Developmental barcoding of whole mouse via homing CRISPR
Open accessPublished version of a preprint
Abstract
Lineage tracing in mouse using CRISPR: A homing guide RNA (hgRNA) that directs CRISPR-Cas9 to its own DNA locus can diversify its sequence and act as an expressed genetic barcode. Kalhor et al. engineered a mouse line carrying 60 independent loci of hgRNAs, thus generating a large number of unique barcodes in various embryonic and extraembryonic tissues in fully developed mice. This method demonstrates lineage tracing from the very first branches of the development tree up to organogenesis events and was used to elucidate embryonic brain patterning. Science , this issue p. eaat9804
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Direct capture of sgRNA molecules lets ECCITE-seq avoid the barcode-swapping problems reported for Perturb-seq.
“ECCITE-seq is readily applicable to any sgRNA library with the Cas9 S. pyogenes scaffold sequence and, by allowing direct capture of sgRNA molecules, overcomes documented problems of barcode swapping events observed with Perturb-seq that have the potential to confound single cell perturbation screens17–20.”
From Multiplexed detection of proteins, transcriptomes, clonotypes and CRISPR perturbations in single cells (2019) · cites this paper as [20]
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References 95 · Cited by 363
Research works printed but not linked: 4
- [3]Riddle DL, Blumenthal T, Meyer BJ, Priess JR, in C. elegans II 2nd edition (Cold Spring Harbor Laboratory Press, 1997). 21413221
- [29]Rossant J, Cross JC, in Mouse Development (2002), pp. 155– 180.11782409
- [35]Molnár Z, Price DJ, in Kaufman’s Atlas of Mouse Development Supplement (Elsevier, 2016), pp. 239– 252.
- [61]Church G, Marblestone A, Kalhor R, in The Future of the Brain, Marcus G, Freeman J, Eds. (Princeton University Press, 2014), pp. 50– 64.
- Authors
- Kalhor, R., Kalhor, K., Mejia, L., Leeper, K., Graveline, A., Mali, P., & Church, G. M.
- Affiliations
- Harvard University (US)
- Sharif University of Technology (IR)
- University of California San Diego (US)
- Corresponding author
- Kalhor, Reza
- Church, George M.
- ORCID
- Venue
- Science
- Published
- 2018-08-31
- Volume
- 361
- Issue
- 6405
- ISSN
- 0036-8075 (ISSN-L)
- 1095-9203
- PMC
- PMC6139672
- OpenAlex
- W2885735662
- Cited by
- 363
- References
- 95
- Citations by year
- 2026: 31 · 2025: 41 · 2024: 41 · 2023: 28 · 2022: 44 · 2021: 61 · 2020: 60 · 2019: 45 · 2018: 12
- FWCI
- 15.83
- Type
- journal article
- Language
- en
- Open access
- green
- doi.org
- Locations
- Science (publishedVersion)
- bioRxiv (Cold Spring Harbor Laboratory) (acceptedVersion)
- PubMed (publishedVersion)
- Europe PMC (PubMed Central) (acceptedVersion)
- PubMed Central (acceptedVersion)
- Funders
- National Institutes of Health (MH103910, HG005550)
- Intelligence Advanced Research Projects Activity (D16PC00008)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › CRISPR and Genetic Engineering
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Developmental Biology and Gene Regulation
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Single-cell and spatial transcriptomics
- Keywords
- mouse development, lineage reconstruction
- MeSH terms
- RNA, Guide, CRISPR-Cas Systems, Alleles, Animals, Mutation, RNA, Guide, Kinetoplastida, Cell Lineage, Gene Expression Profiling, Embryonic Development, Mice, Embryonic Stem Cells, CRISPR-Cas Systems
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