Abstract
Common fragile sites (CFSs) are genomic loci prone to the formation of breaks or gaps on metaphase chromosomes. They are hotspots for chromosome rearrangements and structural variations, which have been extensively implicated in carcinogenesis, aging, and other pathological processes. Although many CFSs were identified decades ago, a consensus is still lacking for why they are particularly unstable and sensitive to replication perturbations. This is in part due to the lack of high-resolution mapping data for the vast majority of the CFSs, which has hindered mechanistic interrogations. Here, we seek to map human CFSs with high resolution on a genome-wide scale by sequencing the sites of mitotic DNA synthesis (MiDASeq) that are specific for CFSs. We generated a nucleotide-resolution atlas of MiDAS sites (MDSs) that covered most of the known CFSs, and comprehensively analyzed their sequence characteristics and genomic features. Our data on MDSs tallied well with long-standing hypotheses to explain CFS fragility while highlighting the contributions of late replication timing and large transcription units. Notably, the MDSs also encompassed most of the recurrent double-strand break clusters previously identified in mouse neural stem/progenitor cells, thus bridging evolutionarily conserved break points across species. Moreover, MiDAseq provides an important resource that can stimulate future research on CFSs to further unravel the mechanisms and biological relevance underlying these labile genomic regions.
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Data availability
The data have been deposited in the NCBI Gene Expression Omnibus under accession number GSE149376.
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Acknowledgements
This work was supported by grants to Songmin Ying from the Ministry of Science and Technology of China (2016YFA0100301), the National Natural Science Foundation of China (81870007, 81920108001), the Zhejiang Provincial Natural Science Foundation (LD19H160001), and the Zhejiang Provincial Program for the Cultivation of High‐Level Innovative Health Talents (2016‐63). We thank Prof. Ian Hickson (University of Copenhagen, Denmark) for advice on the analysis of MiDAS, and Dr. Jianming Zeng (University of Macau) for valuable suggestions on bioinformatics. We deeply thank Prof. Cheng Li (Peking University) for the courtesy of data on TAD. Thanks for the technical support by the Core Facilities, Zhejiang University School of Medicine.
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F. Ji and H.L. designed the experiments. F. Ji, H.L., F.Z., X.G., S.L., M.Z.S. and H.C. conducted the experiments. S.P., L.O., F. Jia and Z.F. performed bioinformatics analysis. H.L. and F. Ji wrote the manuscript. X.W. and T.L. generated and analyzed the Hi-C data. W.L. and Z.C. analyzed, interpreted the data. S.Y. and H.S. initiated the study, instructed the project and interpreted the data. All authors edited the manuscript and proofread it.
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Ji, F., Liao, H., Pan, S. et al. Genome-wide high-resolution mapping of mitotic DNA synthesis sites and common fragile sites by direct sequencing. Cell Res 30, 1009–1023 (2020). https://doi.org/10.1038/s41422-020-0357-y
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DOI: https://doi.org/10.1038/s41422-020-0357-y
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