TY - JOUR T1 - BLISS: quantitative and versatile genome-wide profiling of DNA breaks <em>in situ</em> JF - bioRxiv DO - 10.1101/091629 SP - 091629 AU - Winston X. Yan AU - Reza Mirzazadeh AU - Silvano Garnerone AU - David Scott AU - Martin W. Schneider AU - Tomasz Kallas AU - Joaquin Custodio AU - Erik Wernersson AU - Linyi Gao AU - Yinqing Li AU - Yana Federova AU - Bernd Zetsche AU - Feng Zhang AU - Magda Bienko AU - Nicola Crosetto Y1 - 2016/01/01 UR - http://biorxiv.org/content/early/2016/12/04/091629.abstract N2 - 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. ER -