Genomic instability in fragile sites—still adding the pieces

Sinai, Michal Irony-Tur; Kerem, Batsheva

doi:10.1002/gcc.22715

Cited by 15 publications

(25 citation statements)

References 106 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…However, in lymphocytes, these regions fully completed replication of both alleles by the end of S-phase, especially under unperturbed conditions, implying that additional mechanisms-perhaps tissue specific transcriptional and epigenetic programs-are final contributors toward chromosomal breakages [71]. Alternatively, or in addition, lymphocytes may have capabilities to complete replication or repair potential damage in G2 phase [74][75][76] that are absent in fibroblasts, where these sites ultimately result in breaks. Although we cannot exclude the fact that replication of these CFS may continue in G2 and/or into mitosis in fibroblasts, delayed replication still has deleterious consequences to genome integrity, as reported for other late replicating regions.…”

Section: Discussionmentioning

confidence: 99%

Impaired Replication Timing Promotes Tissue-Specific Expression of Common Fragile Sites

Maccaroni

Balzano

Mirimao

et al. 2020

Genes

View full text Add to dashboard Cite

Common fragile sites (CFSs) are particularly vulnerable regions of the genome that become visible as breaks, gaps, or constrictions on metaphase chromosomes when cells are under replicative stress. Impairment in DNA replication, late replication timing, enrichment of A/T nucleotides that tend to form secondary structures, the paucity of active or inducible replication origins, the generation of R-loops, and the collision between replication and transcription machineries on particularly long genes are some of the reported characteristics of CFSs that may contribute to their tissue-specific fragility. Here, we validated the induction of two CFSs previously found in the human fetal lung fibroblast line, Medical Research Council cell strain 5 (MRC-5), in another cell line derived from the same fetal tissue, Institute for Medical Research-90 cells (IMR-90). After induction of CFSs through aphidicolin, we confirmed the expression of the CFS 1p31.1 on chromosome 1 and CFS 3q13.3 on chromosome 3 in both fetal lines. Interestingly, these sites were found to not be fragile in lymphocytes, suggesting a role for epigenetic or transcriptional programs for this tissue specificity. Both these sites contained late-replicating genes NEGR1 (neuronal growth regulator 1) at 1p31.1 and LSAMP (limbic system-associated membrane protein) at 3q13.3, which are much longer, 0.880 and 1.4 Mb, respectively, than the average gene length. Given the established connection between long genes and CFS, we compiled information from the literature on all previously identified CFSs expressed in fibroblasts and lymphocytes in response to aphidicolin, including the size of the genes contained in each fragile region. Our comprehensive analysis confirmed that the genes found within CFSs are longer than the average human gene; interestingly, the two longest genes in the human genome are found within CFSs: Contactin Associated Protein 2 gene (CNTNAP2) in a lymphocytes’ CFS, and Duchenne muscular dystrophy gene (DMD) in a CFS expressed in both lymphocytes and fibroblasts. This indicates that the presence of very long genes is a unifying feature of all CFSs. We also obtained replication profiles of the 1p31.1 and 3q13.3 sites under both perturbed and unperturbed conditions using a combination of fluorescent in situ hybridization (FISH) and immunofluorescence against bromodeoxyuridine (BrdU) on interphase nuclei. Our analysis of the replication dynamics of these CFSs showed that, compared to lymphocytes where these regions are non-fragile, fibroblasts display incomplete replication of the fragile alleles, even in the absence of exogenous replication stress. Our data point to the existence of intrinsic features, in addition to the presence of long genes, which affect DNA replication of the CFSs in fibroblasts, thus promoting chromosomal instability in a tissue-specific manner.

show abstract

Section: Discussionmentioning

confidence: 99%

Impaired Replication Timing Promotes Tissue-Specific Expression of Common Fragile Sites

Maccaroni

Balzano

Mirimao

et al. 2020

Genes

View full text Add to dashboard Cite

show abstract

“…CFS instability has been proposed to result from fork barriers raised by sequences prone to form secondary structures 18,19,36 . At least 4 types of observations argue against this model; i) Analysis of the nucleotide sequence of several FISH-mapped CFSs has provided contrasted results regarding the presence of such roadblocks in a substantial proportion of the sites 37 .…”

Section: Discussionmentioning

confidence: 99%

“…Formation of cruciform and hairpin structures in regions enriched in stretches of ATdinucleotide repeats has long been proposed to contribute to CFS instability because secondary structures could delay the progression of replication forks and eventually lead to under-replication 18,19 . We therefore compared the RI profiles to the localisation of ATdinucleotide repeats reported in the chromosome regions hosting FRA3B and FRA16D (Fig.…”

Section: Formation Of Sequence-dependent Fork Barriers Does Not Accoumentioning

confidence: 99%

“…A variant of this model proposes that stressinduced uncoupling of the replicative helicase from DNA polymerases gives rise to singlestranded DNA, which elicits formation of DNA secondary structures at particular sequences, notably at stretches of AT-dinucleotides. These structures would further delay polymerase progression, increasing the frequency of replication-transcription encounters 18,19 .…”

Section: Introductionmentioning

confidence: 99%

See 1 more Smart Citation

Transcription-mediated organization of the replication initiation program across large genes sets up common fragile sites genome-wide

Brison

Koundrioukoff

Schmidt

et al. 2019

Preprint

View full text Add to dashboard Cite

Running title (50 characters or less, including spaces)CFSs: a view through Repli-Seq, GRO-seq and OK-Seq ABSTRACT Common Fragile Sites (CFSs) are chromosome regions prone to breakage under replication stress, known to drive chromosome rearrangements during oncogenesis. Most CFSs nest in large expressed genes, suggesting that transcription elicits their instability but the underlying mechanisms remained elusive. Analyses of genome-wide replication timing of human lymphoblasts here show that stress-induced delayed/under-replication is the hallmark of CFSs. Extensive genome-wide analyses of nascent transcripts, replication origin positioning and fork directionality reveal that 80% of CFSs nest in large transcribed domains poor in initiation events, thus replicated by long-traveling forks. In contrast to formation of sequence-dependent fork barriers or head-on transcription-replication conflicts, travelinglong in late S phase explains CFS replication features. We further show that transcription inhibition during the S phase, which excludes the setting of new replication origins, fails to rescue CFS stability. Altogether, results show that transcription-dependent suppression of initiation events delays replication of large gene body, committing them to instability.

show abstract

“…The existence of mechanisms that that normally select a small group of active replication initiation sites from a pool of potential replication origins can facilitate genomic stability, allowing for the complete duplication of the genome when replication stalls. Under such circumstances, excess origin activation prevents under-replication, which can lead to cell cycle perturbations, chromosomal translocations, and DNA breakage in regions with low origin density 1,8,50,55,56 . However, excess initiation of DNA replication can have deleterious consequences, including oncogenic transformation of normal cells and increased genomic instability in cancer 28,44,45,47 , consistent with our observations suggesting that massive overreplication can lead to senescence.…”

Section: Discussionmentioning

confidence: 99%

Dynamics of replication origin over-activation

Redon

Utani

et al. 2020

Preprint

View full text Add to dashboard Cite

We determined replication patterns in cancer cells in which the controls that normally prevent excess replication were disrupted ("re-replicating cells"). Single-fiber analyses suggested that replication origins were activated at a higher frequency in re-replicating cells. However, nascent strand sequencing demonstrated that re-replicating cells utilized the same pool of potential replication origins as normally replicating cells. Surprisingly, rereplicating cells exhibited a skewed initiation frequency correlating with replication timing.These patterns differed from the replication profiles observed in non-re-replicating cells exposed to replication stress, which activated a novel group of dormant origins not typically activated during normal mitotic growth. Hence, disruption of the molecular interactions that regulates origin initiation can activate two distinct pools of potential replication origins: rereplicating cells over-activate flexible origins while replication stress in normal mitotic growth activates dormant origins.Our previous studies have shown that RepID, a replicator-specific binding protein essential for site-specific initiation of DNA replication in mammalian cells 25 , recruits CRL4 to chromatin in a PCNA-independent manner prior to the onset of S phase and promotes CDT1 degradation.RepID deficiency is associated with delayed CDT1 degradation, resulting in limited genome rereplication 26 . Partial genome re-replication can also be caused by inhibition of DOT1L, a methyltransferase which catalyzes the demethylation of histone H3 on lysine 79 (H3K79Me2), thereby removing a histone modification typically associated with a group of replication origins 27 . Because massive re-replication can drive cell death specifically in checkpointcompromised cancer cells, both CDT1 stabilization by inactivation of ubiquitin-mediated degradation and inhibition of DOT1L are currently being explored as novel anti-cancer therapeutic strategies [28][29][30][31][32][33] .Given that genome re-replication is a common avenue to genomic instability and considering its potential as a strategy for chemotherapy, it is important to understand in detail its mechanics and downstream consequences. Here, we report that re-replication exhibits aberrant replication fork dynamics and occurs more slowly than the routine genome duplication that takes place during normal growth. The consequences of the persistent presence of pre-replication complexes on chromatin include massive DNA damage and the induction of senescence. Unlike other instances of replication origin over-activation, such as when replication slows down as a result of nucleotide depletion or in cells exposed to DNA damaging conditions, the re-replication process preferentially utilizes a subset of the replication origin pool typically used during normal growth. Results:

show abstract

Genomic instability in fragile sites—still adding the pieces

Cited by 15 publications

References 106 publications

Impaired Replication Timing Promotes Tissue-Specific Expression of Common Fragile Sites

Impaired Replication Timing Promotes Tissue-Specific Expression of Common Fragile Sites

Transcription-mediated organization of the replication initiation program across large genes sets up common fragile sites genome-wide

Dynamics of replication origin over-activation

Contact Info

Product

Resources

About