid Exchange ◽  
Large Scale ◽  
Fragile Site ◽  
Replication Stress ◽  
Fragile Sites ◽  
Repair Pathway ◽  
Genomic Location ◽  
Pathway Choice

Abstract Chromosomal fragile sites are genomic loci sensitive to replication stress which accumulate high levels of DNA damage, and are frequently mutated in cancers. Fragile site damage is thought to arise from the aberrant repair of spontaneous replication stress, however successful fragile site repair cannot be calculated using existing techniques. Here, we report a new assay measuring recombination-mediated repair at endogenous genomic loci by combining a sister chromatid exchange (SCE) assay with fluorescent in situ hybridization (SCE-FISH). Using SCE-FISH, we find that endogenous and exogenous replication stress generated unrepaired breaks and SCEs at fragile sites. We also find that distinct sources of replication stress induce distinct patterns of breakage: ATR inhibition induces more breaks at early replicating fragile sites (ERFS), while ERFS and late-replicating common fragile sites (CFS) are equally fragile in response to aphidicolin. Furthermore, SCEs were suppressed at fragile sites near centromeres in response to replication stress, suggesting that genomic location influences DNA repair pathway choice. SCE-FISH also measured successful recombination in human primary lymphocytes, and identificed the proto-oncogene BCL2 as a replication stress-induced fragile site. These findings demonstrate that SCE-FISH frequency at fragile sites is a sensitive indicator of replication stress, and that large-scale genome organization influences DNA repair pathway choice.

scholarly journals Werner syndrome helicase activity is essential in maintaining fragile site stability

2008 ◽  
Vol 180 (2) ◽  
pp. 305-314 ◽  
Author(s):  
Livia Maria Pirzio ◽  
Pietro Pichierri ◽  
Margherita Bignami ◽  
Annapaola Franchitto
Keyword(s):  
Werner Syndrome ◽  
Fragile Site ◽  
Chromosome Breakage ◽  
Fragile Sites ◽  
Helicase Activity ◽  
Dna Helicases ◽  
Replication Checkpoint ◽  
Replicative Stress ◽  
Fork Stalling ◽  
The Stability

WRN is a member of the RecQ family of DNA helicases implicated in the resolution of DNA structures leading to the stall of replication forks. Fragile sites have been proposed to be DNA regions particularly sensitive to replicative stress. Here, we establish that WRN is a key regulator of fragile site stability. We demonstrate that in response to mild doses of aphidicolin, WRN is efficiently relocalized in nuclear foci in replicating cells and that WRN deficiency is associated with accumulation of gaps and breaks at common fragile sites even under unperturbed conditions. By expressing WRN isoforms impaired in either helicase or exonuclease activity in defective cells, we identified WRN helicase activity as the function required for maintaining the stability of fragile sites. Finally, we find that WRN stabilizes fragile sites acting in a common pathway with the ataxia telangiectasia and Rad3 related replication checkpoint. These findings provide the first evidence of a crucial role for a helicase in protecting cells against chromosome breakage at normally occurring replication fork stalling sites.

scholarly journals Nucleosides rescue replication-mediated genome instability of human pluripotent stem cells

2019 ◽  
Author(s):  
Jason A. Halliwell ◽  
Thomas J. R. Frith ◽  
Owen Laing ◽  
Christopher J Price ◽  
Oliver J. Bower ◽  
...  
Keyword(s):  
Stem Cells ◽  
Regenerative Medicine ◽  
Pluripotent Stem Cells ◽  
Genome Instability ◽  
Culture Media ◽  
Replication Stress ◽  
Human Pluripotent Stem Cells ◽  
Genetic Changes ◽  
Genomic Damage ◽  
Selection Of

Human pluripotent stem cells (PSC) often acquire genetic changes on prolonged culture, which pose concerns for their use in research and regenerative medicine (Amps et al., 2011, Seth et al., 2011). The acquisition of these changes during culture necessarily first requires mutation and then selection of those mutations that provide a growth advantage. Whilst selection accounts for the recurrent nature of the variants commonly reported (Draper et al., 2004, Olariu et al., 2010), the mechanisms of mutation in PSC remain largely elusive. Here we show that, in contrast to somatic cells, human PSC have an increased susceptibility to DNA damage and mitotic errors, both of which are caused by heightened replication stress in PSC and this can be alleviated by culture with exogenous nucleosides. These results reflect the requirement for rapid replication of human PSC enabled by a truncated G1 (Becker et al., 2006, Becker et al., 2010) that impairs the preparation of these cells for the ensuing DNA replication. A similar relationship has been shown in relation to chromosomal instability in cancer cells (Burrell et al., 2013, Wilhelm et al., 2019) but PSC differ by replication stress triggering apoptosis (Desmarais et al., 2012, Desmarais et al., 2016). Nevertheless, evasion of this response still leads to the appearance of genetic variants that are of concern for regenerative medicine. The inclusion of nucleosides into culture media greatly improves the efficiency of human PSC culture and minimises the acquisition of genomic damage.

scholarly journals AT-dinucleotide rich sequences drive fragile site formation

2019 ◽  
Vol 47 (18) ◽  
pp. 9685-9695 ◽  
Author(s):  
Michal Irony-Tur Sinai ◽  
Anita Salamon ◽  
Noemie Stanleigh ◽  
Tchelet Goldberg ◽  
Aryeh Weiss ◽  
...  
Keyword(s):  
Dna Replication ◽  
Human Genome ◽  
Dna Sequences ◽  
Fragile Site ◽  
Integration Site ◽  
Replication Stress ◽  
Secondary Structures ◽  
Fragile Sites ◽  
Stable Region ◽  
Site Formation

Abstract Common fragile sites (CFSs) are genomic regions prone to breakage under replication stress conditions recurrently rearranged in cancer. Many CFSs are enriched with AT-dinucleotide rich sequences (AT-DRSs) which have the potential to form stable secondary structures upon unwinding the double helix during DNA replication. These stable structures can potentially perturb DNA replication progression, leading to genomic instability. Using site-specific targeting system, we show that targeted integration of a 3.4 kb AT-DRS derived from the human CFS FRA16C into a chromosomally stable region within the human genome is able to drive fragile site formation under conditions of replication stress. Analysis of >1300 X chromosomes integrated with the 3.4 kb AT-DRS revealed recurrent gaps and breaks at the integration site. DNA sequences derived from the integrated AT-DRS showed in vitro a significantly increased tendency to fold into branched secondary structures, supporting the predicted mechanism of instability. Our findings clearly indicate that intrinsic DNA features, such as complexed repeated sequence motifs, predispose the human genome to chromosomal instability.

scholarly journals Genome Maintenance by DNA Helicase B

Genes ◽  
2020 ◽  
Vol 11 (5) ◽  
pp. 578
Author(s):  
Lindsey Hazeslip ◽  
Maroof Khan Zafar ◽  
Muhammad Zain Chauhan ◽  
Alicia K. Byrd
Keyword(s):  
Dna Damage ◽  
Dna Replication ◽  
Stress Responses ◽  
Fragile Site ◽  
Replication Stress ◽  
Dna Helicase ◽  
S Phase ◽  
Fragile Sites ◽  
Topoisomerase 2 ◽  
Initiation Of Dna Replication

DNA Helicase B (HELB) is a conserved helicase in higher eukaryotes with roles in the initiation of DNA replication and in the DNA damage and replication stress responses. HELB is a predominately nuclear protein in G1 phase where it is involved in initiation of DNA replication through interactions with DNA topoisomerase 2-binding protein 1 (TOPBP1), cell division control protein 45 (CDC45), and DNA polymerase α-primase. HELB also inhibits homologous recombination by reducing long-range end resection. After phosphorylation by cyclin-dependent kinase 2 (CDK2) at the G1 to S transition, HELB is predominately localized to the cytosol. However, this cytosolic localization in S phase is not exclusive. HELB has been reported to localize to chromatin in response to replication stress and to localize to the common fragile sites 16D (FRA16D) and 3B (FRA3B) and the rare fragile site XA (FRAXA) in S phase. In addition, HELB is phosphorylated in response to ionizing radiation and has been shown to localize to chromatin in response to various types of DNA damage, suggesting it has a role in the DNA damage response.

scholarly journals FANCD2 modulates the mitochondrial stress response to prevent common fragile site instability

2021 ◽  
Vol 4 (1) ◽  
Author(s):  
Philippe Fernandes ◽  
Benoit Miotto ◽  
Claude Saint-Ruf ◽  
Maha Said ◽  
Viviana Barra ◽  
...  
Keyword(s):  
Stress Response ◽  
Genome Instability ◽  
Fragile Site ◽  
Fragile Sites ◽  
Human Cells ◽  
Mitochondrial Stress ◽  
Stress Response Pathway ◽  
Stress Dependent ◽  
Large Genes ◽  
Genomic Regions

AbstractCommon fragile sites (CFSs) are genomic regions frequently involved in cancer-associated rearrangements. Most CFSs lie within large genes, and their instability involves transcription- and replication-dependent mechanisms. Here, we uncover a role for the mitochondrial stress response pathway in the regulation of CFS stability in human cells. We show that FANCD2, a master regulator of CFS stability, dampens the activation of the mitochondrial stress response and prevents mitochondrial dysfunction. Genetic or pharmacological activation of mitochondrial stress signaling induces CFS gene expression and concomitant relocalization to CFSs of FANCD2. FANCD2 attenuates CFS gene transcription and promotes CFS gene stability. Mechanistically, we demonstrate that the mitochondrial stress-dependent induction of CFS genes is mediated by ubiquitin-like protein 5 (UBL5), and that a UBL5-FANCD2 dependent axis regulates the mitochondrial UPR in human cells. We propose that FANCD2 coordinates nuclear and mitochondrial activities to prevent genome instability.

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