BLISS is a versatile and quantitative method for genome-wide profiling of DNA double-strand breaks

Winston X. Yan, Reza Mirzazadeh, Silvano Garnerone, David Scott, Martin W. Schneider, Tomasz Kallas, Joaquin Custodio, Erik Wernersson, Yinqing Li, Linyi Gao, Yana Federova, Bernd Zetsche, Feng Zhang (), Magda Bienko () and Nicola Crosetto ()
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Winston X. Yan: Broad Institute of MIT and Harvard
Reza Mirzazadeh: Science for Life Laboratory, Karolinska Institutet
Silvano Garnerone: Science for Life Laboratory, Karolinska Institutet
David Scott: Broad Institute of MIT and Harvard
Martin W. Schneider: Broad Institute of MIT and Harvard
Tomasz Kallas: Science for Life Laboratory, Karolinska Institutet
Joaquin Custodio: Science for Life Laboratory, Karolinska Institutet
Erik Wernersson: Science for Life Laboratory, Karolinska Institutet
Yinqing Li: Broad Institute of MIT and Harvard
Linyi Gao: Broad Institute of MIT and Harvard
Yana Federova: Broad Institute of MIT and Harvard
Bernd Zetsche: Broad Institute of MIT and Harvard
Feng Zhang: Broad Institute of MIT and Harvard
Magda Bienko: Science for Life Laboratory, Karolinska Institutet
Nicola Crosetto: Science for Life Laboratory, Karolinska Institutet

Nature Communications, 2017, vol. 8, issue 1, 1-9

Abstract: Abstract Precisely measuring the location and frequency of DNA double-strand breaks (DSBs) along the genome is instrumental to understanding genomic fragility, but current methods are limited in versatility, sensitivity or practicality. Here we present Breaks Labeling In Situ and Sequencing (BLISS), featuring the following: (1) direct labelling of DSBs in fixed cells or tissue sections on a solid surface; (2) low-input requirement by linear amplification of tagged DSBs by in vitro transcription; (3) quantification of DSBs through unique molecular identifiers; and (4) easy scalability and multiplexing. We apply BLISS to profile endogenous and exogenous DSBs in low-input samples of cancer cells, embryonic stem cells and liver tissue. We demonstrate the sensitivity of BLISS by assessing the genome-wide off-target activity of two CRISPR-associated RNA-guided endonucleases, Cas9 and Cpf1, observing that Cpf1 has higher specificity than Cas9. Our results establish BLISS as a versatile, sensitive and efficient method for genome-wide DSB mapping in many applications.

Date: 2017
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DOI: 10.1038/ncomms15058

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