Increasing intracellular dNTP levels improves prime editing efficiency – Nature Biotechnology

Increasing intracellular dNTP levels improves prime editing efficiency – Nature Biotechnology


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

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Chen, P. J. et al. Enhanced prime editing systems by manipulating cellular determinants of editing outcomes. Cell 184, 5635–5652.e29 (2021).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Doman, J. L., Sousa, A. A., Randolph, P. B., Chen, P. J. & Liu, D. R. Designing and executing prime editing experiments in mammalian cells. Nat. Protoc. 17, 2431–2468 (2022).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    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 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Nelson, J. W. et al. Engineered pegRNAs improve prime editing efficiency. Nat. Biotechnol. 40, 402–410 (2022).

    Article 
    CAS 
    PubMed 

    Google Scholar 

  • Li, X. et al. Highly efficient prime editing by introducing same-sense mutations in pegRNA or stabilizing its structure. Nat. Commun. 13, 1669 (2022).

    Article 
    CAS 
    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 
    CAS 
    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 (2023).

    Article 
    CAS 
    PubMed 

    Google Scholar 

  • Grunewald, J. et al. Engineered CRISPR prime editors with compact, untethered reverse transcriptases. Nat. Biotechnol. 41, 337–343 (2023).

    Article 
    CAS 
    PubMed 

    Google Scholar 

  • Feng, Y. et al. Enhancing prime editing efficiency and flexibility with tethered and split pegRNAs. Protein Cell 14, 304–308 (2023).

    CAS 
    PubMed 

    Google Scholar 

  • Doman, J. L. et al. Phage-assisted evolution and protein engineering yield compact, efficient prime editors. Cell 186, 3983–4002.e26 (2023).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    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 (2023).

  • da Silva, J. F. et al. Click editing enables programmable genome writing using DNA polymerases and HUH endonucleases. Nat. Biotechnol. https://doi.org/10.1038/s41587-024-02324-x (2024).

  • Petri, K. et al. CRISPR prime editing with ribonucleoprotein complexes in zebrafish and primary human cells. Nat. Biotechnol. 40, 189–193 (2022).

    Article 
    CAS 
    PubMed 

    Google Scholar 

  • Davis, J. R. et al. Efficient prime editing in mouse brain, liver and heart with dual AAVs. Nat. Biotechnol. 42, 253–264 (2023).

  • Diamond, T. L. et al. Macrophage tropism of HIV-1 depends on efficient cellular dNTP utilization by reverse transcriptase. J. Biol. Chem. 279, 51545–51553 (2004).

    Article 
    CAS 
    PubMed 

    Google Scholar 

  • Gao, W. Y., Cara, A., Gallo, R. C. & Lori, F. Low levels of deoxynucleotides in peripheral blood lymphocytes: a strategy to inhibit human immunodeficiency virus type 1 replication. Proc. Natl Acad. Sci. USA 90, 8925–8928 (1993).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Hakansson, P., Hofer, A. & Thelander, L. Regulation of mammalian ribonucleotide reduction and dNTP pools after DNA damage and in resting cells. J. Biol. Chem. 281, 7834–7841 (2006).

    Article 
    CAS 
    PubMed 

    Google Scholar 

  • Traut, T. W. Physiological concentrations of purines and pyrimidines. Mol. Cell. Biochem. 140, 1–22 (1994).

    Article 
    CAS 
    PubMed 

    Google Scholar 

  • Skasko, M. et al. Mechanistic differences in RNA-dependent DNA polymerization and fidelity between murine leukemia virus and HIV-1 reverse transcriptases. J. Biol. Chem. 280, 12190–12200 (2005).

    Article 
    CAS 
    PubMed 

    Google Scholar 

  • Oscorbin, I. P. & Filipenko, M. L. M-MuLV reverse transcriptase: selected properties and improved mutants. Comput. Struct. Biotechnol. J. 19, 6315–6327 (2021).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Paliksa, S., Alzbutas, G. & Skirgaila, R. Decreased Km to dNTPs is an essential M-MuLV reverse transcriptase adoption required to perform efficient cDNA synthesis in one-step RT–PCR assay. Protein Eng. Des. Sel. 31, 79–89 (2018).

    Article 
    CAS 
    PubMed 

    Google Scholar 

  • Kaushik, N., Chowdhury, K., Pandey, V. N. & Modak, M. J. Valine of the YVDD motif of moloney murine leukemia virus reverse transcriptase: role in the fidelity of DNA synthesis. Biochemistry 39, 5155–5165 (2000).

    Article 
    CAS 
    PubMed 

    Google Scholar 

  • Operario, D. J., Reynolds, H. M. & Kim, B. Comparison of DNA polymerase activities between recombinant feline immunodeficiency and leukemia virus reverse transcriptases. Virology 335, 106–121 (2005).

    Article 
    CAS 
    PubMed 

    Google Scholar 

  • Ni, P. et al. Efficient and versatile multiplex prime editing in hexaploid wheat. Genome Biol. 24, 156 (2023).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Halperin, S.O. Methods and compositions for directed genome editing. US patent 20230076357A1 (2023).

  • Das, D. & Georgiadis, M. M. A directed approach to improving the solubility of Moloney murine leukemia virus reverse transcriptase. Protein Sci. 10, 1936–1941 (2001).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Liang, S. Q. et al. Genome-wide profiling of prime editor off-target sites in vitro and in vivo using PE-tag. Nat. Methods 20, 898–907 (2023).

    Article 
    CAS 
    PubMed 

    Google Scholar 

  • Guo, D. et al. iMyoblasts for ex vivo and in vivo investigations of human myogenesis and disease modeling. eLife 11, e70341 (2022).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Mathews, C. K. Deoxyribonucleotide metabolism, mutagenesis and cancer. Nat. Rev. Cancer 15, 528–539 (2015).

    Article 
    CAS 
    PubMed 

    Google Scholar 

  • Goldstone, D. C. et al. HIV-1 restriction factor SAMHD1 is a deoxynucleoside triphosphate triphosphohydrolase. Nature 480, 379–382 (2011).

    Article 
    CAS 
    PubMed 

    Google Scholar 

  • Laguette, N. et al. SAMHD1 is the dendritic- and myeloid-cell-specific HIV-1 restriction factor counteracted by VPX. Nature 474, 654–657 (2011).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Deutschmann, J. & Gramberg, T. SAMHD1 … and viral ways around it. Viruses 13, 395 (2021).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Bergamaschi, A. et al. The human immunodeficiency virus type 2 VPX protein usurps the CUL4A–DDB1 DCAF1 ubiquitin ligase to overcome a postentry block in macrophage infection. J. Virol. 83, 4854–4860 (2009).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Srivastava, S. et al. Lentiviral VPX accessory factor targets VprBP/DCAF1 substrate adaptor for cullin 4 E3 ubiquitin ligase to enable macrophage infection. PLoS Pathog. 4, e1000059 (2008).

    Article 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Hrecka, K. et al. VPX relieves inhibition of HIV-1 infection of macrophages mediated by the SAMHD1 protein. Nature 474, 658–661 (2011).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Korin, Y. D. & Zack, J. A. Nonproductive human immunodeficiency virus type 1 infection in nucleoside-treated G0 lymphocytes. J. Virol. 73, 6526–6532 (1999).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Meyerhans, A. et al. Restriction and enhancement of human immunodeficiency virus type 1 replication by modulation of intracellular deoxynucleoside triphosphate pools. J. Virol. 68, 535–540 (1994).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Plesa, G. et al. Addition of deoxynucleosides enhances human immunodeficiency virus type 1 integration and 2LTR formation in resting CD4+ T cells. J. Virol. 81, 13938–13942 (2007).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Chabes, A. & Stillman, B. Constitutively high dNTP concentration inhibits cell cycle progression and the DNA damage checkpoint in yeast Saccharomyces cerevisiae. Proc. Natl Acad. Sci. USA 104, 1183–1188 (2007).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Pajalunga, D. et al. A defective dNTP pool hinders DNA replication in cell cycle-reactivated terminally differentiated muscle cells. Cell Death Differ. 24, 774–784 (2017).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Sawa, C. et al. High concentration of extracellular nucleotides suppresses cell growth via delayed cell cycle progression in cancer and noncancer cell lines. Heliyon 7, e08318 (2021).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Wakade, A. R., Przywara, D. A., Palmer, K. C., Kulkarni, J. S. & Wakade, T. D. Deoxynucleoside induces neuronal apoptosis independent of neurotrophic factors. J. Biol. Chem. 270, 17986–17992 (1995).

    Article 
    CAS 
    PubMed 

    Google Scholar 

  • Purhonen, J., Banerjee, R., McDonald, A. E., Fellman, V. & Kallijarvi, J. A sensitive assay for dNTPs based on long synthetic oligonucleotides, EvaGreen dye and inhibitor-resistant high-fidelity DNA polymerase. Nucleic Acids Res. 48, e87 (2020).

    Article 
    CAS 
    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 (2022).

    Article 
    CAS 
    PubMed 

    Google Scholar 

  • Nishimasu, H. et al. Engineered CRISPR–Cas9 nuclease with expanded targeting space. Science 361, 1259–1262 (2018).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Dean, M. et al. Genetic restriction of HIV-1 infection and progression to AIDS by a deletion allele of the CKR5 structural gene. Hemophilia Growth and Development Study, Multicenter AIDS Cohort Study, Multicenter Hemophilia Cohort Study, San Francisco City Cohort, ALIVE Study. Science 273, 1856–1862 (1996).

    Article 
    CAS 
    PubMed 

    Google Scholar 

  • Liu, R. et al. Homozygous defect in HIV-1 coreceptor accounts for resistance of some multiply-exposed individuals to HIV-1 infection. Cell 86, 367–377 (1996).

    Article 
    CAS 
    PubMed 

    Google Scholar 

  • Samson, M. et al. Resistance to HIV-1 infection in Caucasian individuals bearing mutant alleles of the CCR-5 chemokine receptor gene. Nature 382, 722–725 (1996).

    Article 
    CAS 
    PubMed 

    Google Scholar 

  • Pagliuca, F. W. et al. Generation of functional human pancreatic β cells in vitro. Cell 159, 428–439 (2014).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Rezania, A. et al. Reversal of diabetes with insulin-producing cells derived in vitro from human pluripotent stem cells. Nat. Biotechnol. 32, 1121–1133 (2014).

    Article 
    CAS 
    PubMed 

    Google Scholar 

  • Philippe, C. et al. Spectrum and distribution of MECP2 mutations in 424 Rett syndrome patients: a molecular update. Eur. J. Med. Genet. 49, 9–18 (2006).

    Article 
    CAS 
    PubMed 

    Google Scholar 

  • Kerem, B. S. et al. Identification of mutations in regions corresponding to the two putative nucleotide (ATP)-binding folds of the cystic fibrosis gene. Proc. Natl Acad. Sci. USA 87, 8447–8451 (1990).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Myerowitz, R. & Costigan, F. C. The major defect in Ashkenazi Jews with Tay–Sachs disease is an insertion in the gene for the α-chain of β-hexosaminidase. J. Biol. Chem. 263, 18587–18589 (1988).

    Article 
    CAS 
    PubMed 

    Google Scholar 

  • Levesque, S., Cosentino, A., Verma, A., Genovese, P. & Bauer, D. E. Enhancing prime editing in hematopoietic stem and progenitor cells by modulating nucleotide metabolism. Nat. Biotechnol. https://doi.org/10.1038/s41587-024-02266-4 (2024).

  • Madigan, V., Zhang, F. & Dahlman. J. E. Drug delivery systems for CRISPR-based genome editors. Nat. Rev. Drug Discov. 22, 875–894 (2023).

  • Hopfner, K.-P. & Hornung, V. Molecular mechanisms and cellular functions of cGAS–STING signalling. Nat. Rev. Mol. Cell Biol. 21, 501–521 (2020).

    Article 
    CAS 
    PubMed 

    Google Scholar 

  • Dumousseau, M., Rodriguez, N., Juty, N. & Le Novere, N. MELTING, a flexible platform to predict the melting temperatures of nucleic acids. BMC Bioinformatics 13, 101 (2012).

    Article 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Guo, D., Daman, K., Durso, D. F., Yan, J. & Emerson, C. P. Generation of iMyoblasts from human induced pluripotent stem cells. Bio Protoc. 12, e4500 (2022).

    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Veres, A. et al. Charting cellular identity during human in vitro β-cell differentiation. Nature 569, 368–373 (2019).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Balboa, D. et al. Functional, metabolic and transcriptional maturation of human pancreatic islets derived from stem cells. Nat. Biotechnol. 40, 1042–1055 (2022).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Baiersdorfer, M. et al. A facile method for the removal of dsRNA contaminant from in vitro-transcribed mRNA. Mol. Ther. Nucleic Acids 15, 26–35 (2019).

    Article 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Sabnis, S. et al. A novel amino lipid series for mRNA delivery: improved endosomal escape and sustained pharmacology and safety in non-human primates. Mol. Ther. 26, 1509–1519 (2018).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 

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

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Liu, P. et al. Increasing intracellular dNTP levels improves prime editing efficiency. Sequence Read Archive https://www.ncbi.nlm.nih.gov/bioproject/?term=PRJNA1024467 (2024).



  • Source link

    More From Author

    湯米李的妻子佈列塔尼弗蘭從郊狼手中奪回了狗。她說,胖胖的拯救了狗

    湯米李的妻子佈列塔尼弗蘭從郊狼手中奪回了狗。她說,胖胖的拯救了狗

    Tellez,4 PA 獎金不足 20 萬美元,被 Pirates 削減

    Tellez,4 PA 獎金不足 20 萬美元,被 Pirates 削減

    Leave a Reply

    Your email address will not be published. Required fields are marked *

    Recent Comments

    No comments to show.

    Categories