Home NATURALEZA Rapid generation of long, chemically modified pegRNAs for prime editing

Rapid generation of long, chemically modified pegRNAs for prime editing

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  • Anzalone, A. V., Koblan, L. W. & Liu, D. R. Genome editing with CRISPR–Cas nucleases, base editors, transposases and prime editors. Nat. Biotechnol. 38, 824–844 (2020).

    Article 
    PubMed 
    CAS 

    Google Scholar
     

  • Hsu, P. D., Lander, E. S. & Zhang, F. Development and applications of CRISPR–Cas9 for genome engineering. Cell 157, 1262–1278 (2014).

    Article 
    PubMed 
    PubMed Central 
    CAS 

    Google Scholar
     

  • Doudna, J. A. & Charpentier, E. Genome editing. The new frontier of genome engineering with CRISPR–Cas9. Science 346, 1258096 (2014).

    Article 
    PubMed 

    Google Scholar
     

  • Rees, H. A. & Liu, D. R. Base editing: precision chemistry on the genome and transcriptome of living cells. Nat. Rev. Genet. 19, 770–788 (2018).

    Article 
    PubMed 
    PubMed Central 
    CAS 

    Google Scholar
     

  • Anzalone, A. V. et al. Search-and-replace genome editing without double-strand breaks or donor DNA. Nature 576, 149–157 (2019).

    Article 
    PubMed 
    PubMed Central 
    CAS 

    Google Scholar
     

  • Nelson, J. W. et al. Engineered pegRNAs improve prime editing efficiency. Nat. Biotechnol. 40, 402–410 (2021).

    Article 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Zhang, G. et al. Enhancement of prime editing via xrRNA motif-joined pegRNA. Nat. Commun. 13, 1856 (2022).

    Article 
    PubMed 
    PubMed Central 
    CAS 

    Google Scholar
     

  • Liu, Y. et al. Enhancing prime editing by Csy4-mediated processing of pegRNA. Cell Research 31, 1134–1136 (2021).

    Article 
    PubMed 
    PubMed Central 
    CAS 

    Google Scholar
     

  • Yin, H. et al. Structure-guided chemical modification of guide RNA enables potent non-viral in vivo genome editing. Nat. Biotechnol. 35, 1179–1187 (2017).

    Article 
    PubMed 
    PubMed Central 
    CAS 

    Google Scholar
     

  • Hendel, A. et al. Chemically modified guide RNAs enhance CRISPR–Cas genome editing in human primary cells. Nat. Biotechnol. 33, 985–989 (2015).

    Article 
    PubMed 
    PubMed Central 
    CAS 

    Google Scholar
     

  • Ryan, D. E. et al. Improving CRISPR–Cas specificity with chemical modifications in single-guide RNAs. Nucleic Acids Res. 46, 792–803 (2018).

    Article 
    PubMed 
    CAS 

    Google Scholar
     

  • Chen, Q., Zhang, Y. & Yin, H. Recent advances in chemical modifications of guide RNA, mRNA and donor template for CRISPR-mediated genome editing. Adv. Drug Deliv. Rev. 168, 246–258 (2021).

    Article 
    PubMed 
    CAS 

    Google Scholar
     

  • Meisel, R. CRISPR–Cas9 gene editing for sickle cell disease and β-thalassemia. N. Engl. J. Med. 384, e91 (2021).

    PubMed 

    Google Scholar
     

  • Wang, J. et al. Efficient targeted insertion of large DNA fragments without DNA donors. Nat. Methods 19, 331–340 (2022).

    Article 
    PubMed 
    CAS 

    Google Scholar
     

  • Solomon, A. CRISPR–Cas9 in vivo gene editing for transthyretin amyloidosis. N. Engl. J. Med. 385, 1721–1722 (2021).

    Article 
    PubMed 
    CAS 

    Google Scholar
     

  • Finn, J. D. et al. A single administration of CRISPR/Cas9 lipid nanoparticles achieves robust and persistent in vivo genome editing. Cell Rep. 22, 2227–2235 (2018).

    Article 
    PubMed 
    CAS 

    Google Scholar
     

  • Chen, P. J. et al. Enhanced prime editing systems by manipulating cellular determinants of editing outcomes. Cell 184, 5635–5652.e5629 (2021).

    Article 
    PubMed 
    PubMed Central 
    CAS 

    Google Scholar
     

  • Everette, K. A. et al. Ex vivo prime editing of patient haematopoietic stem cells rescues sickle-cell disease phenotypes after engraftment in mice. Nat. Biomed. Eng. 7, 616–628 (2023).

    Article 
    PubMed 
    PubMed Central 
    CAS 

    Google Scholar
     

  • Liu, B. et al. Targeted genome editing with a DNA-dependent DNA polymerase and exogenous DNA-containing templates. Nat. Biotechnol. 42, 1039–1045 (2024).

    Article 
    PubMed 
    CAS 

    Google Scholar
     

  • Petri, K. et al. CRISPR prime editing with ribonucleoprotein complexes in zebrafish and primary human cells. Nat. Biotechnol. 40, 189–193 (2021).

    Article 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Ponnienselvan, K. et al. Reducing the inherent auto-inhibitory interaction within the pegRNA enhances prime editing efficiency. Nucleic Acids Res. 51, 6966–6980 (2023).

    Article 
    PubMed 
    PubMed Central 
    CAS 

    Google Scholar
     

  • Zhang, W. et al. Enhancing CRISPR prime editing by reducing misfolded pegRNA interactions. eLife https://doi.org/10.7554/eLife.90948.2 (2024).

  • Beaucage, S. L. & Caruthers, M. H. Deoxynucleoside phosphoramidites—a new class of key intermediates for deoxypolynucleotide synthesis. Tetrahedron Lett. 22, 1859–1862 (1981).

    Article 
    CAS 

    Google Scholar
     

  • Ryczek, M., Pluta, M., Blaszczyk, L. & Kiliszek, A. Overview of methods for large-scale RNA synthesis. Appl. Sci. 12, 1543 (2022).

    Article 
    CAS 

    Google Scholar
     

  • Wang, G. et al. mRNA produced by VSW-3 RNAP has high-level translation efficiency with low inflammatory stimulation. Cell Insight 1, 100056 (2022).

    Article 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Dousis, A., Ravichandran, K., Hobert, E. M., Moore, M. J. & Rabideau, A. E. An engineered T7 RNA polymerase that produces mRNA free of immunostimulatory byproducts. Nat. Biotechnol. 41, 560–568 (2023).

    Article 
    PubMed 
    CAS 

    Google Scholar
     

  • Karikó, K. et al. Incorporation of pseudouridine into mRNA yields superior nonimmunogenic vector with increased translational capacity and biological stability. Mol. Ther. 16, 1833–1840 (2008).

    Article 
    PubMed 

    Google Scholar
     

  • Kormann, M. S. et al. Expression of therapeutic proteins after delivery of chemically modified mRNA in mice. Nat. Biotechnol. 29, 154–157 (2011).

    Article 
    PubMed 
    CAS 

    Google Scholar
     

  • Warren, L. et al. Highly efficient reprogramming to pluripotency and directed differentiation of human cells with synthetic modified mRNA. Cell Stem Cell 7, 618–630 (2010).

    Article 
    PubMed 
    PubMed Central 
    CAS 

    Google Scholar
     

  • Pardi, N., Hogan, M. J., Porter, F. W. & Weissman, D. mRNA vaccines – a new era in vaccinology. Nat. Rev. Drug Discov. 17, 261–279 (2018).

    Article 
    PubMed 
    PubMed Central 
    CAS 

    Google Scholar
     

  • Hertler, J. et al. Synthesis of point-modified mRNA. Nucleic Acids Res. 50, e115 (2022).

    Article 
    PubMed 
    PubMed Central 
    CAS 

    Google Scholar
     

  • Kao, C., Zheng, M. & Rüdisser, S. A simple and efficient method to reduce nontemplated nucleotide addition at the 3 terminus of RNAs transcribed by T7 RNA polymerase. RNA 5, 1268–1272 (1999).

    Article 
    PubMed 
    PubMed Central 
    CAS 

    Google Scholar
     

  • Liu, Y. et al. Synthesis and applications of RNAs with position-selective labelling and mosaic composition. Nature 522, 368–372 (2015).

    Article 
    PubMed 
    PubMed Central 
    CAS 

    Google Scholar
     

  • Moody, E. R., Obexer, R., Nickl, F., Spiess, R. & Lovelock, S. L. An enzyme cascade enables production of therapeutic oligonucleotides in a single operation. Science 380, 1150–1154 (2023).

    Article 
    PubMed 
    CAS 

    Google Scholar
     

  • Stark, M. R. & Rader, S. D. Efficient splinted ligation of synthetic RNA using RNA ligase. Methods Mol. Biol. 1126, 137–149 (2014).

    Article 
    PubMed 
    CAS 

    Google Scholar
     

  • Bartosik, K., Debiec, K., Czarnecka, A., Sochacka, E. & Leszczynska, G. Synthesis of nucleobase-modified RNA oligonucleotides by post-synthetic approach. Molecules 25, 3344 (2020).

    Article 
    PubMed 
    PubMed Central 
    CAS 

    Google Scholar
     

  • Flamme, M., McKenzie, L. K., Sarac, I. & Hollenstein, M. Chemical methods for the modification of RNA. Methods 161, 64–82 (2019).

    Article 
    PubMed 
    CAS 

    Google Scholar
     

  • Kurschat, W. C., Müller, J., Wombacher, R. & Helm, M. Optimizing splinted ligation of highly structured small RNAs. RNA 11, 1909–1914 (2005).

    Article 
    PubMed 
    PubMed Central 
    CAS 

    Google Scholar
     

  • Wang, S., Chen, D., Gao, L. & Liu, Y. Short oligonucleotides facilitate co-transcriptional labeling of RNA at specific positions. J. Am. Chem. Soc. 144, 5494–5502 (2022).

    Article 
    PubMed 
    CAS 

    Google Scholar
     

  • Van Giesen, K. J. D., Thompson, M. J., Meng, Q. & Lovelock, S. L. Biocatalytic synthesis of antiviral nucleosides, cyclic dinucleotides, and oligonucleotide therapies. JACS Au 3, 13–24 (2023).

    Article 
    PubMed 

    Google Scholar
     

  • Hengesbach, M. et al. RNA intramolecular dynamics by single-molecule FRET. Curr. Protoc. Nucleic Acid Chem. Ch. 11, Unit 11.12 (2008).


    Google Scholar
     

  • Stark, M. R., Pleiss, J. A., Deras, M., Scaringe, S. A. & Rader, S. D. An RNA ligase-mediated method for the efficient creation of large, synthetic RNAs. RNA 12, 2014–2019 (2006).

    Article 
    PubMed 
    PubMed Central 
    CAS 

    Google Scholar
     

  • Nandakumar, J. & Shuman, S. How an RNA ligase discriminates RNA versus DNA damage. Mol. Cell 16, 211–221 (2004).

    Article 
    PubMed 
    CAS 

    Google Scholar
     

  • Chakravarty, A. K. & Shuman, S. The sequential 2′,3′-cyclic phosphodiesterase and 3′-phosphate/5′-OH ligation steps of the RtcB RNA splicing pathway are GTP-dependent. Nucleic Acids Res. 40, 8558–8567 (2012).

    Article 
    PubMed 
    PubMed Central 
    CAS 

    Google Scholar
     

  • Gamper, H. et al. Enzymatic synthesis of RNA standards for mapping and quantifying RNA modifications in sequencing analysis. Methods Enzymol. 692, 127–153 (2023).

    Article 
    PubMed 

    Google Scholar
     

  • Bullard, D. R. & Bowater, R. P. Direct comparison of nick-joining activity of the nucleic acid ligases from bacteriophage T4. Biochem. J. 398, 135–144 (2006).

    Article 
    PubMed 
    PubMed Central 
    CAS 

    Google Scholar
     

  • Viollet, S., Fuchs, R. T., Munafo, D. B., Zhuang, F. & Robb, G. B. T4 RNA ligase 2 truncated active site mutants: improved tools for RNA analysis. BMC Biotechnol. 11, 72 (2011).

    Article 
    PubMed 
    PubMed Central 
    CAS 

    Google Scholar
     

  • Li, X. et al. Enhancing prime editing efficiency by modified pegRNA with RNA G-quadruplexes. J. Mol. Cell. Biol. 14, mjac022 (2022).

    Article 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Anzalone, A. V. et al. Programmable deletion, replacement, integration and inversion of large DNA sequences with twin prime editing. Nat. Biotechnol. 40, 731–740 (2021).

    Article 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Yarnall, M. T. N. et al. Drag-and-drop genome insertion of large sequences without double-strand DNA cleavage using CRISPR-directed integrases. Nat. Biotechnol. 41, 500–512 (2022).

    Article 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Zheng, C. et al. A flexible split prime editor using truncated reverse transcriptase improves dual-AAV delivery in mouse liver. Mol. Ther. 30, 1343–1351 (2022).

    Article 
    PubMed 
    PubMed Central 
    CAS 

    Google Scholar
     

  • Gao, Z. et al. A truncated reverse transcriptase enhances prime editing by split AAV vectors. Mol. Ther. 30, 2942–2951 (2022).

    Article 
    PubMed 
    PubMed Central 
    CAS 

    Google Scholar
     

  • Doman, J. L. et al. Phage-assisted evolution and protein engineering yield compact, efficient prime editors. Cell 186, 3983–4002.e3926 (2023).

    Article 
    PubMed 
    PubMed Central 
    CAS 

    Google Scholar
     

  • An, J. et al. Enhancement of the viability of T cells electroporated with DNA via osmotic dampening of the DNA-sensing cGAS–STING pathway. Nat. Biomed. Eng. 8, 149–164 (2023).

    Article 
    PubMed 

    Google Scholar
     

  • Han, W. et al. Base editing of the HBG promoter induces potent fetal hemoglobin expression with no detectable off-target mutations in human HSCs. Cell Stem Cell 30, 1624–1639.e1628 (2023).

    Article 
    PubMed 
    CAS 

    Google Scholar
     

  • Qiu, H. Y., Ji, R. J. & Zhang, Y. Current advances of CRISPR-Cas technology in cell therapy. Cell Insight. 1, 100067 (2022).

    Article 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Yin, H. et al. Genome editing with Cas9 in adult mice corrects a disease mutation and phenotype. Nat. Biotechnol. 32, 551–553 (2014).

    Article 
    PubMed 
    PubMed Central 
    CAS 

    Google Scholar
     

  • Yin, H. et al. Therapeutic genome editing by combined viral and non-viral delivery of CRISPR system components in vivo. Nat. Biotechnol. 34, 328–333 (2016).

    Article 
    PubMed 
    PubMed Central 
    CAS 

    Google Scholar
     

  • Yin, H. et al. Non-viral vectors for gene-based therapy. Nat. Rev. Genet. 15, 541–555 (2014).

    Article 
    PubMed 
    CAS 

    Google Scholar
     

  • Sun, C. et al. Precise integration of large DNA sequences in plant genomes using PrimeRoot editors. Nat. Biotechnol. 42, 316–327 (2023).

    Article 
    PubMed 

    Google Scholar
     

  • Katrekar, D. et al. In vivo RNA editing of point mutations via RNA-guided adenosine deaminases. Nat. Methods 16, 239–242 (2019).

    Article 
    PubMed 
    PubMed Central 
    CAS 

    Google Scholar
     

  • Khosravi, H. M. & Jantsch, M. F. Site-directed RNA editing: recent advances and open challenges. RNA Biol. 18, 41–50 (2021).

    Article 
    PubMed 
    PubMed Central 
    CAS 

    Google Scholar
     

  • Fu, Y. et al. CRISPR-dCas9 and sgRNA scaffolds enable dual-colour live imaging of satellite sequences and repeat-enriched individual loci. Nat. Commun. 7, 11707 (2016).

    Article 
    PubMed 
    PubMed Central 
    CAS 

    Google Scholar
     

  • Zalatan, J. G. et al. Engineering complex synthetic transcriptional programs with CRISPR RNA scaffolds. Cell 160, 339–350 (2015).

    Article 
    PubMed 
    CAS 

    Google Scholar
     

  • Liang, Z. et al. Efficient DNA-free genome editing of bread wheat using CRISPR/Cas9 ribonucleoprotein complexes. Nat. Commun. 8, 14261 (2017).

    Article 
    PubMed 
    PubMed Central 
    CAS 

    Google Scholar
     

  • Nishimasu, H. et al. Crystal structure of Cas9 in complex with guide RNA and target DNA. Cell 156, 935–949 (2014).

    Article 
    PubMed 
    PubMed Central 
    CAS 

    Google Scholar
     

  • Liu, P. et al. Improved prime editors enable pathogenic allele correction and cancer modelling in adult mice. Nat. Commun. 12, 2121 (2021).

    Article 
    PubMed 
    PubMed Central 
    CAS 

    Google Scholar
     

  • Park, S.-J. et al. Targeted mutagenesis in mouse cells and embryos using an enhanced prime editor. Genome Biol. 22, 170 (2021).

    Article 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Lu, S. et al. Fast and sensitive detection of SARS-CoV-2 RNA using suboptimal protospacer adjacent motifs for Cas12a. Nat. Biomed. Eng. 6, 286–297 (2022).

    Article 
    PubMed 
    CAS 

    Google Scholar
     

  • Wu, J. et al. Characterization of a thermostable Cas12a ortholog. Cell Insight. 2, 100126 (2023).

    Article 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Zhang, H. X. et al. Cas12a-based one-pot SNP detection with high accuracy. Cell Insight. 2, 100080 (2023).

    Article 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Shi, Y.-J. et al. DNA topology regulates PAM-Cas9 interaction and DNA unwinding to enable near-PAMless cleavage by thermophilic Cas9. Mol. Cell 82, 4160–4175.e4166 (2022).

    Article 
    PubMed 
    CAS 

    Google Scholar
     

  • Xia, H. et al. Psychrophilic phage VSW-3 RNA polymerase reduces both terminal and full-length dsRNA byproducts in in vitro transcription. RNA Biol. 19, 1130–1142 (2022).

    Article 
    PubMed 
    PubMed Central 
    CAS 

    Google Scholar
     

  • Yi, J. et al. Co-delivery of Cas9 mRNA and guide RNAs edits hepatitis B virus episomal and integration DNA in mouse and tree shrew models. Antiviral Res. 215, 105618 (2023).

    Article 
    PubMed 
    CAS 

    Google Scholar
     

  • Zhang, C.-P. et al. Efficient non-viral delivery of macromolecules in human primary hematopoietic stem cells and lymphocytes. J. Mol. Cell. Biol. 15, mjad018 (2023).

    Article 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Chen, S., Zhou, Y., Chen, Y. & Gu, J. fastp: an ultra-fast all-in-one FASTQ preprocessor. Bioinformatics 34, i884–i890 (2018).

    Article 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Bolger, A. M., Lohse, M. & Usadel, B. Trimmomatic: a flexible trimmer for Illumina sequence data. Bioinformatics 30, 2114–2120 (2014).

    Article 
    PubMed 
    PubMed Central 
    CAS 

    Google Scholar
     

  • Clement, K. et al. CRISPResso2 provides accurate and rapid genome editing sequence analysis. Nat. Biotechnol. 37, 224–226 (2019).

    Article 
    PubMed 
    PubMed Central 
    CAS 

    Google Scholar
     

  • Lei, X. et al. Rapid generation of long, chemically modified pegRNAs for prime editing. NCBI Bioproject www.ncbi.nlm.nih.gov/bioproject/1067838 (2024).



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