Chromatin context-dependent regulation and epigenetic manipulation of prime editing

[1]  B. van Steensel,et al.  Predicting prime editing efficiency across diverse edit types and chromatin contexts with machine learning , 2023, bioRxiv.

[2]  Jordan L. Doman,et al.  Phage-assisted evolution and protein engineering yield compact, efficient prime editors , 2023, Cell.

[3]  H. Kim,et al.  Prediction of efficiencies for diverse prime editing systems in multiple cell types , 2023, Cell.

[4]  Stephan J Sanders,et al.  Multiplex, single-cell CRISPRa screening for cell type specific regulatory elements , 2023, bioRxiv.

[5]  Elin Madli Peets,et al.  Prediction of prime editing insertion efficiencies using sequence features and DNA repair determinants , 2023, Nature Biotechnology.

[6]  M. Krauthammer,et al.  Predicting prime editing efficiency and product purity by deep learning , 2022, Nature Biotechnology.

[7]  David R. Liu,et al.  Prime editing for precise and highly versatile genome manipulation , 2022, Nature Reviews Genetics.

[8]  Brian J. Beliveau,et al.  Optimized single-nucleus transcriptional profiling by combinatorial indexing , 2022, Nature Protocols.

[9]  R. Medema,et al.  Widespread chromatin context-dependencies of DNA double-strand break repair proteins , 2022, bioRxiv.

[10]  Guangchuang Yu,et al.  Exploring Epigenomic Datasets by ChIPseeker , 2022, Current protocols.

[11]  Isaac B. Hilton,et al.  Quantification of Genome Editing and Transcriptional Control Capabilities Reveals Hierarchies among Diverse CRISPR/Cas Systems in Human Cells , 2022, ACS synthetic biology.

[12]  Beth K. Martin,et al.  A time-resolved, multi-symbol molecular recorder via sequential genome editing , 2022, Nature.

[13]  S. Gasser,et al.  Establishment of H3K9-methylated heterochromatin and its functions in tissue differentiation and maintenance , 2022, Nature Reviews Molecular Cell Biology.

[14]  Francisco J. Sánchez-Rivera,et al.  Genome-wide CRISPR guide RNA design and specificity analysis with GuideScan2 , 2022, bioRxiv.

[15]  Tomás C. Rodríguez,et al.  A split prime editor with untethered reverse transcriptase and circular RNA template , 2022, Nature Biotechnology.

[16]  David R. Liu,et al.  Programmable deletion, replacement, integration, and inversion of large DNA sequences with twin prime editing , 2021, Nature Biotechnology.

[17]  Paul Theodor Pyl,et al.  Analysing high-throughput sequencing data in Python with HTSeq 2.0 , 2021, Bioinform..

[18]  T. B. Loveless,et al.  Open-ended molecular recording of sequential cellular events into DNA , 2021, bioRxiv.

[19]  Beth K. Martin,et al.  Multiplex genomic recording of enhancer and signal transduction activity in mammalian cells , 2021, bioRxiv.

[20]  Z. Weng,et al.  Deletion and replacement of long genomic sequences using prime editing , 2021, Nature Biotechnology.

[21]  David R. Liu,et al.  Enhanced prime editing systems by manipulating cellular determinants of editing outcomes , 2021, Cell.

[22]  J. Loizou,et al.  Prime editing efficiency and fidelity are enhanced in the absence of mismatch repair , 2021, bioRxiv.

[23]  Chang Sik Cho,et al.  Application of prime editing to the correction of mutations and phenotypes in adult mice with liver and eye diseases , 2021, Nature Biomedical Engineering.

[24]  Simon P. Shen,et al.  Engineered pegRNAs improve prime editing efficiency , 2021, Nature Biotechnology.

[25]  Jeffrey A. Hussmann,et al.  Mapping the genetic landscape of DNA double-strand break repair , 2021, Cell.

[26]  L. Pelletier,et al.  Saturation variant interpretation using CRISPR prime editing , 2021, Nature Biotechnology.

[27]  Howard Y. Chang,et al.  Genome-wide programmable transcriptional memory by CRISPR-based epigenome editing , 2021, Cell.

[28]  Beth K. Martin,et al.  Precise genomic deletions using paired prime editing , 2021, Nature Biotechnology.

[29]  Thomas M. Keane,et al.  Twelve years of SAMtools and BCFtools , 2020, GigaScience.

[30]  Raphael Gottardo,et al.  Integrated analysis of multimodal single-cell data , 2020, Cell.

[31]  Sungroh Yoon,et al.  Predicting the efficiency of prime editing guide RNAs in human cells , 2020, Nature Biotechnology.

[32]  Michael J. Purcaro,et al.  Expanded encyclopaedias of DNA elements in the human and mouse genomes , 2020, Nature.

[33]  Sayed Hadi Hashemi,et al.  Genome-wide CRISPRi/a screens in human neurons link lysosomal failure to ferroptosis , 2020, Nature Neuroscience.

[34]  R. Medema,et al.  Impact of chromatin context on Cas9-induced DNA double-strand break repair pathway balance , 2020, bioRxiv.

[35]  William Stafford Noble,et al.  High-Throughput Single-Cell Sequencing with Linear Amplification. , 2019, Molecular cell.

[36]  Mark W. Budde,et al.  In situ readout of DNA barcodes and single base edits facilitated by in vitro transcription , 2019, Nature Biotechnology.

[37]  David R. Liu,et al.  Search-and-replace genome editing without double-strand breaks or donor DNA , 2019, Nature.

[38]  Marco Y. Hein,et al.  Compromised function of the ESCRT pathway promotes endolysosomal escape of tau seeds and propagation of tau aggregation , 2019, The Journal of Biological Chemistry.

[39]  Joana P. Gonçalves,et al.  Multiplexed Cas9 targeting reveals genomic location effects and gRNA-based staggered breaks influencing mutation efficiency , 2019, Nature Communications.

[40]  M. Gonçalves,et al.  The Chromatin Structure of CRISPR-Cas9 Target DNA Controls the Balance between Mutagenic and Homology-Directed Gene-Editing Events , 2019, Molecular therapy. Nucleic acids.

[41]  Dana Carroll,et al.  Nucleosomes inhibit target cleavage by CRISPR-Cas9 in vivo , 2018, Proceedings of the National Academy of Sciences.

[42]  Waseem Akhtar,et al.  Kinetics and Fidelity of the Repair of Cas9-Induced Double-Strand DNA Breaks , 2018, Molecular cell.

[43]  Ji-Young Kim,et al.  KDM2B is a histone H3K79 demethylase and induces transcriptional repression via sirtuin‐1‐mediated chromatin silencing , 2018, FASEB journal : official publication of the Federation of American Societies for Experimental Biology.

[44]  A. Ribas,et al.  Selective targeting of engineered T cells using orthogonal IL-2 cytokine-receptor complexes , 2018, Science.

[45]  A. McKenna,et al.  FlashFry: a fast and flexible tool for large-scale CRISPR target design , 2017, BMC Biology.

[46]  David A. Brafman,et al.  The Impact of Chromatin Dynamics on Cas9-Mediated Genome Editing in Human Cells. , 2017, ACS synthetic biology.

[47]  Geet Duggal,et al.  Salmon: fast and bias-aware quantification of transcript expression using dual-phase inference , 2017, Nature Methods.

[48]  Gunnar Rätsch,et al.  Prediction of ultra-potent shRNAs with a sequential classification algorithm , 2017, Nature Biotechnology.

[49]  André F. Rendeiro,et al.  Pooled CRISPR screening with single-cell transcriptome read-out , 2017, Nature Methods.

[50]  Thomas M. Norman,et al.  A Multiplexed Single-Cell CRISPR Screening Platform Enables Systematic Dissection of the Unfolded Protein Response , 2016, Cell.

[51]  Thomas M. Norman,et al.  Perturb-Seq: Dissecting Molecular Circuits with Scalable Single-Cell RNA Profiling of Pooled Genetic Screens , 2016, Cell.

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

[53]  W. Lim,et al.  Nucleosome breathing and remodeling constrain CRISPR-Cas9 function , 2016, eLife.

[54]  J. Michael Cherry,et al.  ENCODE data at the ENCODE portal , 2015, Nucleic Acids Res..

[55]  Qing-Yu He,et al.  ChIPseeker: an R/Bioconductor package for ChIP peak annotation, comparison and visualization , 2015, Bioinform..

[56]  Aleksandra Markovets,et al.  Acquired EGFR C797S mediates resistance to AZD9291 in advanced non-small cell lung cancer harboring EGFR T790M , 2015, Nature Medicine.

[57]  Kristian Vlahovicek,et al.  Genomation: a Toolkit to Summarize, Annotate and Visualize Genomic Intervals , 2015, Bioinform..

[58]  Michael Q. Zhang,et al.  Integrative analysis of 111 reference human epigenomes , 2015, Nature.

[59]  Alexandro E. Trevino,et al.  Genome-scale transcriptional activation by an engineered CRISPR-Cas9 complex , 2014, Nature.

[60]  W. Huber,et al.  Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2 , 2014, Genome Biology.

[61]  Joana A. Vidigal,et al.  In vivo engineering of oncogenic chromosomal rearrangements with the CRISPR/Cas9 system , 2014, Nature.

[62]  Neville E. Sanjana,et al.  Improved vectors and genome-wide libraries for CRISPR screening , 2014, Nature Methods.

[63]  J. Zuber,et al.  An optimized microRNA backbone for effective single-copy RNAi. , 2013, Cell reports.

[64]  David A. Scott,et al.  Genome engineering using the CRISPR-Cas9 system , 2013, Nature Protocols.

[65]  E. Olhava,et al.  Potent inhibition of DOT1L as treatment of MLL-fusion leukemia. , 2013, Blood.

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

[67]  Wei Shi,et al.  featureCounts: an efficient general purpose program for assigning sequence reads to genomic features , 2013, Bioinform..

[68]  A. D’Andrea,et al.  Chromatin Remodeling at DNA Double-Strand Breaks , 2013, Cell.

[69]  Richard S. Sandstrom,et al.  BEDOPS: high-performance genomic feature operations , 2012, Bioinform..

[70]  Raymond K. Auerbach,et al.  An Integrated Encyclopedia of DNA Elements in the Human Genome , 2012, Nature.

[71]  Marcel Martin Cutadapt removes adapter sequences from high-throughput sequencing reads , 2011 .

[72]  Jia-Ren Lin,et al.  SHPRH and HLTF act in a damage-specific manner to coordinate different forms of postreplication repair and prevent mutagenesis. , 2011, Molecular cell.

[73]  Lan Huang,et al.  Quantitative Profiling of In Vivo-assembled RNA-Protein Complexes Using a Novel Integrated Proteomic Approach* , 2011, Molecular & Cellular Proteomics.

[74]  A. Bradley,et al.  A hyperactive piggyBac transposase for mammalian applications , 2011, Proceedings of the National Academy of Sciences.

[75]  Helga Thorvaldsdóttir,et al.  Integrative Genomics Viewer , 2011, Nature Biotechnology.

[76]  C. Glass,et al.  Simple combinations of lineage-determining transcription factors prime cis-regulatory elements required for macrophage and B cell identities. , 2010, Molecular cell.

[77]  L. Luo,et al.  Splinkerette PCR for Mapping Transposable Elements in Drosophila , 2010, PloS one.

[78]  Heng Li,et al.  BIOINFORMATICS ORIGINAL PAPER , 2022 .

[79]  Michael W. Davidson,et al.  Photoconversion in orange and red fluorescent proteins , 2009, Nature Methods.

[80]  J. Hurwitz,et al.  Human HLTF functions as a ubiquitin ligase for proliferating cell nuclear antigen polyubiquitination , 2008, Proceedings of the National Academy of Sciences.

[81]  M. Lazar,et al.  DOT1L/KMT4 Recruitment and H3K79 Methylation Are Ubiquitously Coupled with Gene Transcription in Mammalian Cells , 2008, Molecular and Cellular Biology.

[82]  Won-Tak Choi,et al.  Distinct Functional Sites for Human Immunodeficiency Virus Type 1 and Stromal Cell-Derived Factor 1α on CXCR4 Transmembrane Helical Domains , 2005, Journal of Virology.

[83]  Min Han,et al.  Efficient Transposition of the piggyBac (PB) Transposon in Mammalian Cells and Mice , 2005, Cell.

[84]  T. Kunkel,et al.  DNA mismatch repair. , 2005, Annual review of biochemistry.

[85]  Yi Zhang,et al.  hDOT1L Links Histone Methylation to Leukemogenesis , 2005, Cell.

[86]  G. Crooks,et al.  WebLogo: a sequence logo generator. , 2004, Genome research.

[87]  J. Martens,et al.  Partitioning and plasticity of repressive histone methylation states in mammalian chromatin. , 2003, Molecular cell.

[88]  Hengbin Wang,et al.  Role of Histone H3 Lysine 27 Methylation in X Inactivation , 2003, Science.

[89]  C. von Kalle,et al.  Polyclonal long-term repopulating stem cell clones in a primate model. , 2002, Blood.

[90]  Kevin Struhl,et al.  Methylation of H3-Lysine 79 Is Mediated by a New Family of HMTases without a SET Domain , 2002, Current Biology.

[91]  J B Lawrence,et al.  Molecular cloning and functional analysis of the adenovirus E1A-associated 300-kD protein (p300) reveals a protein with properties of a transcriptional adaptor. , 1994, Genes & development.

[92]  D. Hartl,et al.  Genetic applications of an inverse polymerase chain reaction. , 1988, Genetics.

[93]  J. Kruskal An Overview of Sequence Comparison: Time Warps, String Edits, and Macromolecules , 1983 .

[94]  S. B. Needleman,et al.  A general method applicable to the search for similarities in the amino acid sequence of two proteins. , 1970, Journal of molecular biology.

[95]  Florian Hahne,et al.  Visualizing Genomic Data Using Gviz and Bioconductor , 2016, Statistical Genomics.

[96]  Thomas R. Gingeras,et al.  STAR: ultrafast universal RNA-seq aligner , 2013, Bioinform..

[97]  Alfred L George,et al.  PiggyBac transposon-mediated gene transfer in human cells. , 2007, Molecular therapy : the journal of the American Society of Gene Therapy.