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qDSB-Seq is a general method for genome-wide quantification of DNA double-strand breaks using sequencing

Measuring relative frequencies of DNA double-strand breaks between loci does not provide the full physiological relevance of those breaks. Here Rowicka and colleagues present qDSB-Seq method which uses spike-in double-strand breaks induced by a restriction enzyme to accurately quantify DNA damage.

Yingjie Zhu
Anna Biernacka
Maga Rowicka
ResearchOpen Access24 May 2019
Nature Communications

Volume: 10, P: 1-11
Nucleotide-resolution DNA double-strand break mapping by next-generation sequencing

Biotinylated tags bind double-strand breaks in genomic DNA; after enrichment and sequencing, this allows precise, genome-wide mapping of the breaks.

Nicola Crosetto
Abhishek Mitra
Ivan Dikic
Research17 Mar 2013
Nature Methods

Volume: 10, P: 361-365
Topoisomerase 1 prevents replication stress at R-loop-enriched transcription termination sites

While R-loops can alter cell homeostasis, it is unclear what determines their toxicity. Here, the authors, by using Top1 knockdown as a tool to enhance the formation of R-loops at certain genomic sites, reveal and characterize a proportion of R-loops that are more toxic to the cell by causing DNA damage.

Alexy Promonet
Ismaël Padioleau
Philippe Pasero
ResearchOpen Access07 Aug 2020
Nature Communications

Volume: 11, P: 1-12
Genome-wide mapping of long-range contacts unveils clustering of DNA double-strand breaks at damaged active genes

Capture Hi-C analysis reveals that DNA double-strand breaks within transcriptionally active regions of the human genome form clusters that exhibit delayed repair in the G1 phase of the cell cycle.

François Aymard
Marion Aguirrebengoa
Gaëlle Legube
Research06 Mar 2017
Nature Structural & Molecular Biology

Volume: 24, P: 353-361
Let the data speak

Benjamin P. Tu
Andrzej Kudlicki
Steven L. McKnight
Correspondence01 Dec 2006
Nature Reviews Molecular Cell Biology

Volume: 7, P: 1-2
High-resolution, ultrasensitive and quantitative DNA double-strand break labeling in eukaryotic cells using i-BLESS

This protocol describes a genome-wide approach for ultrasensitive and quantitative detection of DNA double-strand breaks (DSBs) that relies on encapsulating cells in agarose beads and labeling breaks with biotinylated adapters.

Anna Biernacka
Magdalena Skrzypczak
Krzysztof Ginalski
Protocols21 Dec 2020
Nature Protocols

Volume: 16, P: 1034-1061
i-BLESS is an ultra-sensitive method for detection of DNA double-strand breaks

Anna Biernacka, Yingjie Zhu et al. present i-BLESS, a universal method for detecting genome-wide DNA double strand breaks, optimized here for yeast. By immobilizing cells on agarose beads, the authors are able to achieve efficient diffusion of reagents and labeling of double strand breaks, including ultra-rare breaks such as those at G-quadruplexes.

Anna Biernacka
Yingjie Zhu
Krzysztof Ginalski
ResearchOpen Access31 Oct 2018
Communications Biology

Volume: 1, P: 1-9
Predicting proteome dynamics using gene expression data

Krzysztof Kuchta
Joanna Towpik
Maga Rowicka
ResearchOpen Access14 Sept 2018
Scientific Reports

Volume: 8, P: 1-13

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