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Keywords {🔍}

fig, pubmed, bss, backsplice, cell, base, article, exons, rnas, rna, circrna, sites, cas, circrnas, linear, google, scholar, cdrascirs, backspliced, exon, cells, circular, editing, splice, expression, bes, additional, targeted, file, gene, predominantly, sequences, haaebeyf, central, genomic, chen, canonical, locus, cognate, zhang, biogenesis, circznfnov, genome, splicing, dna, previously, proliferation, yang, screening, top,

Topics {✒️}

bsai-linearized pgl3-u6-sgrna-pgk-puromycin fasta-order --bowtie1 --nocoverage-search eliminating base-editor-induced genome-wide base-editor-mediated circrna knockout high-confidence back-spliced exons crispr/cas9 genome-editing system crispr/cas9-mediated circrna ko rnaser-treated rna-seq datasets agei/ecori-linearized plko engineered crispr-cas9 nuclease distinct crispr/cas proteins cas9 rna-guided endonucleases crispr/cas9-mediated deletion [37 millex-gp filter unit diverse alternative back-splicing engineered ha3a-ebe3-y130f back-spliced cdr1as/cirs-7 exon sponging mir-23b-3p crispr/cas9 systems article download pdf age-dependent neural accumulation double-stranded dna cleavage cell-type specific features tophat2 -fusion-search requires nrn/nyn pam crispr-guided cytidine deaminase crispr-cas nucleases high-confidence bsjs identified rnaser-treated rna-seq human apobec3a-cas9 fusion grch38/hg38 reference genome org/node/project/detail/oep002843 rnaser rna-seq datasets protein-coding genes shifts potentially disrupt back-splice entire back-spliced exon mapped rna-seq signals engineered cas proteins rnaser-treated rna samples targeting back-splice sites conducting large-scale screening back-splice sites predominantly including ha3a-ebe-y130f [45] including ha3a-ebe-y130f predominantly back-spliced exon predominantly back-spliced exons reported rfxcas13/shrna/rnai ha3a-ebe-y130f repressed rna-seq library preparation gov/geo/query/acc

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         headline:Knockout of circRNAs by base editing back-splice sites of circularized exons
         description:Many circular RNAs (circRNAs) are produced from back-splicing of exons of precursor mRNAs and are generally co-expressed with cognate linear RNAs. Methods for circRNA-specific knockout are lacking, largely due to sequence overlaps between forms. Here, we use base editors (BEs) for circRNA depletion. By targeting splice sites involved in both back-splicing and canonical splicing, BEs can repress circular and linear RNAs. Targeting sites predominantly for circRNA biogenesis, BEs could efficiently repress the production of circular but not linear RNAs. As hundreds of exons are predominantly back-spliced to produce circRNAs, this provides an efficient method to deplete circRNAs for functional study.
         datePublished:2022-01-10T00:00:00Z
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      headline:Knockout of circRNAs by base editing back-splice sites of circularized exons
      description:Many circular RNAs (circRNAs) are produced from back-splicing of exons of precursor mRNAs and are generally co-expressed with cognate linear RNAs. Methods for circRNA-specific knockout are lacking, largely due to sequence overlaps between forms. Here, we use base editors (BEs) for circRNA depletion. By targeting splice sites involved in both back-splicing and canonical splicing, BEs can repress circular and linear RNAs. Targeting sites predominantly for circRNA biogenesis, BEs could efficiently repress the production of circular but not linear RNAs. As hundreds of exons are predominantly back-spliced to produce circRNAs, this provides an efficient method to deplete circRNAs for functional study.
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         Human Genetics
         Plant Genetics and Genomics
         Microbial Genetics and Genomics
         Bioinformatics
         Evolutionary Biology
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      name:Xiang Gao
      affiliation:
            name:State Key Laboratory of Molecular Biology, Shanghai Key Laboratory of Molecular Andrology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology , University of Chinese Academy of Sciences, Chinese Academy of Sciences
            address:
               name:State Key Laboratory of Molecular Biology, Shanghai Key Laboratory of Molecular Andrology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology , University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, China
               type:PostalAddress
            type:Organization
            name:School of Life Science and Technology, ShanghaiTech University
            address:
               name:School of Life Science and Technology, ShanghaiTech University, Shanghai, China
               type:PostalAddress
            type:Organization
      name:Xu-Kai Ma
      affiliation:
            name:CAS Key Laboratory of Computational Biology, Shanghai Institute of Nutrition and Health , University of Chinese Academy of Sciences, Chinese Academy of Sciences
            address:
               name:CAS Key Laboratory of Computational Biology, Shanghai Institute of Nutrition and Health , University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, China
               type:PostalAddress
            type:Organization
      name:Xiang Li
      affiliation:
            name:State Key Laboratory of Molecular Biology, Shanghai Key Laboratory of Molecular Andrology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology , University of Chinese Academy of Sciences, Chinese Academy of Sciences
            address:
               name:State Key Laboratory of Molecular Biology, Shanghai Key Laboratory of Molecular Andrology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology , University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, China
               type:PostalAddress
            type:Organization
            name:Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences
            address:
               name:Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, Hangzhou, China
               type:PostalAddress
            type:Organization
      name:Guo-Wei Li
      affiliation:
            name:CAS Key Laboratory of Computational Biology, Shanghai Institute of Nutrition and Health , University of Chinese Academy of Sciences, Chinese Academy of Sciences
            address:
               name:CAS Key Laboratory of Computational Biology, Shanghai Institute of Nutrition and Health , University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, China
               type:PostalAddress
            type:Organization
      name:Chu-Xiao Liu
      affiliation:
            name:State Key Laboratory of Molecular Biology, Shanghai Key Laboratory of Molecular Andrology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology , University of Chinese Academy of Sciences, Chinese Academy of Sciences
            address:
               name:State Key Laboratory of Molecular Biology, Shanghai Key Laboratory of Molecular Andrology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology , University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, China
               type:PostalAddress
            type:Organization
      name:Jun Zhang
      affiliation:
            name:State Key Laboratory of Molecular Biology, Shanghai Key Laboratory of Molecular Andrology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology , University of Chinese Academy of Sciences, Chinese Academy of Sciences
            address:
               name:State Key Laboratory of Molecular Biology, Shanghai Key Laboratory of Molecular Andrology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology , University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, China
               type:PostalAddress
            type:Organization
      name:Ying Wang
      affiliation:
            name:State Key Laboratory of Molecular Biology, Shanghai Key Laboratory of Molecular Andrology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology , University of Chinese Academy of Sciences, Chinese Academy of Sciences
            address:
               name:State Key Laboratory of Molecular Biology, Shanghai Key Laboratory of Molecular Andrology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology , University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, China
               type:PostalAddress
            type:Organization
      name:Jia Wei
      affiliation:
            name:CAS Key Laboratory of Computational Biology, Shanghai Institute of Nutrition and Health , University of Chinese Academy of Sciences, Chinese Academy of Sciences
            address:
               name:CAS Key Laboratory of Computational Biology, Shanghai Institute of Nutrition and Health , University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, China
               type:PostalAddress
            type:Organization
      name:Jia Chen
      affiliation:
            name:School of Life Science and Technology, ShanghaiTech University
            address:
               name:School of Life Science and Technology, ShanghaiTech University, Shanghai, China
               type:PostalAddress
            type:Organization
            name:CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences
            address:
               name:CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, Shanghai, China
               type:PostalAddress
            type:Organization
      name:Ling-Ling Chen
      affiliation:
            name:State Key Laboratory of Molecular Biology, Shanghai Key Laboratory of Molecular Andrology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology , University of Chinese Academy of Sciences, Chinese Academy of Sciences
            address:
               name:State Key Laboratory of Molecular Biology, Shanghai Key Laboratory of Molecular Andrology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology , University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, China
               type:PostalAddress
            type:Organization
            name:Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences
            address:
               name:Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, Hangzhou, China
               type:PostalAddress
            type:Organization
      name:Li Yang
      url:http://orcid.org/0000-0001-8833-7473
      affiliation:
            name:CAS Key Laboratory of Computational Biology, Shanghai Institute of Nutrition and Health , University of Chinese Academy of Sciences, Chinese Academy of Sciences
            address:
               name:CAS Key Laboratory of Computational Biology, Shanghai Institute of Nutrition and Health , University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, China
               type:PostalAddress
            type:Organization
      email:[email protected]
PostalAddress:
      name:State Key Laboratory of Molecular Biology, Shanghai Key Laboratory of Molecular Andrology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology , University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, China
      name:School of Life Science and Technology, ShanghaiTech University, Shanghai, China
      name:CAS Key Laboratory of Computational Biology, Shanghai Institute of Nutrition and Health , University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, China
      name:State Key Laboratory of Molecular Biology, Shanghai Key Laboratory of Molecular Andrology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology , University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, China
      name:Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, Hangzhou, China
      name:CAS Key Laboratory of Computational Biology, Shanghai Institute of Nutrition and Health , University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, China
      name:State Key Laboratory of Molecular Biology, Shanghai Key Laboratory of Molecular Andrology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology , University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, China
      name:State Key Laboratory of Molecular Biology, Shanghai Key Laboratory of Molecular Andrology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology , University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, China
      name:State Key Laboratory of Molecular Biology, Shanghai Key Laboratory of Molecular Andrology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology , University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, China
      name:CAS Key Laboratory of Computational Biology, Shanghai Institute of Nutrition and Health , University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, China
      name:School of Life Science and Technology, ShanghaiTech University, Shanghai, China
      name:CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, Shanghai, China
      name:State Key Laboratory of Molecular Biology, Shanghai Key Laboratory of Molecular Andrology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology , University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, China
      name:Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, Hangzhou, China
      name:CAS Key Laboratory of Computational Biology, Shanghai Institute of Nutrition and Health , University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, China

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