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

Nature Communications
Winston X YanNicola Crosetto

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.

References

Mar 1, 1990·Proceedings of the National Academy of Sciences of the United States of America·R N Van GelderJ H Eberwine
Feb 9, 2010·Nature Structural & Molecular Biology·Rachel K SzilardDaniel Durocher
Feb 24, 2010·Nature Reviews. Molecular Cell Biology·Simona NegriniThanos D Halazonetis
Aug 23, 2011·Annual Review of Genetics·David G Schatz, Patrick C Swanson
Nov 22, 2011·Nature Methods·Teemu KiviojaJussi Taipale
Sep 4, 2012·Cell Reports·Tamar HashimshonyItai Yanai
Jul 23, 2013·Nature Biotechnology·Patrick D HsuFeng Zhang
Oct 19, 2013·Nature Reviews. Genetics·Frédéric BaudatBernard de Massy
Dec 17, 2014·Nature Biotechnology·Richard L FrockFrederick W Alt
Dec 17, 2014·Nature Biotechnology·Shengdar Q TsaiJ Keith Joung
Feb 24, 2015·Mutation Research. Fundamental and Molecular Mechanisms of Mutagenesis·Fan YangSteven Henikoff
Apr 2, 2015·Nature·F Ann RanFeng Zhang
Dec 3, 2015·Science·Ian M SlaymakerFeng Zhang
Feb 14, 2016·Proceedings of the National Academy of Sciences of the United States of America·Bjoern SchwerFrederick W Alt
Jun 9, 2016·Nature Biotechnology·Daesik KimJin-Soo Kim
Jun 28, 2016·Nature Biotechnology·Benjamin P KleinstiverJ Keith Joung
Aug 2, 2016·Molecular Cell·Andres CanelaAndré Nussenzweig
Aug 16, 2016·Nature Methods·Stefanie V LensingShankar Balasubramanian

❮ Previous
Next ❯

Citations

Mar 20, 2018·Nature Biotechnology·Xiaosa LiJia Chen
Sep 5, 2017·International Journal of Environmental Research and Public Health·Vanessa M MaciasJason L Rasgon
Aug 2, 2018·Chemical Record : an Official Publication of the Chemical Society of Japan ... [et Al.]·Wataru Nomura
Jul 8, 2018·Applied and Environmental Microbiology·Lei LiYinhua Lu
Sep 2, 2018·Medicinal Research Reviews·Wenyi WuHetian Lei
Nov 6, 2018·Genes, Chromosomes & Cancer·Elisa Palumbo, Antonella Russo
Aug 2, 2017·Nature Medicine·David A Scott, Feng Zhang
Apr 24, 2019·Journal of Neuroimmune Pharmacology : the Official Journal of the Society on NeuroImmune Pharmacology·Sudhanshu P RaikwarAsgar Zaheer
Nov 12, 2019·Briefings in Functional Genomics·Elena Herrera-CarrilloBen Berkhout
Sep 22, 2017·Neurology·Nicolas N MadiganEduardo E Benarroch
Feb 23, 2020·Environmental and Molecular Mutagenesis·Wentao Li, Aziz Sancar
Jun 6, 2020·Nucleic Acids Research·Karol SzlachtaYuh-Hwa Wang
Jun 9, 2020·Clinical and Translational Medicine·Nannan ZhengXiangdong Wang
Aug 25, 2020·The CRISPR Journal·Lavina Sierra TayPrashant Mali
Sep 18, 2020·Nucleic Acids Research·Do Yon KimDaesik Kim
Feb 10, 2019·Genome Biology·Tracy J BallingerColin A Semple
Jan 10, 2019·Nature Communications·Puping LiangZhou Songyang
Mar 1, 2020·Nucleic Acids Research·Kelly M HarkinsRichard E Green
Mar 22, 2020·Nucleic Acids Research·Francesca GoriniStefano Amente
May 15, 2020·TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik·Sukumar BiswasJianxin Shi
Jun 26, 2020·Radiation and Environmental Biophysics·Britta LangenEva Forssell-Aronsson
Jul 1, 2020·Advanced Science·Xiaofeng DaiKostya Ken Ostrikov
May 8, 2020·Physiology and Molecular Biology of Plants : an International Journal of Functional Plant Biology·Banashree SaikiaChannakeshavaiah Chikkaputtaiah
Sep 2, 2017·Annual Review of Genomics and Human Genetics·Valerio VitelliFabrizio d'Adda di Fagagna
Apr 17, 2019·Nature Biotechnology·D Dewran KocakCharles A Gersbach
Dec 7, 2018·Genome Biology·Nadia AmraniErik J Sontheimer
Jun 22, 2019·The CRISPR Journal·Nicholas C HustonBarrett E Steinberg
May 12, 2020·Molecular & Cellular Oncology·Sara Oster, Rami I Aqeilan
Dec 13, 2017·Proceedings of the National Academy of Sciences of the United States of America·Samuel LessardMatthew C Canver
Oct 21, 2018·Nature Protocols·Cicera R LazzarottoShengdar Q Tsai
Nov 6, 2018·Communications Biology·Anna BiernackaKrzysztof Ginalski
Jan 24, 2019·Brain Sciences·Carolyn M Yrigollen, Beverly L Davidson

❮ Previous
Next ❯

Datasets Mentioned

BETA
SRP099132

Methods Mentioned

BETA
immunoprecipitation
PCR
BLISS
Illumina sequencing
BLESS
biopsies
GUIDEseq
transfection
transfections
in vitro transcription

Software Mentioned

MATLAB
Biopython Python package
GUIDEseq
Cpf1
OFFinder
BLISS
Cas
Gorilla
Elements
BLESS

Related Concepts

Related Feeds

CRISPR Ribonucleases Deactivation

CRISPR-Cas system enables the editing of genes to create or correct mutations. This feed focuses on mechanisms that underlie deactivation of CRISPR ribonucleases. Here is the latest research.

CRISPR (general)

Clustered regularly interspaced short palindromic repeats (CRISPR) are DNA sequences in the genome that are recognized and cleaved by CRISPR-associated proteins (Cas). CRISPR-Cas system enables the editing of genes to create or correct mutations. Discover the latest research on CRISPR here.

CRISPR for Genome Editing

Genome editing technologies enable the editing of genes to create or correct mutations. Clustered regularly interspaced short palindromic repeats (CRISPR) are DNA sequences in the genome that are recognized and cleaved by CRISPR-associated proteins (Cas). Here is the latest research on the use of CRISPR-Cas system in gene editing.