An efficient CRISPR–Cas12a promoter editing system for crop improvement

[1]  Zhe Zhang,et al.  Loss‐function mutants of OsCKX gene family based on CRISPR‐Cas systems revealed their diversified roles in rice , 2023, The plant genome.

[2]  Yiping Qi,et al.  Hypercompact CRISPR–Cas12j2 (CasΦ) enables genome editing, gene activation, and epigenome editing in plants , 2022, Plant communications.

[3]  Yonghong Wang,et al.  Targeting a gene regulatory element enhances rice grain yield by decoupling panicle number and size , 2022, Nature Biotechnology.

[4]  I. Mila,et al.  The auxin-responsive transcription factor SlDOF9 regulates inflorescence and flower development in tomato , 2022, Nature Plants.

[5]  Yiping Qi,et al.  Genome‐wide analyses of PAM‐relaxed Cas9 genome editors reveal substantial off‐target effects by ABE8e in rice , 2022, bioRxiv.

[6]  Guoliang Li,et al.  The landscape of promoter-centred RNA–DNA interactions in rice , 2022, Nature Plants.

[7]  W. Greenleaf,et al.  NEAT-seq: simultaneous profiling of intra-nuclear proteins, chromatin accessibility and gene expression in single cells , 2021, Nature Methods.

[8]  Tao Zhang,et al.  CRISPR‐BETS: a base‐editing design tool for generating stop codons , 2021, Plant biotechnology journal.

[9]  Q. Qian,et al.  CRISPR‐Cas9 mediated OsMIR168a knockout reveals its pleiotropy in rice , 2021, Plant biotechnology journal.

[10]  D. Downes,et al.  A gain-of-function single nucleotide variant creates a new promoter which acts as an orientation-dependent enhancer-blocker , 2021, Nature Communications.

[11]  Peter J. Bradbury,et al.  Conserved noncoding sequences provide insights into regulatory sequence and loss of gene expression in maize , 2021, Genome research.

[12]  Tao Zhang,et al.  Improved plant cytosine base editors with high editing activity, purity, and specificity , 2021, Plant biotechnology journal.

[13]  Z. Lippman,et al.  Dissecting cis-regulatory control of quantitative trait variation in a plant stem cell circuit , 2021, Nature Plants.

[14]  Stephen M. Mount,et al.  Expanding the scope of plant genome engineering with Cas12a orthologs and highly multiplexable editing systems , 2021, Nature Communications.

[15]  Jiming Jiang,et al.  Genomic Editing of Intronic Enhancers Unveils Their Role in Fine-Tuning Tissue-Specific Gene Expression in Arabidopsis thaliana. , 2021, The Plant cell.

[16]  Z. Lippman,et al.  Conserved pleiotropy of an ancient plant homeobox gene uncovered by cis-regulatory dissection , 2021, Cell.

[17]  Qingyu Wu,et al.  Enhancing grain-yield-related traits by CRISPR–Cas9 promoter editing of maize CLE genes , 2021, Nature Plants.

[18]  Q. Qian,et al.  Efficient deletion of multiple circle RNA loci by CRISPR‐Cas9 reveals Os06circ02797 as a putative sponge for OsMIR408 in rice , 2021, Plant biotechnology journal.

[19]  Yiping Qi,et al.  PAM-less plant genome editing using a CRISPR–SpRY toolbox , 2021, Nature Plants.

[20]  N. Sreenivasulu,et al.  Waxy Editing: Old Meets New. , 2020, Trends in plant science.

[21]  Masatomo Kobayashi,et al.  Antagonistic regulation of the gibberellic acid response during stem growth in rice , 2020, Nature.

[22]  Xingliang Ma,et al.  Quantitative regulation of Waxy expression by CRISPR/Cas9‐based promoter and 5'UTR‐intron editing improves grain quality in rice , 2020, Plant biotechnology journal.

[23]  Qiaoquan Liu,et al.  Creating novel Wx alleles with fine‐tuned amylose levels and improved grain quality in rice by promoter editing using CRISPR/Cas9 system , 2020, Plant biotechnology journal.

[24]  Qiuxiang Pang,et al.  Deacetylase-independent function of SIRT6 couples GATA4 transcription factor and epigenetic activation against cardiomyocyte apoptosis , 2020, Nucleic acids research.

[25]  Q. Qian,et al.  A strigolactones biosynthesis gene contributed to the Green Revolution in rice. , 2020, Molecular plant.

[26]  Wenli Zhang,et al.  MH-seq for Functional Characterization of Open Chromatin in Plants. , 2020, Trends in plant science.

[27]  Q. Qian,et al.  Production of novel beneficial alleles of a rice yield‐related QTL by CRISPR/Cas9 , 2020, Plant biotechnology journal.

[28]  Yiping Qi,et al.  Intron-Based Single Transcript Unit CRISPR Systems for Plant Genome Editing , 2020, Rice.

[29]  Jiming Jiang,et al.  Genome-wide MNase hypersensitivity assay unveils distinct classes of open chromatin associated with H3K27me3 and DNA methylation in Arabidopsis thaliana , 2020, Genome Biology.

[30]  Jinpu Jin,et al.  PlantRegMap: charting functional regulatory maps in plants , 2019, Nucleic Acids Res..

[31]  Phillip A. Richmond,et al.  JASPAR 2020: update of the open-access database of transcription factor binding profiles , 2019, Nucleic Acids Res..

[32]  Xiuxiu Li,et al.  MBKbase for rice: an integrated omics knowledgebase for molecular breeding in rice , 2019, Nucleic Acids Res..

[33]  V. Fellman,et al.  A sensitive assay for dNTPs based on long synthetic oligonucleotides, EvaGreen dye and inhibitor-resistant high-fidelity DNA polymerase , 2019, bioRxiv.

[34]  Daniel L. Vera,et al.  The regulatory landscape of early maize inflorescence development , 2019, bioRxiv.

[35]  Robert J. Schmitz,et al.  The prevalence, evolution and chromatin signatures of plant regulatory elements , 2019, Nature Plants.

[36]  B. Ren,et al.  An ultra high-throughput method for single-cell joint analysis of open chromatin and transcriptome , 2019, Nature Structural & Molecular Biology.

[37]  A. Sandelin,et al.  Determinants of enhancer and promoter activities of regulatory elements , 2019, Nature Reviews Genetics.

[38]  Linda V. Bakker,et al.  An improved de novo assembly and annotation of the tomato reference genome using single-molecule sequencing, Hi-C proximity ligation and optical maps , 2019, bioRxiv.

[39]  Zachary B. Lippman,et al.  Revolutions in agriculture chart a course for targeted breeding of old and new crops , 2019, Science.

[40]  Steven L Salzberg,et al.  Graph-based genome alignment and genotyping with HISAT2 and HISAT-genotype , 2019, Nature Biotechnology.

[41]  Geo Pertea,et al.  Transcriptome assembly from long-read RNA-seq alignments with StringTie2 , 2019, Genome Biology.

[42]  Tao Zhang,et al.  Improving Plant Genome Editing with High-Fidelity xCas9 and Non-canonical PAM-Targeting Cas9-NG. , 2019, Molecular plant.

[43]  M. Tester,et al.  Breeding crops to feed 10 billion , 2019, Nature Biotechnology.

[44]  Jun S. Liu,et al.  Convergent regulatory evolution and loss of flight in paleognathous birds , 2019, Science.

[45]  Zheng Xuelian,et al.  Targeted Mutagenesis of NAC Transcription Factor Gene, OsNAC041, Leading to Salt Sensitivity in Rice , 2019, Rice Science.

[46]  Kan Wang,et al.  Application of CRISPR-Cas12a temperature sensitivity for improved genome editing in rice, maize, and Arabidopsis , 2019, BMC Biology.

[47]  Sandy L. Klemm,et al.  Chromatin accessibility and the regulatory epigenome , 2019, Nature Reviews Genetics.

[48]  Tao Zhang,et al.  Single transcript unit CRISPR 2.0 systems for robust Cas9 and Cas12a mediated plant genome editing , 2019, Plant biotechnology journal.

[49]  Sayed Abdul Akher,et al.  Multiplex QTL editing of grain-related genes improves yield in elite rice varieties , 2019, Plant Cell Reports.

[50]  Q. Qian,et al.  Xiaowei, a New Rice Germplasm for Large-Scale Indoor Research. , 2018, Molecular plant.

[51]  L. Tian,et al.  A large-scale whole-genome sequencing analysis reveals highly specific genome editing by both Cas9 and Cpf1 (Cas12a) nucleases in rice , 2018, Genome biology.

[52]  S. Mundlos,et al.  Structural variation in the 3D genome , 2018, Nature Reviews Genetics.

[53]  Tao Zhang,et al.  Plant Genome Editing Using FnCpf1 and LbCpf1 Nucleases at Redefined and Altered PAM Sites. , 2018, Molecular plant.

[54]  Yong Zhang,et al.  MIGS as a Simple and Efficient Method for Gene Silencing in Rice , 2018, Front. Plant Sci..

[55]  Peter J. Bradbury,et al.  Dysregulation of expression correlates with rare-allele burden and fitness loss in maize , 2018, Nature.

[56]  Zachary B. Lippman,et al.  Engineering Quantitative Trait Variation for Crop Improvement by Genome Editing , 2017, Cell.

[57]  Tao Zhang,et al.  CRISPR-Cas9 Based Genome Editing Reveals New Insights into MicroRNA Function and Regulation in Rice , 2017, Front. Plant Sci..

[58]  Jian‐Kang Zhu,et al.  Multiplex Gene Editing in Rice Using the CRISPR-Cpf1 System. , 2017, Molecular plant.

[59]  Tao Zhang,et al.  A CRISPR–Cpf1 system for efficient genome editing and transcriptional repression in plants , 2017, Nature Plants.

[60]  Kevin L. Schneider,et al.  Improved maize reference genome with single-molecule technologies , 2017, Nature.

[61]  E. M. DeGennaro,et al.  Multiplex gene editing by CRISPR-Cpf1 through autonomous processing of a single crRNA array , 2016, Nature Biotechnology.

[62]  Yunhai Li,et al.  SMALL GRAIN 11 Controls Grain Size, Grain Number and Grain Yield in Rice , 2016, Rice.

[63]  B. Deplancke,et al.  The Genetics of Transcription Factor DNA Binding Variation , 2016, Cell.

[64]  Yiping Qi,et al.  A Single Transcript CRISPR-Cas9 System for Efficient Genome Editing in Plants. , 2016, Molecular plant.

[65]  Fidel Ramírez,et al.  deepTools2: a next generation web server for deep-sequencing data analysis , 2016, Nucleic Acids Res..

[66]  Colin M. Diesh,et al.  JBrowse: a dynamic web platform for genome visualization and analysis , 2016, Genome Biology.

[67]  Dengwei Zhang,et al.  Effective screen of CRISPR/Cas9-induced mutants in rice by single-strand conformation polymorphism , 2016, Plant Cell Reports.

[68]  Tao Zhang,et al.  PlantDHS: a database for DNase I hypersensitive sites in plants , 2015, Nucleic Acids Res..

[69]  Zuofeng Zhu,et al.  CLUSTERED PRIMARY BRANCH 1, a new allele of DWARF11, controls panicle architecture and seed size in rice. , 2016, Plant biotechnology journal.

[70]  A. Regev,et al.  Cpf1 Is a Single RNA-Guided Endonuclease of a Class 2 CRISPR-Cas System , 2015, Cell.

[71]  J. Doudna,et al.  The new frontier of genome engineering with CRISPR-Cas9 , 2014, Science.

[72]  D. Schwartz,et al.  Improvement of the Oryza sativa Nipponbare reference genome using next generation sequence and optical map data , 2013, Rice.

[73]  Tao Zhang,et al.  Genome-Wide Identification of Regulatory DNA Elements and Protein-Binding Footprints Using Signatures of Open Chromatin in Arabidopsis[C][W][OA] , 2012, Plant Cell.

[74]  Steven L Salzberg,et al.  Fast gapped-read alignment with Bowtie 2 , 2012, Nature Methods.

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

[76]  William Stafford Noble,et al.  FIMO: scanning for occurrences of a given motif , 2011, Bioinform..

[77]  Jialing Yao,et al.  Linking differential domain functions of the GS3 protein to natural variation of grain size in rice , 2010, Proceedings of the National Academy of Sciences.

[78]  Aaron R. Quinlan,et al.  Bioinformatics Applications Note Genome Analysis Bedtools: a Flexible Suite of Utilities for Comparing Genomic Features , 2022 .

[79]  Mark D. Robinson,et al.  edgeR: a Bioconductor package for differential expression analysis of digital gene expression data , 2009, Bioinform..

[80]  Qian Qian,et al.  Allelic diversities in rice starch biosynthesis lead to a diverse array of rice eating and cooking qualities , 2009, Proceedings of the National Academy of Sciences.

[81]  C. Bustamante,et al.  Evolutionary History of GS3, a Gene Conferring Grain Length in Rice , 2009, Genetics.

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

[83]  Bartek Wilczynski,et al.  Biopython: freely available Python tools for computational molecular biology and bioinformatics , 2009, Bioinform..

[84]  Cole Trapnell,et al.  Ultrafast and memory-efficient alignment of short DNA sequences to the human genome , 2009, Genome Biology.

[85]  Hitoshi Sakakibara,et al.  DWARF10, an RMS1/MAX4/DAD1 ortholog, controls lateral bud outgrowth in rice. , 2007, The Plant journal : for cell and molecular biology.

[86]  Bin Han,et al.  GS3, a major QTL for grain length and weight and minor QTL for grain width and thickness in rice, encodes a putative transmembrane protein , 2006, Theoretical and Applied Genetics.

[87]  M. Ellis,et al.  Semidwarf (sd-1), “green revolution” rice, contains a defective gibberellin 20-oxidase gene , 2002, Proceedings of the National Academy of Sciences of the United States of America.

[88]  G. S. Khush,et al.  Green revolution: A mutant gibberellin-synthesis gene in rice , 2002, Nature.

[89]  P. Christou,et al.  ‘Green revolution’ genes encode mutant gibberellin response modulators , 1999, Nature.