Cancer genomes exhibit numerous deletions, some of which inactivate tumor suppressor genes and/or correspond to unstable genomic regions, notably common fragile sites (CFSs). However, 70%-80% of recurrent deletions cataloged in tumors remain unexplained. Recent findings that CFS setting is cell-type dependent prompted us to reevaluate the contribution of CFS to cancer deletions. By combining extensive CFS molecular mapping and a comprehensive analysis of CFS features, we show that the pool of CFSs for all human cell types consists of chromosome regions with genes over 300 kb long, and different subsets of these loci are committed to fragility in different cell types. Interestingly, we find that transcription of large genes does not dictate CFS fragility. We further demonstrate that, like CFSs, cancer deletions are significantly enriched in genes over 300 kb long. We now provide evidence that over 50% of recurrent cancer deletions originate from CFSs associated with large genes.

Replication stress is a primary threat to genome stability and has been implicated in tumorigenesis 1,2 . Common fragile sites (CFSs) are loci hypersensitive to replication stress 3 and are hotspots for chromosomal rearrangements in cancers 4 . CFSs replicate late in S-phase 3 , are cell-type dependent 4-6 and nest within very large genes 4,[7][8][9] . The mechanisms responsible for CFS instability are still discussed, notably the relative impact of transcription-replication conflicts 7,8,10 versus their low density in replication initiation events 5,6 . Here we address the relationships between transcription, replication, gene size and instability by manipulating the transcription of three endogenous large genes, two in chicken and one in human cells.Remarkably, moderate transcription destabilises large genes whereas high transcription levels alleviate their instability. Replication dynamics analyses showed that transcription quantitatively shapes the replication program of large genes, setting both their initiation profile and their replication timing as well as regulating internal fork velocity. Noticeably, high transcription levels advance the replication time of large genes from late to mid S-phase, which most likely gives cells more time to complete replication before mitotic entry.Transcription can therefore contribute to maintaining the integrity of some difficult-toreplicate loci, challenging the dominant view that it is exclusively a threat to genome stability.It is largely agreed that CFSs tend to remain incompletely replicated until mitosis upon replication stress. Incompletely replicated regions are processed by specific endonucleases promoting mitotic DNA synthesis and sister chromatid separation, eventually at the cost of chromosomal rearrangements [11][12][13][14][15] . Two main mechanisms have been suggested to explain this delayed replication completion. One postulates that secondary DNA structures 10 or transcription-dependent replication barriers, notably R-loops 7,8,10 , lead to fork stalling and collapse. The other proposes that replication of the core of the CFSs by long-travelling forks due to their paucity in initiation events is specifically delayed upon fork slowing 5,6 . Here we .

Back to Main Page1. Please note that only one statement of equally contributing authors is allowed (as well as one statement of joint supervision, if appropriate), so the two present statements have been amalgamated into one for now. If the two pairs of authors need to be diffentiated, a statement can be added to the author contributions section to explain. If you would like to do this, please provide some text to add.The meer fact that two different statements were made was because they were not the same. So they must not be amalgamated.I have added a line in the Author Contribution section.2. First para of main text, sentence beginning "In yeast", please check that "SlX4" is correct. Should it be SLX4?It should be Slx4 with lowercase L and lowercase X 3. Please check your article carefully, coordinate with any co-authors and enter all final edits clearly in the eproof, remembering to save frequently. Once corrections are submitted, we cannot routinely make further changes to the article. OK 4. Note that the eproof should be amended in only one browser window at any one time; otherwise changes will be overwritten.OK 5. Author surnames have been highlighted. Please check these carefully and adjust if the first name or surname is marked up incorrectly. Note that changes here will affect indexing of your article in public repositories such as PubMed. Also, carefully check the spelling and numbering of all author names and affiliations, and the corresponding email address(es). OK 6. You cannot alter accepted Supplementary Information files except for critical changes to scientific content. If you do resupply any files, please also provide a brief (but complete) list of changes. If these are not considered scientific changes, any altered Supplementary files will not be used, only the originally accepted version will be published. OK 7. Para beginning "Here, we unravel" -please check that PCNA has been expanded correctly at first mention. e.Proofing https://eproofing.springer.com/journals_v2/printpage.php?token... 1 of 64 22/04/2020, 15:41 OK 8. Results section, first para, please define YFP at first mention Yellow fluorescent protein (YFP) Figure 1b -please define IgCThis is a typo. It should be IgG in the figure and the following definition added to the legend:IgG: Immunoglobulin G 10. Figure 1c, bottom axes of plots -please check that the jump from 10 h to 12 h is correct (the other time points are in increments of 1 h). Please also check that the labels added to the right of the immunoblots in panel c are correct.All is correct Figure 1 caption -please define HA at first mentionHemagglutinin (HA) Figure 1 -Please check carefully that the caption for panel c is correct as edited to match the new figure.All is OK In the caption to Figure 2g,h -please differentiate (by inserting (g) and (h) what the two panels show.The caption is the same for g and h. The only difference is that the mutations in g are missense mutations while they are nonsense mutations in h. I have changed the caption to:Co-immunoprecipitation of en...

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Background Genome-wide association studies (GWASs) have identified genes influencing skin ageing and mole count in Europeans, but little is known about the relevance of these (or other genes) in non-Europeans. Objectives To conduct a GWAS for facial skin ageing and mole count in adults < 40 years old, of mixed European, Native American and African ancestry, recruited in Latin America. Methods Skin ageing and mole count scores were obtained from facial photographs of over 6000 individuals. After quality control checks, three wrinkling traits and mole count were retained for genetic analyses. DNA samples were genotyped with Illumina's HumanOmniExpress chip. Association testing was performed on around 8 703 729 single-nucleotide polymorphisms (SNPs) across the autosomal genome.

The treatment of malignant brain gliomas remains a challenge, despite the availability of the classical triad of surgery, radiotherapy, and chemotherapy. There is thus the need for investigations into other forms of treatment strategies, such as gene therapy. Using antisense technology we have targeted glycogen metabolism, since malignant astrocytes present a high content of glycogen. In vitro rat C6-glioma cells, transfected with antisense glycogen synthase (C6-AS cells) exhibited a decreased expression of glycogen synthase and reduced activity of glycogen synthesis, along with attenuated invasiveness. In vivo tumors induced by C6-AS cells in nude mice exhibited a significant reduction in tumor growth compared with controls. This reduction could be mediated by the induction of MCH-I expression. The inhibition of glycogen synthesis by antisense glycogen synthase validates a putative target and a new approach for further study to advance the much-needed efficacy of intervention strategies for malignant gliomas.

Replication stress is a primary threat to genome stability and has been implicated in tumorigenesis1, 2. Common fragile sites (CFSs) are loci hypersensitive to replication stress3 and are hotspots for chromosomal rearrangements in cancers4. CFSs replicate late in S-phase3, are cell-type dependent4–6 and nest within very large genes4, 7–9. The mechanisms responsible for CFS instability are still discussed, notably the relative impact of transcription-replication conflicts7, 8, 10versus their low density in replication initiation events5, 6. Here we address the relationships between transcription, replication, gene size and instability by manipulating the transcription of three endogenous large genes, two in chicken and one in human cells. Remarkably, moderate transcription destabilises large genes whereas high transcription levels alleviate their instability. Replication dynamics analyses showed that transcription quantitatively shapes the replication program of large genes, setting both their initiation profile and their replication timing as well as regulating internal fork velocity. Noticeably, high transcription levels advance the replication time of large genes from late to mid S-phase, which most likely gives cells more time to complete replication before mitotic entry. Transcription can therefore contribute to maintaining the integrity of some difficult-to-replicate loci, challenging the dominant view that it is exclusively a threat to genome stability.

The tumour suppressor SLX4 plays multiple roles in the maintenance of genome stability, acting as a scaffold for structure-specific endonucleases and other DNA repair proteins. It directly interacts with the mismatch repair (MMR) protein MSH2 but the significance of this interaction remained unknown until recent findings showing that MutSβ (MSH2-MSH3) stimulates in vitro the SLX4-dependent Holliday junction resolvase activity. Here, we characterize the mode of interaction between SLX4 and MSH2, which relies on an MSH2-interacting peptide (SHIP box) that drives interaction of SLX4 with both MutSβ and MutSα (MSH2-MSH6). While we show that this MSH2 binding domain is dispensable for the well-established role of SLX4 in interstrand crosslink repair, we find that it mediates inhibition of MutSα-dependent MMR by SLX4, unravelling an unanticipated function of SLX4.