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

Supplementary information

Reporting Summary

Genetic manipulation and immortalized culture of ex vivo primary human germinal center B cells

The cell-line-derived subcutaneous tumor model in preclinical cancer research

Subcellular patch-clamp techniques for single-bouton stimulation and simultaneous pre- and postsynaptic recording at cortical synapses

NovoSpaRc: flexible spatial reconstruction of single-cell gene expression with optimal transport

Genome-wide pooled CRISPR screening in neurospheres

High-throughput cultivation and identification of bacteria from the plant root microbiota

Viral crosslinking and solid-phase purification enables discovery of ribonucleoprotein complexes on incoming RNA virus genomes

Mitochondrial single-cell ATAC-seq for high-throughput multi-omic detection of mitochondrial genotypes and chromatin accessibility

Addendum: Micro-CT acquisition and image processing to track and characterize pulmonary nodules in mice

Multiplexed single-cell proteomics using SCoPE2

查看全部

Sections

Figures

References

Supplementary information

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)

Supplementary information

推荐阅读