Engineering megabase-sized genomic deletions with MACHETE (Molecular Alteration of Chromosomes with Engineered Tandem Elements)

Francisco M. Barriga, Scott W. Lowe

Published: 2024-02-07 DOI: 10.1038/s41596-024-00953-9

CRISPR-Cas9

MACHETE

genomic deletions

selection cassette

site-specific nucleases

AI 解读

CRISPR-Combo–mediated orthogonal genome editing and transcriptional activation for plant breeding

Profiling human brain vascular cells using single-cell transcriptomics and organoids

Luciferase- and HaloTag-based reporter assays to measure small-molecule-induced degradation pathway in living cells

Publisher Correction: A reconstituted cell-free assay for the evaluation of the intrinsic activity of purified human ribosomes

RNA-extraction-free nano-amplified colorimetric test for point-of-care clinical diagnosis of COVID-19

Optimized whole-genome sequencing workflow for tumor diagnostics in routine pathology practice

Tracking endocytosis and intracellular distribution of spherical nucleic acids with correlative single-cell imaging

Optofluidic Raman-activated cell sorting for targeted genome retrieval or cultivation of microbial cells with specific functions

Desynchronizing the sleep–wake cycle from circadian timing to assess their separate contributions to physiology and behaviour and to estimate intrinsic circadian period

Imaging and optogenetic modulation of vascular mural cells in the live brain

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References

Kim, Y. G., Cha, J. & Chandrasegaran, S. Hybrid restriction enzymes: zinc finger fusions to Fok I cleavage domain. Proc. Natl Acad. Sci. USA 93, 1156–1160 (1996).
Cermak, T. et al. Efficient design and assembly of custom TALEN and other TAL effector-based constructs for DNA targeting. Nucleic Acids Res. 39, e82–e82 (2011).
Jinek, M. et al. A programmable dual-RNA–guided DNA endonuclease in adaptive bacterial immunity. Science 337, 816–821 (2012).
Wood, A. J. et al. Targeted genome editing across species using ZFNs and TALENs. Science 333, 307–307 (2011).
Miller, J. C. et al. An improved zinc-finger nuclease architecture for highly specific genome editing. Nat. Biotechnol. 25, 778–785 (2007).
Doudna, J. A. The promise and challenge of therapeutic genome editing. Nature 578, 229–236 (2020).
Joung, J. et al. Genome-scale CRISPR–Cas9 knockout and transcriptional activation screening. Nat. Protoc. 12, 828–863 (2017).
Fauser, F., Schiml, S. & Puchta, H. Both CRISPR/Cas-based nucleases and nickases can be used efficiently for genome engineering in Arabidopsis thaliana. Plant J. 79, 348–359 (2014).
Friedland, A. E. et al. Heritable genome editing in C. elegans via a CRISPR–Cas9 system. Nat. Methods 10, 741–743 (2013).
Shalem, O., Sanjana, N. E. & Zhang, F. High-throughput functional genomics using CRISPR–Cas9. Nat. Rev. Genet. 16, 299–311 (2015).
Feng, S. et al. Strategies for high-efficiency mutation using the CRISPR/Cas system. Front. Cell Dev. Biol. 9, 803252 (2022).
Varshney, G. K. et al. High-throughput gene targeting and phenotyping in zebrafish using CRISPR/Cas9. Genome Res. 25, 1030–1042 (2015).
Canver, M. C. et al. Characterization of genomic deletion efficiency mediated by clustered regularly interspaced palindromic repeats (CRISPR)/Cas9 nuclease system in mammalian cells. J. Biol. Chem. 289, 21312–21324 (2014).
Barriga, F. M. et al. MACHETE identifies interferon-encompassing chromosome 9p21.3 deletions as mediators of immune evasion and metastasis. Nat. Cancer 3, 1367–1385 (2022).
Spiliopoulou, P. et al. All is not lost: learning from 9p21 loss in cancer. Trends Immunol. 43, 379–390 (2022).
Sherr, C. J. The INK4a/ARF network in tumour suppression. Nat. Rev. Mol. Cell Biol. 2, 731–737 (2001).
Cai, Y. et al. Loss of chromosome 8p governs tumor progression and drug response by altering lipid metabolism. Cancer Cell 29, 751–766 (2016).
Carroll, D. Genome engineering with targetable nucleases. Annu. Rev. Biochem. 83, 409–439 (2014).
He, Z. et al. Highly efficient targeted chromosome deletions using CRISPR/Cas9: highly efficient targeted chromosome deletions. Biotechnol. Bioeng. 112, 1060–1064 (2015).
Boroviak, K., Doe, B., Banerjee, R., Yang, F. & Bradley, A. Chromosome engineering in zygotes with CRISPR/Cas9. Genesis 54, 78–85 (2016).
Shalem, O. et al. Genome-scale CRISPR–Cas9 knockout screening in human cells. Science 343, 84–87 (2014).
Liu, Y. et al. Deletions linked to TP53 loss drive cancer through p53-independent mechanisms. Nature 531, 471–475 (2016).
Taylor, A. M. et al. Genomic and functional approaches to understanding cancer aneuploidy. Cancer Cell 33, 676–689.e3 (2018).
Bosco, N. et al. KaryoCreate: a CRISPR-based technology to study chromosome-specific aneuploidy by targeting human centromeres. Cell 186, 1985–2001.e19 (2023).
Truong, M. A. et al. A kinesin‐based approach for inducing chromosome‐specific mis‐segregation in human cells. EMBO J. 42, e111559 (2023).
Fu, Y. et al. High-frequency off-target mutagenesis induced by CRISPR–Cas nucleases in human cells. Nat. Biotechnol. 31, 822–826 (2013).
Höijer, I. et al. CRISPR–Cas9 induces large structural variants at on-target and off-target sites in vivo that segregate across generations. Nat. Commun. 13, 627 (2022).
Perez, A. R. et al. GuideScan software for improved single and paired CRISPR guide RNA design. Nat. Biotechnol. 35, 347–349 (2017).
Schmidt, H. et al. Genome-wide CRISPR guide RNA design and specificity analysis with GuideScan2. Preprint at bioRxiv https://doi.org/10.1101/2022.05.02.490368 (2022).
Gundry, M. C. et al. Highly efficient genome editing of murine and human hematopoietic progenitor cells by CRISPR/Cas9. Cell Rep. 17, 1453–1461 (2016).
Stewart-Ornstein, J. & Lahav, G. Dynamics of CDKN1A in single cells defined by an endogenous fluorescent tagging toolkit. Cell Rep. 14, 1800–1811 (2016).

Engineering megabase-sized genomic deletions with MACHETE (Molecular Alteration of Chromosomes with Engineered Tandem Elements)

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