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

Yan, W. X.; Mirzazadeh, R.; Garnerone, S.; Scott, D. A.; Schneider, M. W.; Kallas, T.; Custodio, J.; Wernersson, E.; Gao, L.; Li, Y.; Federova, Y.; Zetsche, B.; Zhang, F.; Bienko, M.; Crosetto, N.

doi:10.1101/091629

bioRxiv · 10.1101/091629

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

Yan, W. X.·Mirzazadeh, R.·Garnerone, S.·Scott, D. A.·Schneider, M. W.·Kallas, T.·Custodio, J.·Wernersson, E.·Gao, L.·Li, Y.·Federova, Y.·Zetsche, B.·Zhang, F.·Bienko, M.·Crosetto, N.

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Abstract

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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Yan, W. X., Mirzazadeh, R., Garnerone, S., Scott, D. A., Schneider, M. W., Kallas, T., Custodio, J., Wernersson, E., Gao, L., Li, Y., Federova, Y., Zetsche, B., Zhang, F., Bienko, M., Crosetto, N.. 2016-12-04. BLISS: quantitative and versatile genome-wide profiling of DNA breaks in situ. https://doi.org/10.1101/091629

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