Genome-wide detection of DNA double-strand breaks by in-suspension BLISS

[1]  Robert Gentleman,et al.  rtracklayer: an R package for interfacing with genome browsers , 2009, Bioinform..

[2]  Britta A. M. Bouwman,et al.  Release of paused RNA polymerase II at specific loci favors DNA double-strand-break formation and promotes cancer translocations , 2019, Nature Genetics.

[3]  Martin J. Aryee,et al.  High levels of AAV vector integration into CRISPR-induced DNA breaks , 2019, Nature Communications.

[4]  M. Skrzypczak,et al.  Comprehensive Mapping of Histone Modifications at DNA Double-Strand Breaks Deciphers Repair Pathway Chromatin Signatures , 2018, Molecular cell.

[5]  M. Rowicka,et al.  Nucleotide-resolution DNA double-strand breaks mapping by next-generation sequencing , 2013, Nature Methods.

[6]  Roland Eils,et al.  Complex heatmaps reveal patterns and correlations in multidimensional genomic data , 2016, Bioinform..

[7]  Takashi Yamamoto,et al.  Acceleration of cancer science with genome editing and related technologies , 2018, Cancer science.

[8]  Sabina Sánchez-Hernández,et al.  Biased and Unbiased Methods for the Detection of Off-Target Cleavage by CRISPR/Cas9: An Overview , 2016, International journal of molecular sciences.

[9]  Roland Eils,et al.  circlize implements and enhances circular visualization in R , 2014, Bioinform..

[10]  J. Joung,et al.  CIRCLE-seq: a highly sensitive in vitro screen for genome-wide CRISPR-Cas9 nuclease off-targets , 2017, Nature Methods.

[11]  Britta A. M. Bouwman,et al.  Genome-Wide CRISPR Off-Target DNA Break Detection by the BLISS Method. , 2021, Methods in molecular biology.

[12]  S. Itzkovitz,et al.  Spatial Reconstruction of Single Enterocytes Uncovers Broad Zonation along the Intestinal Villus Axis , 2018, Cell.

[13]  Erik L. G. Wernersson,et al.  BLISS is a versatile and quantitative method for genome-wide profiling of DNA double-strand breaks , 2017, Nature Communications.

[14]  I. Amit,et al.  Comprehensive mapping of long range interactions reveals folding principles of the human genome , 2011 .

[15]  F. Alt,et al.  The role of DNA breaks in genomic instability and tumorigenesis , 2003, Immunological reviews.

[16]  A. Suresh,et al.  Optimal prediction of the number of unseen species , 2016, Proceedings of the National Academy of Sciences.

[17]  Xiaoling Wang,et al.  Unbiased detection of off-target cleavage by CRISPR-Cas9 and TALENs using integrase-defective lentiviral vectors , 2015, Nature Biotechnology.

[18]  Stefano Monti,et al.  Genome-wide Translocation Sequencing Reveals Mechanisms of Chromosome Breaks and Rearrangements in B Cells , 2011, Cell.

[19]  Hanhui Ma,et al.  STRIDE—a fluorescence method for direct, specific in situ detection of individual single- or double-strand DNA breaks in fixed cells , 2019, Nucleic acids research.

[20]  T. Pandita,et al.  Ssb1 and Ssb2 cooperate to regulate mouse hematopoietic stem and progenitor cells by resolving replicative stress. , 2017, Blood.

[21]  S. Balasubramanian,et al.  DSBCapture: in situ capture and direct sequencing of dsDNA breaks , 2016, Nature Methods.

[22]  Tom Misteli,et al.  The biogenesis of chromosome translocations , 2014, Nature Cell Biology.

[23]  Leslie S. Edwards,et al.  Mapping the genomic landscape of CRISPR–Cas9 cleavage , 2017, Nature Methods.

[24]  Michel C. Nussenzweig,et al.  Translocation-Capture Sequencing Reveals the Extent and Nature of Chromosomal Rearrangements in B Lymphocytes , 2011, Cell.

[25]  G. Weinstock,et al.  HCoDES reveals chromosomal DNA end structures with single-nucleotide resolution. , 2014, Molecular cell.

[26]  Aaron R. Quinlan,et al.  BIOINFORMATICS APPLICATIONS NOTE , 2022 .

[27]  R. Wellinger,et al.  Genome-Wide Mapping of DNA Strand Breaks , 2011, PloS one.

[28]  G. Boissonneault,et al.  Quantification and genome-wide mapping of DNA double-strand breaks. , 2016, DNA repair.

[29]  J. Joung,et al.  Defining and improving the genome-wide specificities of CRISPR–Cas9 nucleases , 2016, Nature Reviews Genetics.

[30]  A. Nussenzweig,et al.  DNA Breaks and End Resection Measured Genome-wide by End Sequencing. , 2016, Molecular cell.

[31]  Nguyen Ngoc Hoa,et al.  Mre11 Is Essential for the Removal of Lethal Topoisomerase 2 Covalent Cleavage Complexes. , 2016, Molecular cell.

[32]  B. Haarer,et al.  Break-seq reveals hydroxyurea-induced chromosome fragility as a result of unscheduled conflict between DNA replication and transcription , 2015, Genome research.

[33]  A. Kudlicki,et al.  i-BLESS is an ultra-sensitive method for detection of DNA double-strand breaks , 2018, Communications Biology.

[34]  J. Schug,et al.  Genome-wide Identification of Structure-Forming Repeats as Principal Sites of Fork Collapse upon ATR Inhibition. , 2018, Molecular cell.

[35]  M. J. Neale,et al.  A nucleotide resolution map of Top2-linked DNA breaks in the yeast and human genome , 2019, Nature Communications.

[36]  Daesik Kim,et al.  DIG-seq: a genome-wide CRISPR off-target profiling method using chromatin DNA , 2018, Genome research.

[37]  Martin J. Aryee,et al.  GUIDE-Seq enables genome-wide profiling of off-target cleavage by CRISPR-Cas nucleases , 2014, Nature Biotechnology.

[38]  Kairong Cui,et al.  Mapping DNA Breaks by Next-Generation Sequencing. , 2018, Methods in molecular biology.

[39]  K. Szlachta,et al.  CNCC: an analysis tool to determine genome-wide DNA break end structure at single-nucleotide resolution , 2020, BMC genomics.

[40]  Britta A. M. Bouwman,et al.  Endogenous DNA Double-Strand Breaks during DNA Transactions: Emerging Insights and Methods for Genome-Wide Profiling , 2018, Genes.

[41]  Richard Durbin,et al.  Fast and accurate long-read alignment with Burrows–Wheeler transform , 2010, Bioinform..

[42]  A. Nussenzweig,et al.  Endogenous DNA Damage as a Source of Genomic Instability in Cancer , 2017, Cell.

[43]  Britta A. M. Bouwman,et al.  Modeling double strand break susceptibility to interrogate structural variation in cancer , 2019, Genome Biology.

[44]  Lili Wang,et al.  Correction to: ITR-Seq, a next-generation sequencing assay, identifies genome-wide DNA editing sites in vivo following adeno-associated viral vector-mediated genome editing , 2020, BMC Genomics.

[45]  Feng Zhang,et al.  Engineered Cpf1 variants with altered PAM specificities increase genome targeting range , 2017, Nature Biotechnology.

[46]  Piero Carninci,et al.  A damaged genome’s transcriptional landscape through multilayered expression profiling around in situ-mapped DNA double-strand breaks , 2017, Nature Communications.

[47]  Gonçalo R. Abecasis,et al.  The Sequence Alignment/Map format and SAMtools , 2009, Bioinform..

[48]  Richard Durbin,et al.  Sequence analysis Fast and accurate short read alignment with Burrows – Wheeler transform , 2009 .

[49]  Britta A. M. Bouwman,et al.  Colibactin DNA-damage signature indicates mutational impact in colorectal cancer , 2020, Nature Medicine.

[50]  Yves Pommier,et al.  Topoisomerase II-Induced Chromosome Breakage and Translocation Is Determined by Chromosome Architecture and Transcriptional Activity. , 2019, Molecular cell.

[51]  N. Crosetto,et al.  Genome-Wide Profiling of DNA Double-Strand Breaks by the BLESS and BLISS Methods. , 2018, Methods in molecular biology.

[52]  Gabriela Figueroa-González,et al.  Strategies for the evaluation of DNA damage and repair mechanisms in cancer , 2017, Oncology letters.

[53]  P. Mangeot,et al.  A cohesin/HUSH- and LINC-dependent pathway controls ribosomal DNA double-strand break repair , 2019, Genes & development.

[54]  R. Irizarry ggplot2 , 2019, Introduction to Data Science.

[55]  Richard L. Frock,et al.  Genome-wide detection of DNA double-stranded breaks induced by engineered nucleases , 2014, Nature Biotechnology.

[56]  Job Dekker,et al.  Hi-C 2.0: An optimized Hi-C procedure for high-resolution genome-wide mapping of chromosome conformation. , 2017, Methods.

[57]  Jong-il Kim,et al.  Digenome-seq: genome-wide profiling of CRISPR-Cas9 off-target effects in human cells , 2015, Nature Methods.

[58]  Teresa M. Przytycka,et al.  DNA Break Mapping Reveals Topoisomerase II Activity Genome-Wide , 2014, International journal of molecular sciences.

[59]  E. Lander,et al.  Development and Applications of CRISPR-Cas9 for Genome Engineering , 2014, Cell.

[60]  R. Overbeek,et al.  Searching for patterns in genomic data. , 1997, Trends in genetics : TIG.

[61]  E. Birney,et al.  Mapping identifiers for the integration of genomic datasets with the R/Bioconductor package biomaRt , 2009, Nature Protocols.

[62]  M. Skrzypczak,et al.  qDSB-Seq is a general method for genome-wide quantification of DNA double-strand breaks using sequencing , 2019, Nature Communications.

[63]  E. Soutoglou,et al.  Finding DNA Ends within a Haystack of Chromatin. , 2016, Molecular cell.

[64]  K. Caldecott,et al.  DNA strand break repair and human genetic disease. , 2007, Annual review of genomics and human genetics.

[65]  Britta A. M. Bouwman,et al.  Spatial Chromosome Folding and Active Transcription Drive DNA Fragility and Formation of Oncogenic MLL Translocations. , 2019, Molecular cell.

[66]  Robert Gentleman,et al.  Software for Computing and Annotating Genomic Ranges , 2013, PLoS Comput. Biol..

[67]  Jeffrey C. Miller,et al.  An unbiased genome-wide analysis of zinc-finger nuclease specificity , 2011, Nature Biotechnology.

[68]  J. Hoeijmakers,et al.  Chromosomal stability and the DNA double-stranded break connection , 2001, Nature Reviews Genetics.

[69]  D. S. Pederson,et al.  Mechanisms and Consequences of Double‐Strand DNA Break Formation in Chromatin , 2016, Journal of cellular physiology.