PUBLICATION
Endogenous CRISPR/Cas9 arrays for scalable whole-organism lineage tracing
- Authors
- Cotterell, J., Vila-Cejudo, M., Batlle-Morera, L., Sharpe, J.
- ID
- ZDB-PUB-200514-2
- Date
- 2020
- Source
- Development (Cambridge, England) 147(9): (Journal)
- Registered Authors
- Keywords
- CRISPR, Human, Lineage Tracing, Mouse, Zebrafish
- MeSH Terms
-
- CRISPR-Cas Systems/genetics*
- Zebrafish
- Mice
- Gene Editing/methods
- Clustered Regularly Interspaced Short Palindromic Repeats/genetics
- Mutation/genetics
- Animals
- Genetic Engineering
- Phylogeny
- PubMed
- 32398353 Full text @ Development
Citation
Cotterell, J., Vila-Cejudo, M., Batlle-Morera, L., Sharpe, J. (2020) Endogenous CRISPR/Cas9 arrays for scalable whole-organism lineage tracing. Development (Cambridge, England). 147(9).
Abstract
The past decade has seen a renewed appreciation of the central importance of cellular lineages to many questions in biology (especially organogenesis, stem cells and tumor biology). This has been driven in part by a renaissance in genetic clonal-labeling techniques. Recent approaches are based on accelerated mutation of DNA sequences, which can then be sequenced from individual cells to re-create a 'phylogenetic' tree of cell lineage. However, current approaches depend on making transgenic alterations to the genome in question, which limit their application. Here, we introduce a new method that completely avoids the need for prior genetic engineering, by identifying endogenous CRISPR/Cas9 target arrays suitable for lineage analysis. In both mouse and zebrafish, we identify the highest quality compact arrays as judged by equal base composition, 5' G sequence, minimal likelihood of residing in the functional genome, minimal off targets and ease of amplification. We validate multiple high-quality endogenous CRISPR/Cas9 arrays, demonstrating their utility for lineage tracing. Our pragmatically scalable technique thus can produce deep and broad lineages in vivo, while removing the dependence on genetic engineering.
Genes / Markers
Expression
Phenotype
Mutations / Transgenics
Human Disease / Model
Sequence Targeting Reagents
Fish
Orthology
Engineered Foreign Genes
Mapping