Volume 30, No 11, Nov 2020

ISSN: 1001-0602 
EISSN: 1748-7838 2018 
impact factor 17.848* 
(Clarivate Analytics, 2019)

Volume 30 Issue 11, November 2020: 1009-1023

ORIGINAL ARTICLES

Genome-wide high-resolution mapping of mitotic DNA synthesis sites and common fragile sites by direct sequencing

Fang Ji¹ , Hongwei Liao¹ , Sheng Pan^1,2 , Liujian Ouyang^1,2 , Fang Jia^1,2 , Zaiyang Fu^1,2 , Fengjiao Zhang¹ , Xinwei Geng¹ , Xinming Wang³ , Tingting Li⁴ , Shuangying Liu^1,2 , Madiha Zahra Syeda¹ , Haixia Chen⁵ , Wen Li⁵ , Zhihua Chen⁵ , Huahao Shen^5,6,* , Songmin Ying^1,*

¹Department of Pharmacology & Department of Respiratory and Critical Care Medicine of the Second Affiliated Hospital, Zhejiang University School of Medicine, Key Laboratory of Respiratory Disease of Zhejiang Province, Hangzhou, Zhejiang 310009, China
²Chu Kochen Honors College of Zhejiang University, Hangzhou, Zhejiang, China
³School of Life Sciences, Peking University, Beijing 100871, China
⁴State Key Laboratory of Proteomics, National Center of Biomedical Analysis, Institute of Basic Medical Sciences, Beijing 100850, China
⁵Key Laboratory of Respiratory Disease of Zhejiang Province, Department of Respiratory and Critical Care Medicine, Second Affiliated Hospital of Zhejiang University School of Medicine, Hangzhou, Zhejiang 310009, China
⁶State Key Laboratory of Respiratory Diseases, Guangzhou, Guangdong 510120, China
^†These authors contributed equally: Fang Ji, Hongwei Liao, Sheng Pan
Correspondence: Huahao Shen(huahaoshen@zju.edu.cn)Songmin Ying(yings@zju.edu.cn)

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.

https://doi.org/10.1038/s41422-020-0357-y

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