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Programmable RNA‐guided large DNA transgenesis by CRISPR/Cas9 and site‐specific integrase Bxb1

Hosur, Vishnu, Low, Benjamin E., Wiles, Michael V.·2022·Frontiers in Bioengineering and Biotechnology
DOI 10.3389/fbioe.2022.910151PMC PMC9294445
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Abstract

The inability to insert large DNA constructs into the genome efficiently and precisely is a key challenge in genomic engineering. Random transgenesis, which is widely used, lacks precision, and comes with a slew of drawbacks. Lentiviral and adeno-associated viral methods are plagued by, respectively, DNA toxicity and a payload capacity of less than 5 kb. Homology-directed repair (HDR) techniques based on CRISPR-Cas9 can be effective, but only in the 1–5 kb range. In addition, long homology arms—DNA sequences that permit construct insertion—of lengths ranging from 0.5 to 5 kb are required by currently known HDR-based techniques. A potential new method that uses Cas9-guided transposases to insert DNA structures up to 10 kb in length works well in bacteria, but only in bacteria. Surmounting these roadblocks, a new toolkit has recently been developed that combines RNA-guided Cas9 and the site-specific integrase Bxb1 to integrate DNA constructs ranging in length from 5 to 43 kb into mouse zygotes with germline transmission and into human cells. This ground-breaking toolkit will give researchers a valuable resource for developing novel, urgently needed mouse and human induced pluripotent stem cell (hiPSC) models of cancer and other genetic diseases, as well as therapeutic gene integration and biopharmaceutical applications, such as the development of stable cell lines to produce therapeutic protein products.

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  • CRISPR Cas9, Base and Prime editing, PASTE, and other versions of gene editing are becoming cost effective and may become mainstream services accessible to the general public.

    “CRISPR Cas9, Base and Prime editing, Programmable Addition via Site‐specific Targeting Elements (PASTE), and other versions of gene editing are becoming cost effective and may cause the trajectory of these technologies to become mainstream services that the general public can access easily. 48 , 50 , 51”

    From Three Tiers to biological escape velocity: The quest to outwit aging (2022) · cites this paper as [51]

    The sections on PASTE and Conclusion and Future Directions discuss PASTE, CRISPR-Cas9, base editing, and prime editing. But Available Tools: Strengths and Weaknesses calls the lack of economical techniques for precise large-DNA integration a key obstacle; the paper does not say these technologies are becoming cost-effective or may become easily accessible mainstream services for the general public. (LLM, conf=0.85)

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Research works printed but not linked: 50

  1. Abe, 2020, Pronuclear Microinjection During S-Phase Increases the Efficiency of CRISPR-Cas9-Assisted Knockin of Large DNA Donors in Mouse Zygotes, Cell Rep., 31, 107653, 10.1016/j.celrep.2020.107653 · DOI
  2. Anzalone, 2021, Programmable Large DNA Deletion, Replacement, Integration, and Inversion with Twin Prime Editing and Site-Specific Recombinases, bioRxiv, 10.1101/2021.11.01.466790 · DOI
  3. Anzalone, 2019, Search-and-Replace Genome Editing Without Double-Strand Breaks or Donor DNA, Nature, 576, 149, 10.1038/s41586-019-1711-4 · DOI · Paper page
  4. Brosh, 2021, A Versatile Platform for Locus-Scale Genome Rewriting and Verification, Proc. Natl. Acad. Sci. U.S.A., 118, 10.1073/pnas.2023952118 · DOI
  5. Chaudhari, 2020, A Non-Viral Genome Editing Platform for Site-Specific Insertion of Large Transgenes, Stem Cell Res. Ther., 11, 380, 10.1186/s13287-020-01890-6 · DOI
  6. Chu, 2015, Increasing the Efficiency of Homology-Directed Repair for CRISPR-Cas9-Induced Precise Gene Editing in Mammalian Cells, Nat. Biotechnol., 33, 543, 10.1038/nbt.3198 · DOI · Paper page
  7. Dave, 2017, Mice Deficient of Myc Super-Enhancer Region Reveal Differential Control Mechanism Between Normal and Pathological Growth, Elife, 6, 10.7554/eLife.23382 · DOI
  8. Gilpatrick, 2020, Targeted Nanopore Sequencing with Cas9-Guided Adapter Ligation, Nat. Biotechnol., 38, 433, 10.1038/s41587-020-0407-5 · DOI
  9. Goodwin, 2019, Large-Scale Discovery of Mouse Transgenic Integration Sites Reveals Frequent Structural Variation and Insertional Mutagenesis, Genome Res., 29, 494, 10.1101/gr.233866.117 · DOI
  10. Grandela, 2021, STRAIGHT-IN: A Platform for High-Throughput Targeting of Large DNA Payloads into Human Pluripotent Stem Cells, bioRxiv, 10.1101/2021.12.08.471715 · DOI
  11. Grindley, 2006, Mechanisms of Site-Specific Recombination, Annu. Rev. Biochem., 75, 567, 10.1146/annurev.biochem.73.011303.073908 · DOI
  12. Gu, 2018, Efficient Generation of Targeted Large Insertions by Microinjection into Two-Cell-Stage Mouse Embryos, Nat. Biotechnol., 36, 632, 10.1038/nbt.4166 · DOI
  13. Haruyama, 2009, Overview: Engineering Transgenic Constructs and Mice, Curr. Protoc. Cell Biol., 42, 10.1002/0471143030.cb1910s42 · DOI
  14. Hnisz, 2013, Super-Enhancers in the Control of Cell Identity and Disease, Cell, 155, 934, 10.1016/j.cell.2013.09.05324119843 · DOI
  15. Hnisz, 2015, Convergence of Developmental and Oncogenic Signaling Pathways at Transcriptional Super-Enhancers, Mol. Cell, 58, 362, 10.1016/j.molcel.2015.02.014 · DOI · Paper page
  16. Iacovino, 2011, Inducible Cassette Exchange: A Rapid and Efficient System Enabling Conditional Gene Expression in Embryonic Stem and Primary Cells, Stem Cells, 29, 1580, 10.1002/stem.715 · DOI
  17. Ioannidi, 2021, Drag-and-Drop Genome Insertion Without DNA Cleavage with CRISPR-Directed Integrases, bioRxiv, 10.1101/2021.11.01.466786 · DOI
  18. Jasin, 2016, The Democratization of Gene Editing: Insights from Site-Specific Cleavage and Double-Strand Break Repair, DNA Repair, 44, 6, 10.1016/j.dnarep.2016.05.001 · DOI
  19. Komor, 2016, Programmable Editing of a Target Base in Genomic DNA Without Double-Stranded DNA Cleavage, Nature, 533, 420, 10.1038/nature17946 · DOI · Paper page
  20. Krupke, 2017, The Mouse Tumor Biology Database: A Comprehensive Resource for Mouse Models of Human Cancer, Cancer Res., 77, e67, 10.1158/0008-5472.Can-17-0584 · DOI
  21. Laboulaye, 2018, Mapping Transgene Insertion Sites Reveals Complex Interactions Between Mouse Transgenes and Neighboring Endogenous Genes, Front. Mol. Neurosci., 11, 385, 10.3389/fnmol.2018.00385 · DOI
  22. Lai, 2010, Evidence for the Failure of Adeno-Associated Virus Serotype 5 to Package a Viral Genome ≥8.2 Kb, Mol. Ther., 18, 75, 10.1038/mt.2009.256 · DOI · Paper page
  23. Liu, 2019, Methodologies for Improving HDR Efficiency, Front. Genet., 9, 691, 10.3389/fgene.2018.00691 · DOI · Paper page
  24. Low, 2021, Efficient Targeted Transgenesis of Large Donor DNA into Multiple Mouse Genetic Backgrounds Using Bacteriophage Bxb1 Integrase, Sci. Rep., 10.1038/s41598-022-09445-w · DOI
  25. Menghi, 2018, The Tandem Duplicator Phenotype Is a Prevalent Genome-Wide Cancer Configuration Driven by Distinct Gene Mutations, Cancer Cell, 34, 197, 10.1016/j.ccell.2018.06.00830017478 · DOI
  26. Menghi, 2016, The Tandem Duplicator Phenotype as a Distinct Genomic Configuration in Cancer, Proc. Natl. Acad. Sci. U.S.A., 113, E2373, 10.1073/pnas.1520010113 · DOI
  27. Merrick, 2018, Serine Integrases: Advancing Synthetic Biology, ACS Synth. Biol., 7, 299, 10.1021/acssynbio.7b00308 · DOI
  28. Mitchell, 2021, De Novo assembly and Delivery to Mouse Cells of a 101 Kb Functional Human Gene, Genetics, 218, 10.1093/genetics/iyab038 · DOI · Paper page
  29. Montini, 2006, Hematopoietic Stem Cell Gene Transfer in a Tumor-Prone Mouse Model Uncovers Low Genotoxicity of Lentiviral Vector Integration, Nat. Biotechnol., 24, 687, 10.1038/nbt1216 · DOI
  30. Munoz-Lopez, 2010, DNA Transposons: Nature and Applications in Genomics, Curr. Genomics, 11, 115, 10.2174/138920210790886871 · DOI
  31. Nayak, 2010, Progress and Prospects: Immune Responses to Viral Vectors, Gene Ther., 17, 295, 10.1038/gt.2009.148 · DOI
  32. Peters, 2017, Recruitment of CRISPR-Cas Systems by Tn7-Like Transposons, Proc. Natl. Acad. Sci. U.S.A., 114, E7358, 10.1073/pnas.1709035114 · DOI
  33. Quadros, 2017, Easi-CRISPR: A Robust Method for One-Step Generation of Mice Carrying Conditional and Insertion Alleles Using Long ssDNA Donors and CRISPR Ribonucleoproteins, Genome Biol., 18, 92, 10.1186/s13059-017-1220-4 · DOI
  34. Reilly, 2016, The Effects of Genetic Background of Mouse Models of Cancer: Friend or Foe?, Cold Spring Harb. Protoc., 2016, pdb.top076273, 10.1101/pdb.top076273 · DOI
  35. Rivera, 2008, Genetic Background and the Dilemma of Translating Mouse Studies to Humans, Immunity, 28, 1, 10.1016/j.immuni.2007.12.008 · DOI
  36. Stark, 2017, Making Serine Integrases Work for Us, Curr. Opin. Microbiol., 38, 130, 10.1016/j.mib.2017.04.006 · DOI
  37. Strecker, 2019, RNA-Guided DNA Insertion with CRISPR-Associated Transposases, Science, 365, 48, 10.1126/science.aax9181 · DOI
  38. Tang, 2020, Super-Enhancer Function and its Application in Cancer Targeted Therapy, npj Precis. Onc., 4, 2, 10.1038/s41698-020-0108-z · DOI
  39. 2012, An Integrated Encyclopedia of DNA Elements in the Human Genome, Nature, 489, 57, 10.1038/nature11247 · DOI · Paper page
  40. Tipanee, 2017, Transposons: Moving Forward from Preclinical Studies to Clinical Trials, Hum. Gene Ther., 28, 1087, 10.1089/hum.2017.128 · DOI
  41. Vo, 2020, CRISPR RNA-Guided Integrases for High-Efficiency, Multiplexed Bacterial Genome Engineering, Nat. Biotechnol., 39, 480, 10.1038/s41587-020-00745-y · DOI
  42. Wallace, 2007, Manipulating the Mouse Genome to Engineer Precise Functional Syntenic Replacements with Human Sequence, Cell, 128, 197, 10.1016/j.cell.2006.11.044 · DOI
  43. Wang, 2015, Highly Efficient CRISPR/HDR-Mediated Knock-In for Mouse Embryonic Stem Cells and Zygotes, Biotechniques, 59, 201, 10.2144/000114339 · DOI
  44. Wang, 2013, One-Step Generation of Mice Carrying Mutations in Multiple Genes by CRISPR/Cas-Mediated Genome Engineering, Cell, 153, 910, 10.1016/j.cell.2013.04.025 · DOI · Paper page
  45. Wang, 2008, Chromosomal Transposition of PiggyBac in Mouse Embryonic Stem Cells, Proc. Natl. Acad. Sci. U.S.A., 105, 9290, 10.1073/pnas.0801017105 · DOI
  46. Wang, 2019, Super-Enhancers in Transcriptional Regulation and Genome Organization, Nucleic Acids Res., 47, 11481, 10.1093/nar/gkz1038 · DOI · Paper page
  47. Willis, 2017, Mechanism of Tandem Duplication Formation in BRCA1-Mutant Cells, Nature, 551, 590, 10.1038/nature24477 · DOI
  48. Yan, 2013, Mechanism of Random Integration of Foreign DNA in Transgenic Mice, Transgenic Res., 22, 983, 10.1007/s11248-013-9701-z · DOI
  49. Yang, 2020, Methods Favoring Homology-Directed Repair Choice in Response to CRISPR/Cas9 Induced-Double Strand Breaks, Ijms, 21, 6461, 10.3390/ijms21186461 · DOI · Paper page
  50. Yang, 2013, One-Step Generation of Mice Carrying Reporter and Conditional Alleles by CRISPR/Cas-Mediated Genome Engineering, Cell, 154, 1370, 10.1016/j.cell.2013.08.022 · DOI · Paper page

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Metadata

Authors
Hosur, V., Low, B. E., & Wiles, M. V.
Venue
Frontiers in Bioengineering and Biotechnology
Publisher
Frontiers Media SA
Published
2022-07-05
Volume
10
ISSN
2296-4185
DOI
10.3389/fbioe.2022.910151
PMC
PMC9294445
Cited by
20
References
0
Licence
creativecommons.org/licenses/by/4.0/ (vor)
Funders
National Institutes of Health

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