Applications of and considerations for using CRISPR–Cas9-mediated gene conversion systems in rodents

Hannah A. Grunwald, Alexander J. Weitzel, Kimberly L. Cooper

Published: 2021-12-22 DOI: 10.1038/s41596-021-00646-7

CRISPR-Cas9

gene conversion

rodents

gene drive

Lyme disease

AI 解读

Efficient and safe single-cell cloning of human pluripotent stem cells using the CEPT cocktail

Profiling native pulmonary basement membrane stiffness using atomic force microscopy

Genetic circuit design automation with Cello 2.0

Synthesis of siRNA nanoparticles to silence plaque-destabilizing gene in atherosclerotic lesional macrophages

Scalable dual-omics profiling with single-nucleus chromatin accessibility and mRNA expression sequencing 2 (SNARE-seq2)

A practical guide to scanning light-field microscopy with digital adaptive optics

Effective high-throughput isolation of fully human antibodies targeting infectious pathogens

Improved sampling and DNA extraction procedures for microbiome analysis in food-processing environments

MOF-derived nanoporous carbons with diverse tunable nanoarchitectures

Tutorial: a statistical genetics guide to identifying HLA alleles driving complex disease

查看全部

Sections

Figures

References

Genetic elements that are inherited at super-Mendelian frequencies could be used in a ‘gene drive’ to spread an allele to high prevalence in a population with the goal of eliminating invasive species or disease vectors. We recently demonst
Main
An introduction to active genetics in mice
The meiotic window is critical for interchromosomal HDR
Population modification and wild release
Possible applications of active genetics in the laboratory
Strategies to convert alleles to homozygosity
Technical considerations when designing an active genetic system in rodents
The unknown mechanics of mobilizing multiple elements at once
Conclusion
- Reporting Summary
- References
References
ACKNOWLEDGMENTS

Ericsson, A. C., Crim, M. J. & Franklin, C. L. A brief history of animal modeling. Mo. Med. 110, 201–205 (2013).
Meerburg, B. G., Singleton, G. R. & Kijlstra, A. Rodent-borne diseases and their risks for public health. Crit. Rev. Microbiol. 35, 221–270 (2009).
Towns, D. R., Atkinson, I. A. E. & Daugherty, C. H. Have the harmful effects of introduced rats on islands been exaggerated? Biol. Invasions 8, 863–891 (2006).
Grunwald, H. A. et al. Super-Mendelian inheritance mediated by CRISPR–Cas9 in the female mouse germline. Nature 566, 105–109 (2019).
Gantz, V. M. & Bier, E. The dawn of active genetics. BioEssays N. Rev. Mol. Cell. Dev. Biol. 38, 50–63 (2016).
Platt, R. J. et al. CRISPR-Cas9 knockin mice for genome editing and cancer modeling. Cell 159, 440–455 (2014).
Bond, S. T. et al. Tissue-specific expression of Cas9 has no impact on whole-body metabolism in four transgenic mouse lines. Mol. Metab. 53, 101292 (2021).
Esvelt, K. M., Smidler, A. L., Catteruccia, F. & Church, G. M. Concerning RNA-guided gene drives for the alteration of wild populations. eLife 3, e03401 (2014).
Callaway, E. Controversial CRISPR ‘gene drives’ tested in mammals for the first time. Nature 559, 164–164 (2018).
Scudellari, M. Self-destructing mosquitoes and sterilized rodents: the promise of gene drives. Nature 571, 160–162 (2019).
Gantz, V. M. & Bier, E. The mutagenic chain reaction: a method for converting heterozygous to homozygous mutations. Science 348, 442–444 (2015).
Gantz, V. M. et al. Highly efficient Cas9-mediated gene drive for population modification of the malaria vector mosquito Anopheles stephensi. Proc. Natl Acad. Sci. USA 112, E6736–E6743 (2015).
Xu, X.-R. S., Gantz, V. M., Siomava, N. & Bier, E. CRISPR/Cas9 and active genetics-based trans-species replacement of the endogenous Drosophila kni-L2 CRM reveals unexpected complexity. eLife 6, e30281 (2017).
López Del Amo, V. et al. A transcomplementing gene drive provides a flexible platform for laboratory investigation and potential field deployment. Nat. Commun. 11, 352 (2020).
DiCarlo, J. E., Chavez, A., Dietz, S. L., Esvelt, K. M. & Church, G. M. Safeguarding CRISPR-Cas9 gene drives in yeast. Nat. Biotechnol. 33, 1250–1255 (2015).
Champer, J. et al. Molecular safeguarding of CRISPR gene drive experiments. eLife 8, e41439 (2019).
Noble, C. et al. Daisy-chain gene drives for the alteration of local populations. Proc. Natl Acad. Sci. USA 116, 8275 (2019).
Singh, P., Schimenti, J. C. & Bolcun-Filas, E. A mouse geneticist’s practical guide to CRISPR applications. Genetics 199, 1–15 (2015).
Mao, Z., Bozzella, M., Seluanov, A. & Gorbunova, V. DNA repair by nonhomologous end joining and homologous recombination during cell cycle in human cells. Cell Cycle 7, 2902–2906 (2008).
Li, G. et al. Small molecules enhance CRISPR/Cas9-mediated homology-directed genome editing in primary cells. Sci. Rep. 7, 8943 (2017).
Hu, Z. et al. Ligase IV inhibitor SCR7 enhances gene editing directed by CRISPR-Cas9 and ssODN in human cancer cells. Cell Biosci. 8, 12–12 (2018).
Janssen, J. M., Chen, X., Liu, J. & Gonçalves, M. A. F. V. The chromatin structure of CRISPR-Cas9 target DNA controls the balance between mutagenic and homology-directed gene-editing events. Mol. Ther. Nucleic Acids 16, 141–154 (2019).
Gu, B., Posfai, E. & Rossant, J. Efficient generation of targeted large insertions by microinjection into two-cell-stage mouse embryos. Nat. Biotechnol. 36, 632–637 (2018).
Raveux, A., Vandormael-Pournin, S. & Cohen-Tannoudji, M. Optimization of the production of knock-in alleles by CRISPR/Cas9 microinjection into the mouse zygote. Sci. Rep. 7, 42661 (2017).
Carlson-Stevermer, J. et al. Assembly of CRISPR ribonucleoproteins with biotinylated oligonucleotides via an RNA aptamer for precise gene editing. Nat. Commun. 8, 1711 (2017).
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. 1, 54 (2018).
Guichard, A. et al. Efficient allelic-drive in Drosophila. Nat. Commun. 10, 1640 (2019).
Romanienko, P. J. & Camerini-Otero, R. D. The mouse Spo11 gene is required for meiotic chromosome synapsis. Mol. Cell 6, 975–987 (2000).
Comeron, J. M., Ratnappan, R. & Bailin, S. The many landscapes of recombination in Drosophila melanogaster. PLoS Genet. 8, e1002905 (2012).
Duret, L. & Galtier, N. Biased gene conversion and the evolution of mammalian genomic landscapes. Annu. Rev. Genomics Hum. Genet. 10, 285–311 (2009).
Osada, N. & Innan, H. Duplication and gene conversion in the Drosophila melanogaster genome. PLoS Genet. 4, e1000305 (2008).
Williams, A. L. et al. Non-crossover gene conversions show strong GC bias and unexpected clustering in humans. eLife 4, e04637 (2015).
de Vries, F. A. T. et al. Mouse Sycp1 functions in synaptonemal complex assembly, meiotic recombination, and XY body formation. Genes Dev. 19, 1376–1389 (2005).
Di Carlo, A. D., Travia, G. & De Felici, M. The meiotic specific synaptonemal complex protein SCP3 is expressed by female and male primordial germ cells of the mouse embryo. Int. J. Dev. Biol. 44, 241–244 (2000).
Goetz, P., Chandley, A. C. & Speed, R. M. Morphological and temporal sequence of meiotic prophase development at puberty in the male mouse. J. Cell Sci. 65, 249 (1984).
Oakberg, E. F. A description of spermiogenesis in the mouse and its use in analysis of the cycle of the seminiferous epithelium and germ cell renewal. Am. J. Anat. 99, 391–413 (1956).
de Kretser, D. M., Loveland, K. L., Meinhardt, A., Simorangkir, D. & Wreford, N. Spermatogenesis. Hum. Reprod. 13, 1–8 (1998).
Weitzel, A. J. et al. Meiotic Cas9 expression mediates gene conversion in the male and female mouse germline. PLoS Biol. 19, e3001478 (2021).
Goedecke, W., Eijpe, M., Offenberg, H. H., van Aalderen, M. & Heyting, C. Mre11 and Ku70 interact in somatic cells, but are differentially expressed in early meiosis. Nat. Genet. 23, 194–198 (1999).
Enguita-Marruedo, A. et al. Transition from a meiotic to a somatic-like DNA damage response during the pachytene stage in mouse meiosis. PLoS Genet. 15, e1007439 (2019).
Ahmed, E. A., Philippens, M. E. P., Kal, H. B., de Rooij, D. G. & de Boer, P. Genetic probing of homologous recombination and non-homologous end joining during meiotic prophase in irradiated mouse spermatocytes. Mutat. Res. 688, 12–18 (2010).
Hammond, A. et al. A CRISPR-Cas9 gene drive system targeting female reproduction in the malaria mosquito vector Anopheles gambiae. Nat. Biotechnol. 34, 78–83 (2016).
Simoni, A. et al. A male-biased sex-distorter gene drive for the human malaria vector Anopheles gambiae. Nat. Biotechnol. http://doi.org/10.1038/s41587-020-0508-1 (2020).
Unckless, R. L., Clark, A. G. & Messer, P. W. Evolution of resistance against CRISPR/Cas9 gene drive. Genetics 205, 827–841 (2017).
Noble, C., Olejarz, J., Esvelt, K. M., Church, G. M. & Nowak, M. A. Evolutionary dynamics of CRISPR gene drives. Sci. Adv. 3, e1601964 (2017).
Champer, S. E. et al. Computational and experimental performance of CRISPR homing gene drive strategies with multiplexed gRNAs. Sci. Adv. 6, eaaz0525 (2020).
Champer, J. et al. A CRISPR homing gene drive targeting a haplolethal gene removes resistance alleles and successfully spreads through a cage population. Proc. Natl Acad. Sci. USA 117, 24377 (2020).
Barbaric, I., Miller, G. & Dear, T. N. Appearances can be deceiving: phenotypes of knockout mice. Brief. Funct. Genomics 6, 91–103 (2007).
Liao, B.-Y. & Zhang, J. Null mutations in human and mouse orthologs frequently result in different phenotypes. Proc. Natl Acad. Sci. USA 105, 6987 (2008).
Mou, H. et al. CRISPR/Cas9-mediated genome editing induces exon skipping by alternative splicing or exon deletion. Genome Biol. 18, 108–108 (2017).
Sui, T. et al. CRISPR-induced exon skipping is dependent on premature termination codon mutations. Genome Biol. 19, 164–164 (2018).
El-Brolosy, M. A. et al. Genetic compensation triggered by mutant mRNA degradation. Nature 568, 193–197 (2019).
Mak, I. W., Evaniew, N. & Ghert, M. Lost in translation: animal models and clinical trials in cancer treatment. Am. J. Transl. Res. 6, 114–118 (2014).
Devoy, A., Bunton-Stasyshyn, R. K. A., Tybulewicz, V. L. J., Smith, A. J. H. & Fisher, E. M. C. Genomically humanized mice: technologies and promises. Nat. Rev. Genet. 13, 14–20 (2011).
Zhu, F., Nair, R. R., Fisher, E. M. C. & Cunningham, T. J. Humanising the mouse genome piece by piece. Nat. Commun. 10, 1845 (2019).
Cooke, G. E. Pharmacogenetics of multigenic disease: heart disease as an example. Pharmacogenet. Heart Dis. 44, 66–74 (2006).
Bertram, L. & Tanzi, R. E. The genetics of Alzheimer’s disease. in Molecular Biology of Neurodegenerative Diseases (ed. Teplow, D. B.) 79–100 (Academic Press, 2012).
Bottino, R. & Trucco, M. Multifaceted therapeutic approaches for a multigenic disease. Diabetes 54, S79–S86 (2005).
Mimitou, E. P. & Symington, L. S. Sae2, Exo1 and Sgs1 collaborate in DNA double-strand break processing. Nature 455, 770–774 (2008).
Zhu, Z., Chung, W.-H., Shim, E. Y., Lee, S. E. & Ira, G. Sgs1 helicase and two nucleases Dna2 and Exo1 resect DNA double-strand break ends. Cell 134, 981–994 (2008).
Hicks, W. M., Yamaguchi, M. & Haber, J. E. Real-time analysis of double-strand DNA break repair by homologous recombination. Proc. Natl Acad. Sci. USA 108, 3108–3115 (2011).
Mehta, A. & Haber, J. E. Sources of DNA double-strand breaks and models of recombinational DNA repair. Cold Spring Harb. Perspect. Biol. 6, a016428–a016428 (2014).
Song, Y., Lai, L. & Li, Z. Large-scale genomic deletions mediated by CRISPR/Cas9 system. Oncotarget 8, 5647–5647 (2017).
Zhang, L. et al. Large genomic fragment deletions and insertions in mouse using CRISPR/Cas9. PLOS One 10, e0120396 (2015).
Hoshijima, K. et al. Highly efficient CRISPR-Cas9-based methods for generating deletion mutations and F0 embryos that lack gene function in zebrafish. Dev. Cell 51, 645–657.e4 (2019).
Zheng, Q. et al. Precise gene deletion and replacement using the CRISPR/Cas9 system in human cells. BioTechniques 57, 115–124 (2014).
Chen, X. et al. Dual sgRNA-directed gene knockout using CRISPR/Cas9 technology in Caenorhabditis elegans. Sci. Rep. 4, 7581 (2014).
Mali, P. et al. CAS9 transcriptional activators for target specificity screening and paired nickases for cooperative genome engineering. Nat. Biotechnol. 31, 833–838 (2013).
Anderson, E. M. et al. Systematic analysis of CRISPR–Cas9 mismatch tolerance reveals low levels of off-target activity. J. Biotechnol. 211, 56–65 (2015).
Zheng, T. et al. Profiling single-guide RNA specificity reveals a mismatch sensitive core sequence. Sci. Rep. 7, 40638 (2017).
Hsu, P. D. et al. DNA targeting specificity of RNA-guided Cas9 nucleases. Nat. Biotechnol. 31, 827–832 (2013).
Grainger, S. et al. CRISPR guide RNA validation in vitro. Zebrafish 14, 383–386 (2017).
Gallardo, T., Shirley, L., John, G. & Castrillon, D. H. Generation of a germ cell-specific mouse transgenic Cre line, Vasa-Cre. Genesis 45, 413–417 (2007).
Chiou, S.-H. et al. Pancreatic cancer modeling using retrograde viral vector delivery and in vivo CRISPR/Cas9-mediated somatic genome editing. Genes Dev. http://doi.org/10.1101/gad.264861.115 (2015).
Toyooka, Y. et al. Expression and intracellular localization of mouse Vasa-homologue protein during germ cell development. Mech. Dev. 93, 139–149 (2000).
Pfitzner, C. et al. Progress toward zygotic and germline gene drives in mice. CRISPR J. 3, 388–397 (2020).
Bellani, M. A., Boateng, K. A., McLeod, D. & Camerini-Otero, R. D. The expression profile of the major mouse SPO11 isoforms indicates that SPO11β introduces double strand breaks and suggests that SPO11α has an additional role in prophase in both spermatocytes and oocytes. Mol. Cell. Biol. 30, 4391–4403 (2010).
Rose, J. C. et al. Rapidly inducible Cas9 and DSB-ddPCR to probe editing kinetics. Nat. Methods 14, 891–896 (2017).
Kallimasioti-Pazi, E. M. et al. Heterochromatin delays CRISPR-Cas9 mutagenesis but does not influence the outcome of mutagenic DNA repair. PLOS Biol. 16, e2005595 (2018).
Yoshida, K. et al. The mouse RecA-like gene Dmc1 is required for homologous chromosome synapsis during meiosis. Mol. Cell 1, 707–718 (1998).
Kneitz, B. et al. MutS homolog 4 localization to meiotic chromosomes is required for chromosome pairing during meiosis in male and female mice. Genes Dev. 14, 1085–1097 (2000).
de Vries, S. S. et al. Mouse MutS-like protein Msh5 is required for proper chromosome synapsis in male and female meiosis. Genes Dev. 13, 523–531 (1999).
Yuan, L. et al. The murine SCP3 gene is required for synaptonemal complex assembly, chromosome synapsis, and male fertility. Mol. Cell 5, 73–83 (2000).
Zhang, J., Chen, L., Zhang, J. & Wang, Y. Drug inducible CRISPR/Cas systems. Comput. Struct. Biotechnol. J. 17, 1171–1177 (2019).
Maji, B. et al. Multidimensional chemical control of CRISPR-Cas9. Nat. Chem. Biol. 13, 9–11 (2017).
Byrne, S. M., Ortiz, L., Mali, P., Aach, J. & Church, G. M. Multi-kilobase homozygous targeted gene replacement in human induced pluripotent stem cells. Nucleic Acids Res 43, e21–e21 (2015).
Deng, C. & Capecchi, M. R. Reexamination of gene targeting frequency as a function of the extent of homology between the targeting vector and the target locus. Mol. Cell. Biol. 12, 3365–3371 (1992).
Beumer, K. J., Trautman, J. K., Mukherjee, K. & Carroll, D. Donor DNA utilization during gene targeting with zinc-finger nucleases. G3 (Bethesda) 3, 657–664 (2013).
Kuscu, C., Arslan, S., Singh, R., Thorpe, J. & Adli, M. Genome-wide analysis reveals characteristics of off-target sites bound by the Cas9 endonuclease. Nat. Biotechnol. 32, 677–683 (2014).
Wu, X. et al. Genome-wide binding of the CRISPR endonuclease Cas9 in mammalian cells. Nat. Biotechnol. 32, 670–676 (2014).
van Overbeek, M. et al. DNA repair profiling reveals nonrandom outcomes at Cas9-mediated breaks. Mol. Cell 63, 633–646 (2016).

Applications of and considerations for using CRISPR–Cas9-mediated gene conversion systems in rodents

Supplementary information

Reporting Summary

推荐阅读