TY - JOUR
T1 - Dna2 nuclease deficiency results in large and complex DNA insertions at chromosomal breaks
AU - Yu, Yang
AU - Pham, Nhung
AU - Xia, Bo
AU - Papusha, Alma
AU - Wang, Guangyu
AU - Yan, Zhenxin
AU - Peng, Guang
AU - Chen, Kaifu
AU - Ira, Grzegorz
N1 - Funding Information:
Acknowledgements We thank A. Gabriel, D. J. Garfinkel, J. Haber, M. G. Blanco and F. Storici for the gifts of strains and plasmids, and J. Haber and P. Hastings for critical reading of the manuscript. This work was funded by grants from the US National Institutes of Health (GM080600 and GM125650 to G.I., GM125632 and HL133254 to K.C.) and the Cancer Prevention Research Institute of Texas (RP140456 to G.I. and G.P., RP150611 to K.C.).
Publisher Copyright:
© 2018, Springer Nature Limited.
Copyright:
Copyright 2020 Elsevier B.V., All rights reserved.
PY - 2018/12/13
Y1 - 2018/12/13
N2 - Insertions of mobile elements1–4, mitochondrial DNA5 and fragments of nuclear chromosomes6 at DNA double-strand breaks (DSBs) threaten genome integrity and are common in cancer7–9. Insertions of chromosome fragments at V(D)J recombination loci can stimulate antibody diversification10. The origin of insertions of chromosomal fragments and the mechanisms that prevent such insertions remain unknown. Here we reveal a yeast mutant, lacking evolutionarily conserved Dna2 nuclease, that shows frequent insertions of sequences between approximately 0.1 and 1.5 kb in length into DSBs, with many insertions involving multiple joined DNA fragments. Sequencing of around 500 DNA inserts reveals that they originate from Ty retrotransposons (8%), ribosomal DNA (rDNA) (15%) and from throughout the genome, with preference for fragile regions such as origins of replication, R-loops, centromeres, telomeres or replication fork barriers. Inserted fragments are not lost from their original loci and therefore represent duplications. These duplications depend on nonhomologous end-joining (NHEJ) and Pol4. We propose a model in which alternative processing of DNA structures arising in Dna2-deficient cells can result in the release of DNA fragments and their capture at DSBs. Similar DNA insertions at DSBs are expected to occur in any cells with linear extrachromosomal DNA fragments.
AB - Insertions of mobile elements1–4, mitochondrial DNA5 and fragments of nuclear chromosomes6 at DNA double-strand breaks (DSBs) threaten genome integrity and are common in cancer7–9. Insertions of chromosome fragments at V(D)J recombination loci can stimulate antibody diversification10. The origin of insertions of chromosomal fragments and the mechanisms that prevent such insertions remain unknown. Here we reveal a yeast mutant, lacking evolutionarily conserved Dna2 nuclease, that shows frequent insertions of sequences between approximately 0.1 and 1.5 kb in length into DSBs, with many insertions involving multiple joined DNA fragments. Sequencing of around 500 DNA inserts reveals that they originate from Ty retrotransposons (8%), ribosomal DNA (rDNA) (15%) and from throughout the genome, with preference for fragile regions such as origins of replication, R-loops, centromeres, telomeres or replication fork barriers. Inserted fragments are not lost from their original loci and therefore represent duplications. These duplications depend on nonhomologous end-joining (NHEJ) and Pol4. We propose a model in which alternative processing of DNA structures arising in Dna2-deficient cells can result in the release of DNA fragments and their capture at DSBs. Similar DNA insertions at DSBs are expected to occur in any cells with linear extrachromosomal DNA fragments.
UR - http://www.scopus.com/inward/record.url?scp=85058569913&partnerID=8YFLogxK
UR - http://www.scopus.com/inward/citedby.url?scp=85058569913&partnerID=8YFLogxK
U2 - 10.1038/s41586-018-0769-8
DO - 10.1038/s41586-018-0769-8
M3 - Article
C2 - 30518856
AN - SCOPUS:85058569913
SN - 0028-0836
VL - 564
SP - 287
EP - 290
JO - Nature
JF - Nature
IS - 7735
ER -