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BLISS: quantitative and versatile genome-wide profiling of DNA breaks in situ

By Winston X Yan, Reza Mirzazadeh, Silvano Garnerone, David Scott, Martin W. Schneider, Tomasz Kallas, Joaquin Custodio, Erik Wernersson, Linyi Gao, Yinqing Li, Yana Federova, Bernd Zetsche, Feng Zhang, Magda Bienko, Nicola Crosetto

Posted 04 Dec 2016
bioRxiv DOI: 10.1101/091629

We present a method for genome-wide DNA double-strand Breaks (DSBs) Labeling In Situ and Sequencing (BLISS) which, compared to existing methods, introduces several key features: 1) high efficiency and low input requirement by in situ DSB labeling in cells or tissue sections directly on a solid surface; 2) easy scalability by performing in situ reactions in multi-well plates; 3) high sensitivity by linearly amplifying tagged DSBs using in vitro transcription; and 4) accurate DSB quantification and control of PCR biases by using unique molecular identifiers. We demonstrate the ability to use BLISS to quantify natural and drug-induced DSBs in low-input samples of cancer cells, primary mouse embryonic stem cells, and mouse liver tissue sections. Finally, we applied BLISS to compare the specificity of CRISPR-associated RNA-guided endonucleases Cas9 and Cpf1, and found that Cpf1 has higher specificity than Cas9. These results establish BLISS as a versatile, sensitive, and efficient method for genome- wide DSB mapping in many applications.

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