AI Trends & News
Surface Laptop Ultra Pre-orders Open: Price, Release Date and AI Features
Microsoft opens Surface Laptop Ultra pre-orders from US$2,599.99. Explore its launch date, NVIDIA RTX Spark features and implications for Nigerian businesses.
Click editing enables programmable genome writing using DNA polymerases and HUH endonucleases
Technology tamfitronics
Doudna, J. A. The promise and challenge of therapeutic genome editing. Nature 578229–236 (2020).
Anzalone, A. V., Koblan, L. W. & Liu, D. R. Genome editing with CRISPR–Cas nucleases, base editors, transposases and prime editors. Nat. Biotechnol. 38824–844 (2020).
van Overbeek, M. et al. DNA repair profiling reveals nonrandom outcomes at Cas9-mediated breaks. Mol. Cell 63633–646 (2016).
Shen, M. W. et al. Predictable and precise template-free CRISPR editing of pathogenic variants. Nature 563646–651 (2018).
Kosicki, M., Tomberg, K. & Bradley, A. Repair of double-strand breaks induced by CRISPR–Cas9 leads to large deletions and complex rearrangements. Nat. Biotechnol. 36765–771 (2018).
Leibowitz, M. L. et al. Chromothripsis as an on-target consequence of CRISPR–Cas9 genome editing. Nat. Genet. 53895–905 (2021).
Kosicki, M. et al. Cas9-induced large deletions and small indels are controlled in a convergent fashion. Nat. Commun. 133422 (2022).
Alanis-Lobato, G. et al. Frequent loss of heterozygosity in CRISPR–Cas9-edited early human embryos. Proc. Natl Acad. Sci. USA 118e2004832117 (2021).
Enache, O. M. et al. Cas9 activates the p53 pathway and selects for p53-inactivating mutations. Nat. Genet. 52662–668 (2020).
Haapaniemi, E., Botla, S., Persson, J., Schmierer, B. & Taipale, J. CRISPR–Cas9 genome editing induces a p53-mediated DNA damage response. Night. With. 24927–930 (2018).
Ihry, R. J. et al. p53 inhibits CRISPR–Cas9 engineering in human pluripotent stem cells. Night. With. 24939–946 (2018).
Cullot, G. et al. CRISPR–Cas9 genome editing induces megabase-scale chromosomal truncations. Nat. Commun. 101136 (2019).
Cullot, G. et al. Cell cycle arrest and p53 prevent ON-target megabase-scale rearrangements induced by CRISPR–Cas9. Nat. Commun. 144072 (2023).
Boutin, J. et al. CRISPR–Cas9 globin editing can induce megabase-scale copy-neutral losses of heterozygosity in hematopoietic cells. Nat. Commun. 124922 (2021).
Tsai, H.-H. et al. Whole genomic analysis reveals atypical non-homologous off-target large structural variants induced by CRISPR–Cas9-mediated genome editing. Nat. Commun. 145183 (2023).
Hustedt, N. & Durocher, D. The control of DNA repair by the cell cycle. Nat. Cell Biol. 191–9 (2017).
Yeh, C. D., Richardson, C. D. & Corn, J. E. Advances in genome editing through control of DNA repair pathways. Nat. Cell Biol. 211468–1478 (2019).
Komor, A. C., Kim, Y. B., Packer, M. S., Zuris, J. A. & Liu, D. R. Programmable editing of a target base in genomic DNA without double-stranded DNA cleavage. Nature 533420–424 (2016).
Gaudelli, N. M. et al. Programmable base editing of A•T to G•C in genomic DNA without DNA cleavage. Nature 551464–471 (2017).
Rees, H. A. & Liu, D. R. Base editing: precision chemistry on the genome and transcriptome of living cells. Night. Rev. The gene. 19770–788 (2018).
Grünewald, J. et al. Transcriptome-wide off-target RNA editing induced by CRISPR-guided DNA base editors. Nature 569433–437 (2019).
Zuo, E. et al. Cytosine base editor generates substantial off-target single-nucleotide variants in mouse embryos. Science 364289–292 (2019).
Park, S. & Beal, P. A. Off-target editing by CRISPR-guided DNA base editors. Biochemistry 583727–3734 (2019).
Huang, T. P., Newby, G. A. & Liu, D. R. Precision genome editing using cytosine and adenine base editors in mammalian cells. Nat. Protoc. 161089–1128 (2021).
Porto, E. M., Komor, A. C., Slaymaker, I. M. & Yeo, G. W. Base editing: advances and therapeutic opportunities. Nat. Rev. Drug Discovery 19839–859 (2020).
Halperin, S. O. et al. CRISPR-guided DNA polymerases enable diversification of all nucleotides in a tunable window. Nature 560248–252 (2018).
Tou, C. J., Schaffer, D. V. & Dueber, J. E. Targeted diversification in the S. cerevisiae genome with CRISPR-guided DNA polymerase I. ACS Synth. Biol. 91911–1916 (2020).
Long, M. et al. Directed evolution of ornithine cyclodeaminase using an EvolvR-based growth-coupling strategy for efficient biosynthesis of l-proline. ACS Synth. Biol. 91855–1863 (2020).
Gossing, M. et al. Multiplexed guide RNA expression leads to increased mutation frequency in targeted window using a CRISPR-guided error-prone DNA polymerase in Saccharomyces cerevisiae. ACS Synth. Biol. 122271–2277 (2023).
Nakade, S. et al. Frame editors for precise, template-free frameshifting. Preprint at https://doi.org/10.1101/2022.12.05.518807 (2022).
Yang, Q. et al. Phage DNA polymerase prevents on-target damage and enhances precision of CRISPR editing. Preprint at https://doi.org/10.1101/2023.01.10.523496 (2023).
Yoo, K. W., Yadav, M. K., Song, Q., Atala, A. & Lu, B. Targeting DNA polymerase to DNA double-strand breaks reduces DNA deletion size and increases templated insertions generated by CRISPR/Cas9. Nucleic Acids Res. 503944–3957 (2022).
Sharon, E. et al. Functional genetic variants revealed by massively parallel precise genome editing. Cell 175544–557.e16 (2018).
Anzalone, A. V. et al. Search-and-replace genome editing without double-strand breaks or donor DNA. Nature 576149–157 (2019).
Kong, X. et al. Precise genome editing without exogenous donor DNA via retron editing system in human cells. Protein Cell 12899–902 (2021).
Zhao, B., Chen, S.-A. A., Lee, J. & Fraser, H. B. Bacterial retrons enable precise gene editing in human cells. CRISPR J. 531–39 (2022).
Chen, P. J. & Liu, D. R. Prime editing for precise and highly versatile genome manipulation. Night. Rev. The gene. 24161–177 (2023).
Berdis, A. J. Mechanisms of DNA polymerases. Chem. Rev. 1092862–2879 (2009).
Johansson, E. & Dixon, N. Replicative DNA polymerases. Cold Spring Harb. Perspect. Biol. 5a012799 (2013).
Ponnienselvan, K. et al. Addressing the dNTP bottleneck restricting prime editing activity. Preprint at https://doi.org/10.1101/2023.10.21.563443 (2023).
Egli, M. & Manoharan, M. Chemistry, structure and function of approved oligonucleotide therapeutics. Nucleic Acids Res. 512529–2573 (2023).
Chandler, M. et al. Breaking and joining single-stranded DNA: the HUH endonuclease superfamily. Nat. Rev. Microbiol. 11525–538 (2013).
Lovendahl, K. N., Hayward, A. N. & Gordon, W. R. Sequence-directed covalent protein-DNA linkages in a single step using HUH-tags. J. Am. Chem. Soc. 1397030–7035 (2017).
Tompkins, K. J. et al. Molecular underpinnings of ssDNA specificity by Rep HUH-endonucleases and implications for HUH-tag multiplexing and engineering. Nucleic Acids Res. 491046–1064 (2021).
Aird, E. J., Lovendahl, K. N., St. Martin, A., Harris, R. S. & Gordon, W. R. Increasing Cas9-mediated homology-directed repair efficiency through covalent tethering of DNA repair template. Commun. Biol. 154 (2018).
Klenow, H. & Overgaard-Hansen, K. Proteolytic cleavage of DNA polymerase from Escherichia coli B into an exonuclease unit and a polymerase unit. FEBS Lett. 625–27 (1970).
Richardson, C. D., Ray, G. J., DeWitt, M. A., Curie, G. L. & Corn, J. E. Enhancing homology-directed genome editing by catalytically active and inactive CRISPR–Cas9 using asymmetric donor DNA. Nat. Biotechnol. 34339–344 (2016).
Li, L. et al. Multiple diverse circoviruses infect farm animals and are commonly found in human and chimpanzee feces. J. Virol. 841674–1682 (2010).
Chandra, A., Hughes, T. R., Nugent, C. I. & Lundblad, V. Cdc13 both positively and negatively regulates telomere replication. Genes Dev. 15404–414 (2001).
Glustrom, L. W. et al. Single-stranded telomere-binding protein employs a dual rheostat for binding affinity and specificity that drives function. Proc. Natl Acad. Sci. USA 11510315–10320 (2018).
Smiley, A. T. et al. Watson–Crick base-pairing requirements for ssDNA recognition and processing in replication-initiating HUH endonucleases. mBio 14e02587-22 (2023).
Lawyer, F. C. et al. High-level expression, purification, and enzymatic characterization of full-length Thermus aquaticus DNA polymerase and a truncated form deficient in 5′ to 3′ exonuclease activity. Genome Res. 2275–287 (1993).
Blanco, L. et al. Highly efficient DNA synthesis by the phage phi 29 DNA polymerase. Symmetrical mode of DNA replication. J. Biol. Chem. 2648935–8940 (1989).
Esteban, J. A., Soengas, M. S., Salas, M. & Blanco, L. 3′ → 5′ exonuclease active site of phi 29 DNA polymerase. Evidence favoring a metal ion-assisted reaction mechanism. J. Biol. Chem. 26931946–31954 (1994).
Thyme, S. B., Akhmetova, L., Montague, T. G., Valen, E. & Schier, A. F. Internal guide RNA interactions interfere with Cas9-mediated cleavage. Nat. Commun. 711750 (2016).
Ponnienselvan, K. et al. Reducing the inherent auto-inhibitory interaction within the pegRNA enhances prime editing efficiency. Nucleic Acids Res. 516966–6980 (2023).
Zhang, W. et al. Enhancing CRISPR prime editing by reducing misfolded pegRNA interactions. eLife 12RP90948 (2024).
Nelson, J. W. et al. Engineered pegRNAs improve prime editing efficiency. Nat. Biotechnol. 40402–410 (2022).
Chen, P. J. et al. Enhanced prime editing systems by manipulating cellular determinants of editing outcomes. Cell 184, 5635–5652.e29 (2021).
Ferreira da Silva, J. et al. Prime editing efficiency and fidelity are enhanced in the absence of mismatch repair. Nat. Commun. 13760 (2022).
Lahue, R. S., Au, K. G. & Modrich, P. DNA mismatch correction in a defined system. Science 245160–164 (1989).
Su, S. S., Lahue, R. S., Au, K. G. & Modrich, P. Mispair specificity of methyl-directed DNA mismatch correction in vitro. J. Biol. Chem. 2636829–6835 (1988).
Mathis, N. et al. Machine learning prediction of prime editing efficiency across diverse chromatin contexts. Nat. Biotechnol. https://doi.org/10.1038/s41587-024-02268-2 (2024).
Mathis, N. et al. Predicting prime editing efficiency and product purity by deep learning. Nat. Biotechnol. 411151–1159 (2023).
Paquet, D. et al. Efficient introduction of specific homozygous and heterozygous mutations using CRISPR/Cas9. Nature 533125–129 (2016).
Doman, J. L. et al. Phage-assisted evolution and protein engineering yield compact, efficient prime editors. Cell 1863983–4002.e26 (2023).
Petri, K. et al. CRISPR prime editing with ribonucleoprotein complexes in zebrafish and primary human cells. Nat. Biotechnol. 40189–193 (2022).
Grünewald, J. et al. Engineered CRISPR prime editors with compact, untethered reverse transcriptases. Nat. Biotechnol. 41337–343 (2023).
Li, X. et al. Highly efficient prime editing by introducing same-sense mutations in pegRNA or stabilizing its structure. Nat. Commun. 131669 (2022).
Ricchetti, M. & Buc, H. E. coli DNA polymerase I as a reverse transcriptase. EMBO J. 12387–396 (1993).
Krzywkowski, T., Kühnemund, M., Wu, D. & Nilsson, M. Limited reverse transcriptase activity of phi29 DNA polymerase. Nucleic Acids Res. 463625–3632 (2018).
Kim, D. Y., Moon, S. B., Ko, J.-H., Kim, Y.-S. & Kim, D. Unbiased investigation of specificities of prime editing systems in human cells. Nucleic Acids Res. 4810576–10589 (2020).
Yu, Z. et al. PEAC-seq adopts Prime Editor to detect CRISPR off-target and DNA translocation. Nat. Commun. 137545 (2022).
Liang, S.-Q. et al. Genome-wide detection of CRISPR editing in vivo using GUIDE-tag. Nat. Commun. 13437 (2022).
Liang, S.-Q. et al. Genome-wide profiling of prime editor off-target sites in vitro and in vivo using PE-tag. Nat. Methods 20898–907 (2023).
Bae, S., Park, J. & Kim, J.-S. Cas-OFFinder: a fast and versatile algorithm that searches for potential off-target sites of Cas9 RNA-guided endonucleases. Bioinformatics 301473–1475 (2014).
Kamtekar, S. et al. Insights into strand displacement and processivity from the crystal structure of the protein-primed DNA polymerase of bacteriophage phi29. Mol. Cell 16609–618 (2004).
Rodríguez, I. et al. A specific subdomain in phi29 DNA polymerase confers both processivity and strand-displacement capacity. Proc. Natl Acad. Sci. USA 1026407–6412 (2005).
de Vega, M., Lázaro, J. M., Mencía, M., Blanco, L. & Salas, M. Improvement of φ29 DNA polymerase amplification performance by fusion of DNA binding motifs. Proc. Natl Acad. Sci. USA 10716506–16511 (2010).
Povilaitis, T., Alzbutas, G., Sukackaite, R., Siurkus, J. & Skirgaila, R. In vitro evolution of phi29 DNA polymerase using isothermal compartmentalized self replication technique. Protein Eng. Des. Sel. 29617–628 (2016).
Ong, J., Tanner, N., Zhang, Y., Bei, Y. & Potapov, V. Variant DNA polymerases having improved properties and method for improved isothermal amplification of a target DNA. US Patent 11,371,028 (2021).
Plaper, T. et al. Coiled-coil heterodimers with increased stability for cellular regulation and sensing SARS-CoV-2 spike protein-mediated cell fusion. Sci. Rep. 119136 (2021).
Lainšček, D. et al. Coiled-coil heterodimer-based recruitment of an exonuclease to CRISPR/Cas for enhanced gene editing. Nat. Commun. 133604 (2022).
Liu, B. et al. Targeted genome editing with a DNA-dependent DNA polymerase and exogenous DNA-containing templates. Nat. Biotechnol. https://doi.org/10.1038/s41587-023-01947-w (2023).
Trojan, J. et al. Functional analysis of hMLH1 variants and HNPCC-related mutations using a human expression system. Gastroenterology 122211–219 (2002).
Roberts, T. C., Langer, R. & Wood, M. J. A. Advances in oligonucleotide drug delivery. Nat. Rev. Drug Discov. 19673–694 (2020).
Pan, W. et al. DNA polymerase preference determines PCR priming efficiency. BMC Biotech. 1410 (2014).
Choi, J. et al. Precise genomic deletions using paired prime editing. Nat. Biotechnol. 40218–226 (2022).
Jiang, T., Zhang, X. O., Weng, Z. & Xue, W. Deletion and replacement of long genomic sequences using prime editing. Nat. Biotechnol. 40227–234 (2022).
Anzalone, A. V. et al. Programmable deletion, replacement, integration and inversion of large DNA sequences with twin prime editing. Nat. Biotechnol. 40731–740 (2022).
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. 41500–512 (2023).
Zheng, C. et al. Template-jumping prime editing enables large insertion and exon rewriting in vivo. Nat. Commun. 143369 (2023).
Wang, J. et al. Efficient targeted insertion of large DNA fragments without DNA donors. Nat. Methods 19331–340 (2022).
Gasiunas, G. et al. A catalogue of biochemically diverse CRISPR–Cas9 orthologs. Nat. Commun. 115512 (2020).
Altae-Tran, H. et al. The widespread IS200/IS605 transposon family encodes diverse programmable RNA-guided endonucleases. Science 37457–65 (2021).
Martín-Alonso, S., Frutos-Beltrán, E. & Menéndez-Arias, L. Reverse transcriptase: from transcriptomics to genome editing. Trends Biotechnol. 39194–210 (2021).
Shuto, Y. et al. Structural basis for pegRNA-guided reverse transcription by a prime editor. Nature 631224–231 (2024).
Yang, L. et al. Efficient delivery of antisense oligonucleotides using bioreducible lipid nanoparticles in vitro and in vivo. Mol. Ther. Nucleic Acids 191357–1367 (2020).
Farbiak, L. et al. All‐in‐one dendrimer‐based lipid nanoparticles enable precise HDR‐mediated gene editing in vivo. Adv. Mater. 332006619 (2021).
Dahlman, J. E. et al. Barcoded nanoparticles for high throughput in vivo discovery of targeted therapeutics. Proc. Natl Acad. Sci. USA 1142060–2065 (2017).
Xue, L. et al. High-throughput barcoding of nanoparticles identifies cationic, degradable lipid-like materials for mRNA delivery to the lungs in female preclinical models. Nat. Commun. 151884 (2024).
Chen, K. et al. Lung and liver editing by lipid nanoparticle delivery of a stable CRISPR–Cas9 RNP. Preprint at https://doi.org/10.1101/2023.11.15.566339 (2023).
Wei, T. et al. Lung SORT LNPs enable precise homology-directed repair mediated CRISPR/Cas genome correction in cystic fibrosis models. Nat. Commun. 147322 (2023).
Onuma, H., Sato, Y. & Harashima, H. Lipid nanoparticle-based ribonucleoprotein delivery for in vivo genome editing. J. Controlled Release 355406–416 (2023).
Kazlauskas, D., Varsani, A., Koonin, E. V. & Krupovic, M. Multiple origins of prokaryotic and eukaryotic single-stranded DNA viruses from bacterial and archaeal plasmids. Nat. Commun. 103425 (2019).
Kleinstiver, B. P. et al. Engineered CRISPR–Cas9 nucleases with altered PAM specificities. Nature 523481–485 (2015).
Rohland, N. & Reich, D. Cost-effective, high-throughput DNA sequencing libraries for multiplexed target capture. Genome Res. 22939–946 (2012).
Kleinstiver, B. P. et al. Engineered CRISPR–Cas12a variants with increased activities and improved targeting ranges for gene, epigenetic and base editing. Nat. Biotechnol. 37276–282 (2019).
Clement, K. et al. CRISPResso2 provides accurate and rapid genome editing sequence analysis. Nat. Biotechnol. 37224–226 (2019).
BBMap. SourceForge https://sourceforge.net/projects/bbmap (2022).
Iseli, C., Ambrosini, G., Bucher, P. & Jongeneel, C. V. Indexing strategies for rapid searches of short words in genome sequences. PLoS One 2e579 (2007).
Ferreira da Silva J., et al. Click editing enables programmable genome writing using DNA polymerases and HUH endonucleases. (Dataset. NCBI Sequence Read Archive); https://www.ncbi.nlm.nih.gov/bioproject/PRJNA1015647 (2024).
Originally reported by nature.com. Adapted for our readers.
