High-resolution, ultrasensitive and quantitative DNA double-strand break labeling in eukaryotic cells using i-BLESS

Anna Biernacka, Magdalena Skrzypczak, Yingjie Zhu, Philippe Pasero, Maga Rowicka, Krzysztof Ginalski

Published: 2020-12-20 DOI: 10.1038/s41596-020-00448-3

DNA double-strand breaks

i-BLESS

ultrasensitive detection

genome stability

qDSB-Seq

AI 解读

Supplementary information

Reporting Summary

Supplementary Video 1

Encapsulation of human GM19239 cells in agarose beads.

Using high-resolution microscopy data to generate realistic structures for electromagnetic FDTD simulations from complex biological models

Experimental modulation of physiological force application on leg joint neurons in intactDrosophila melanogaster

Mitochondrial single-cell ATAC-seq for high-throughput multi-omic detection of mitochondrial genotypes and chromatin accessibility

Identification, isolation and analysis of human gut-associated lymphoid tissues

Development of RNA G-quadruplex (rG4)-targetingl-RNA aptamers by rG4-SELEX

Self-assembled ultraflexible probes for long-term neural recordings and neuromodulation

Hyperpolarized water as universal sensitivity booster in biomolecular NMR

Improved sampling and DNA extraction procedures for microbiome analysis in food-processing environments

An analytical workflow for dynamic characterization and quantification of metal-bearing nanomaterials in biological matrices

A flow cytometry-based protocol for syngenic isolation of neurovascular unit cells from mouse and human tissues

查看全部

Sections

Figures

References

Supplementary information

Lensing, S. V. et al. DSBCapture: in situ capture and sequencing of DNA breaks. Nat. Methods 13, 855–857 (2016).
Alt, F. W. & Schwer, B. DNA double-strand breaks as drivers of neural genomic change, function, and disease. DNA Repair 71, 158–163 (2018).
Gothe, H. J., Minneker, V. & Roukos, V. Dynamics of double-strand breaks: implications for the formation of chromosome translocations. Adv. Exp. Med. Biol. 1044, 27–38 (2018).
Mitelman, F., Johansson, B. & Mertens, F. The impact of translocations and gene fusions on cancer causation. Nat. Rev. Cancer 7, 233–245 (2007).
O’Driscoll, M. Diseases associated with defective responses to DNA damage. Cold Spring Harb. Perspect. Biol. 4, a012773 (2012).
White, R. R. & Vijg, J. Do DNA double-strand breaks drive aging? Mol. Cell 63, 729–738 (2016).
Adli, M. The CRISPR tool kit for genome editing and beyond. Nat. Commun. 9, 1911 (2018).
Carroll, D. Genome engineering with zinc-finger nucleases. Genetics 188, 773–782 (2011).
Ma, A. C., Chen, Y., Blackburn, P. R. & Ekker, S. C. TALEN-mediated mutagenesis and genome editing. Methods Mol. Biol. 1451, 17–30 (2016).
Tian, X. et al. CRISPR/Cas9—An evolving biological tool kit for cancer biology and oncology. NPJ Precis. Oncol. 3, 8 (2019).
Martin, S. A., Lord, C. J. & Ashworth, A. DNA repair deficiency as a therapeutic target in cancer. Curr. Opin. Genet. Dev. 18, 80–86 (2008).
Turinetto, V. & Giachino, C. Multiple facets of histone variant H2AX: a DNA double-strand-break marker with several biological functions. Nucleic Acids Res. 43, 2489–2498 (2015).
McManus, K. J. & Hendzel, M. J. ATM-dependent DNA damage-independent mitotic phosphorylation of H2AX in normally growing mammalian cells. Mol. Biol. Cell 16, 5013–5025 (2005).
Wang, F. & Higgins, J. M. Histone modifications and mitosis: countermarks, landmarks, and bookmarks. Trends Cell Biol. 23, 175–184 (2013).
Leduc, F. et al. Genome-wide mapping of DNA strand breaks. PLoS ONE 6, e17353 (2011).
Baranello, L. et al. DNA break mapping reveals topoisomerase II activity genome-wide. Int. J. Mol. Sci. 15, 13111–13122 (2014).
Shastri, N. et al. Genome-wide identification of structure-forming repeats as principal sites of fork collapse upon ATR inhibition. Mol. Cell 72, 222–238 e211 (2018).
Gittens, W. H. et al. A nucleotide resolution map of Top2-linked DNA breaks in the yeast and human genome. Nat. Commun. 10, 4846 (2019).
Pratto, F. et al. DNA recombination. Recombination initiation maps of individual human genomes. Science 346, 1256442 (2014).
Khil, P. P., Smagulova, F., Brick, K. M., Camerini-Otero, R. D. & Petukhova, G. V. Sensitive mapping of recombination hotspots using sequencing-based detection of ssDNA. Genome Res. 22, 957–965 (2012).
Biernacka, A. et al. i-BLESS is an ultra-sensitive method for detection of DNA double-strand breaks. Commun. Biol. 1, 181 (2018).
Hoffman, E. A., McCulley, A., Haarer, B., Arnak, R. & Feng, W. Break-seq reveals hydroxyurea-induced chromosome fragility as a result of unscheduled conflict between DNA replication and transcription. Genome Res. 25, 402–412 (2015).
Crosetto, N. et al. Nucleotide-resolution DNA double-strand break mapping by next-generation sequencing. Nat. Methods 10, 361–365 (2013).
Ran, F. A. et al. In vivo genome editing using Staphylococcus aureus Cas9. Nature 520, 186–191 (2015).
Aymard, F. et al. Genome-wide mapping of long-range contacts unveils clustering of DNA double-strand breaks at damaged active genes. Nat. Struct. Mol. Biol. 24, 353–361 (2017).
Shi, W. et al. Ssb1 and Ssb2 cooperate to regulate mouse hematopoietic stem and progenitor cells by resolving replicative stress. Blood 129, 2479–2492 (2017).
Hu, J. et al. Detecting DNA double-stranded breaks in mammalian genomes by linear amplification-mediated high-throughput genome-wide translocation sequencing. Nat. Protoc. 11, 853–871 (2016).
Canela, A. et al. DNA breaks and end resection measured genome-wide by end sequencing. Mol. Cell 63, 898–911 (2016).
Mimitou, E. P., Yamada, S. & Keeney, S. A global view of meiotic double-strand break end resection. Science 355, 40–45 (2017).
Yamada, S. et al. Molecular structures and mechanisms of DNA break processing in mouse meiosis. Genes Dev. 34, 806–818 (2020).
Wiegand, R. C., Godson, G. N. & Radding, C. M. Specificity of the S1 nuclease from Aspergillus oryzae. J. Biol. Chem. 250, 8848–8855 (1975).
Yan, W. X. et al. BLISS is a versatile and quantitative method for genome-wide profiling of DNA double-strand breaks. Nat. Commun. 8, 15058 (2017).
Promonet, A. et al. Topoisomerase 1 prevents replication stress at R-loop-enriched transcription termination sites. Nat. Commun. 11, 3940 (2020).
Zhu, Y. et al. qDSB-Seq is a general method for genome-wide quantification of DNA double-strand breaks using sequencing. Nat. Commun. 10, 2313 (2019).
Petek, L. M., Russell, D. W. & Miller, D. G. Frequent endonuclease cleavage at off-target locations in vivo. Mol. Ther. 18, 983–986 (2010).
Tsai, S. Q. et al. GUIDE-seq enables genome-wide profiling of off-target cleavage by CRISPR-Cas nucleases. Nat. Biotechnol. 33, 187–197 (2015).
Gabriel, R. et al. An unbiased genome-wide analysis of zinc-finger nuclease specificity. Nat. Biotechnol. 29, 816–823 (2011).
Botstein, D., Chervitz, S. A. & Cherry, J. M. Yeast as a model organism. Science 277, 1259–1260 (1997).
Bassett, D. E. Jr., Boguski, M. S. & Hieter, P. Yeast genes and human disease. Nature 379, 589–590 (1996).
Zhu, Y. et al. Integrated analysis of patterns of DNA breaks reveals break formation mechanisms and their population distribution during replication stress. Preprint at https://www.biorxiv.org/content/10.1101/171439v2 (2017).
Sriramachandran, A. M. et al. Genome-wide nucleotide-resolution mapping of DNA replication patterns, single-strand breaks, and lesions by GLOE-Seq. Mol. Cell 78, 975–985 e977 (2020).
Chung, W. H., Zhu, Z., Papusha, A., Malkova, A. & Ira, G. Defective resection at DNA double-strand breaks leads to de novo telomere formation and enhances gene targeting. PLoS Genet. 6, e1000948 (2010).
Symington, L. S. Mechanism and regulation of DNA end resection in eukaryotes. Crit. Rev. Biochem. Mol. Biol. 51, 195–212 (2016).
Zhou, Y., Caron, P., Legube, G. & Paull, T. T. Quantitation of DNA double-strand break resection intermediates in human cells. Nucleic Acids Res. 42, e19 (2014).
Aymard, F. et al. Transcriptionally active chromatin recruits homologous recombination at DNA double-strand breaks. Nat. Struct. Mol. Biol. 21, 366–374 (2014).
Vieira Braga, F. A. & Miragaia, R. J. Tissue handling and dissociation for single-cell RNA-Seq. Methods Mol. Biol. 1979, 9–21 (2019).
Reichard, A. & Asosingh, K. Best practices for preparing a single cell suspension from solid tissues for flow cytometry. Cytom. A 95, 219–226 (2019).
Leelatian, N. et al. Preparing viable single cells from human tissue and tumors for cytomic analysis. Curr. Protoc. Mol. Biol. 118, 25C 21 21–25C 21 23 (2017).
Cannan, W. J. & Pederson, D. S. Mechanisms and consequences of double-strand DNA break formation in chromatin. J. Cell Physiol. 231, 3–14 (2016).
Li, F. et al. Apn2 resolves blocked 3′ ends and suppresses Top1-induced mutagenesis at genomic rNMP sites. Nat. Struct. Mol. Biol. 26, 155–163 (2019).
Mitra, A., Skrzypczak, M., Ginalski, K. & Rowicka, M. Strategies for achieving high sequencing accuracy for low diversity samples and avoiding sample bleeding using illumina platform. PLoS ONE 10, e0120520 (2015).
Mitra, A. et al. Analyzing and interpreting DNA double-strand break sequencing data. Preprint at https://www.biorxiv.org/content/10.1101/2020.03.05.977801v1 (2020).
Tiwari, S., Wang, S., Hagen, G. & Guilfoyle, T. J. Transfection assays with protoplasts containing integrated reporter genes. Methods Mol. Biol. 323, 237–244 (2006).
Buenrostro, J. D., Wu, B., Chang, H. Y. & Greenleaf, W. J. ATAC-seq: a method for assaying chromatin accessibility genome-wide. Curr. Protoc. Mol. Biol. 109, 21 29 21–21 29 29 (2015).

High-resolution, ultrasensitive and quantitative DNA double-strand break labeling in eukaryotic cells using i-BLESS

Supplementary information

推荐阅读