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.

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 Large Intronic Deletion of the Fragile Site Gene PRKN Dramatically Lowers Its Fragility Without Impacting Gene Expression

2021 ◽  
Vol 12 ◽  
Author(s):  
Sebastian H. N. Munk ◽  
Vasileios Voutsinos ◽  
Vibe H. Oestergaard
Keyword(s):  
Gene Expression ◽  
Reverse Genetics ◽  
Fragile Site ◽  
Fragile Sites ◽  
Metaphase Chromosomes ◽  
Large Gene ◽  
Large Intron ◽  
Chromosomal Fragile Sites ◽  
Large Genes ◽  
Genomic Regions

Common chromosomal fragile sites (CFSs) are genomic regions prone to form breaks and gaps on metaphase chromosomes during conditions of replication stress. Moreover, CFSs are hotspots for deletions and amplifications in cancer genomes. Fragility at CFSs is caused by transcription of extremely large genes, which contributes to replication problems. These extremely large genes do not encode large proteins, but the extreme sizes of the genes originate from vast introns. Intriguingly, the intron sizes of extremely large genes are conserved between mammals and birds. Here, we have used reverse genetics to address the function and significance of the largest intron in the extremely large gene PRKN, which is highly fragile in our model system. Specifically, we have introduced an 80-kilobase deletion in intron 7 of PRKN. We find that gene expression of PRKN is largely unaffected by this intronic deletion. Strikingly, the intronic deletion, which leads to a 12% reduction of the overall size of the PRKN gene body, results in an almost twofold reduction of the PRKN fragility. Our results stress that while the large intron clearly contributes to the fragility of PRKN, it does not play an important role for PRKN expression. Taken together, our findings further add to the mystery concerning conservation of the seemingly non-functional but troublesome large introns in PRKN.

Generation of a new adenovirus type 12-inducible fragile site by insertion of an artificial U2 locus in the human genome

1993 ◽  
Vol 13 (10) ◽  
pp. 6064-6070
Author(s):  
Y P Li ◽  
R Tomanin ◽  
J R Smiley ◽  
S Bacchetti
Keyword(s):  
Human Genome ◽  
Gene Cluster ◽  
Fragile Site ◽  
Adenovirus Type ◽  
Fragile Sites ◽  
Human Cells ◽  
Major Site ◽  
Chromosome 13 ◽  
Direct Assessment

Infection with adenovirus type 12 (Ad12) induces four fragile sites in the human genome (H.F. Stich, G.L. van Hoosier, and J.J. Trentin, Exp. Cell Res. 34:400-403, 1964; H. zur Hausen, J. Virol. 1:1174-1185, 1967). The major site, at 17q21-22, contains the U2 gene cluster, which is specifically disrupted by infection in at least a percentage of the cells (D.M. Durnam, J.C. Menninger, S.H. Chandler, P.P. Smith, and J.K. McDougall, Mol. Cell. Biol. 8:1863-1867, 1988). For direct assessment of whether the U2 locus is the target of the Ad12 effect, an artificial locus, constructed in vitro and consisting of tandem arrays of the U2 6-kbp monomer, was transfected into human cells. We report that integration of this artificial locus on the p arm of chromosome 13 creates a new Ad12-inducible fragile site.

scholarly journals The transcriptionally competent U2 gene is necessary and sufficient for adenovirus type 12 induction of the fragile site at 17q21-22.

1995 ◽  
Vol 15 (11) ◽  
pp. 6256-6261 ◽  
Author(s):  
S Gargano ◽  
P Wang ◽  
E Rusanganwa ◽  
S Bacchetti
Keyword(s):  
Human Genome ◽  
Tandem Repeats ◽  
Fragile Site ◽  
Adenovirus Type ◽  
Fragile Sites ◽  
Human Cells ◽  
Necessary And Sufficient

Adenovirus type 12 induces four fragile sites upon infection of human cells. The U2 locus, consisting of up to 20 tandem repeats of a 5.8-kbp monomer, maps at the most sensitive of these sites at 17q21-22. We have previously shown that an artificial U2 locus integrated into the human genome generates a new virus-induced fragile site. To determine which elements within the U2 monomer are responsible for fragility, we constructed loci consisting of tandem repeats of subfragments of the U2 monomer. With this approach, we demonstrate that a transcriptionally competent U2 gene is necessary and sufficient for virus-induced fragility and that no other element within the 5.8-kbp monomer contributes to this effect.

scholarly journals Proteomic characterization of chromosomal common fragile site (CFS)-associated proteins uncovers ATRX as a regulator of CFS stability

2019 ◽  
Vol 47 (15) ◽  
pp. 8004-8018 ◽  
Author(s):  
David Pladevall-Morera ◽  
Stephanie Munk ◽  
Andreas Ingham ◽  
Lorenza Garribba ◽  
Eliene Albers ◽  
...  
Keyword(s):  
Chromatin Immunoprecipitation ◽  
Fragile Site ◽  
Global Analysis ◽  
Fragile Sites ◽  
Replication Proteins ◽  
Chromosomal Breaks ◽  
Associated Proteins ◽  
Genomic Regions ◽  
Conserved Genomic Regions

Abstract Common fragile sites (CFSs) are conserved genomic regions prone to break under conditions of replication stress (RS). Thus, CFSs are hotspots for rearrangements in cancer and contribute to its chromosomal instability. Here, we have performed a global analysis of proteins that recruit to CFSs upon mild RS to identify novel players in CFS stability. To this end, we performed Chromatin Immunoprecipitation (ChIP) of FANCD2, a protein that localizes specifically to CFSs in G2/M, coupled to mass spectrometry to acquire a CFS interactome. Our strategy was validated by the enrichment of many known regulators of CFS maintenance, including Fanconi Anemia, DNA repair and replication proteins. Among the proteins identified with unknown functions at CFSs was the chromatin remodeler ATRX. Here we demonstrate that ATRX forms foci at a fraction of CFSs upon RS, and that ATRX depletion increases the occurrence of chromosomal breaks, a phenotype further exacerbated under mild RS conditions. Accordingly, ATRX depletion increases the number of 53BP1 bodies and micronuclei, overall indicating that ATRX is required for CFS stability. Overall, our study provides the first proteomic characterization of CFSs as a valuable resource for the identification of novel regulators of CFS stability.

scholarly journals Common Fragile Site Profiling in Epithelial and Erythroid Cells Reveals that Most Recurrent Cancer Deletions Lie in Fragile Sites Hosting Large Genes

Cell Reports ◽  
2013 ◽  
Vol 4 (3) ◽  
pp. 420-428 ◽  
Author(s):  
Benoît Le Tallec ◽  
Gaël Armel Millot ◽  
Marion Esther Blin ◽  
Olivier Brison ◽  
Bernard Dutrillaux ◽  
...  
Keyword(s):  
Fragile Site ◽  
Fragile Sites ◽  
Common Fragile Site ◽  
Erythroid Cells ◽  
Recurrent Cancer ◽  
Large Genes

scholarly journals Generation of a new adenovirus type 12-inducible fragile site by insertion of an artificial U2 locus in the human genome.

1993 ◽  
Vol 13 (10) ◽  
pp. 6064-6070 ◽  
Author(s):  
Y P Li ◽  
R Tomanin ◽  
J R Smiley ◽  
S Bacchetti
Keyword(s):  
Human Genome ◽  
Gene Cluster ◽  
Fragile Site ◽  
Adenovirus Type ◽  
Fragile Sites ◽  
Human Cells ◽  
Major Site ◽  
Chromosome 13 ◽  
Direct Assessment

Infection with adenovirus type 12 (Ad12) induces four fragile sites in the human genome (H.F. Stich, G.L. van Hoosier, and J.J. Trentin, Exp. Cell Res. 34:400-403, 1964; H. zur Hausen, J. Virol. 1:1174-1185, 1967). The major site, at 17q21-22, contains the U2 gene cluster, which is specifically disrupted by infection in at least a percentage of the cells (D.M. Durnam, J.C. Menninger, S.H. Chandler, P.P. Smith, and J.K. McDougall, Mol. Cell. Biol. 8:1863-1867, 1988). For direct assessment of whether the U2 locus is the target of the Ad12 effect, an artificial locus, constructed in vitro and consisting of tandem arrays of the U2 6-kbp monomer, was transfected into human cells. We report that integration of this artificial locus on the p arm of chromosome 13 creates a new Ad12-inducible fragile site.

scholarly journals Molecular Basis for Expression of Common and Rare Fragile Sites

2003 ◽  
Vol 23 (20) ◽  
pp. 7143-7151 ◽  
Author(s):  
Eitan Zlotorynski ◽  
Ayelet Rahat ◽  
Jennifer Skaug ◽  
Neta Ben-Porat ◽  
Efrat Ozeri ◽  
...  
Keyword(s):  
Molecular Basis ◽  
Fragile Site ◽  
Secondary Structures ◽  
Fragile Sites ◽  
Entire Genome ◽  
Common Fragile Sites ◽  
Dna Structures ◽  
Significant Difference ◽  
Minisatellite Repeats ◽  
Genomic Regions

ABSTRACT Fragile sites are specific loci that form gaps, constrictions, and breaks on chromosomes exposed to partial replication stress and are rearranged in tumors. Fragile sites are classified as rare or common, depending on their induction and frequency within the population. The molecular basis of rare fragile sites is associated with expanded repeats capable of adopting unusual non-B DNA structures that can perturb DNA replication. The molecular basis of common fragile sites was unknown. Fragile sites from R-bands are enriched in flexible sequences relative to nonfragile regions from the same chromosomal bands. Here we cloned FRA7E, a common fragile site mapped to a G-band, and revealed a significant difference between its flexibility and that of nonfragile regions mapped to G-bands, similar to the pattern found in R-bands. Thus, in the entire genome, flexible sequences might play a role in the mechanism of fragility. The flexible sequences are composed of interrupted runs of AT-dinucleotides, which have the potential to form secondary structures and hence can affect replication. These sequences show similarity to the AT-rich minisatellite repeats that underlie the fragility of the rare fragile sites FRA16B and FRA10B. We further demonstrate that the normal alleles of FRA16B and FRA10B span the same genomic regions as the common fragile sites FRA16C and FRA10E. Our results suggest that a shared molecular basis, conferred by sequences with a potential to form secondary structures that can perturb replication, may underlie the fragility of rare fragile sites harboring AT-rich minisatellite repeats and aphidicolin-induced common fragile sites.

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.

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