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Defining endogenous barcoding sites for CRISPR/Cas9-based cell lineage tracing in zebrafish.
Chang Ye1, Zhuoxin Chen1, Zhan Liu1
1State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, 510275, China.
Journal of Genetics and Genomics = Yi Chuan Xue Bao
|March 17, 2020
Summary
Researchers identified 78 endogenous genomic sites in zebrafish for CRISPR/Cas9 barcoding. This method enables scalable tracking of developmental cell lineages and simultaneous cell type characterization using single-cell RNA sequencing.
Area of Science:
- Developmental biology
- Genomics
- Molecular biology
Background:
- Tracking developmental cell lineages is crucial for understanding complex organisms.
- CRISPR/Cas9 barcoding shows promise but faces scalability challenges due to exogenous sequences.
- Need for efficient and scalable lineage tracing methods in model organisms.
Purpose of the Study:
- To identify and characterize endogenous genomic sites suitable for CRISPR/Cas9-based lineage barcoding in zebrafish.
- To enable scalable and simultaneous cell type and cell lineage information recovery.
Main Methods:
- Genome-wide characterization of potential barcoding sites.
- Validation using CRISPR/Cas9 technology.
- Analysis of site expression patterns using single-cell RNA sequencing (scRNA-seq) data.
Main Results:
- Identified 78 high-quality endogenous genomic sites in zebrafish for CRISPR/Cas9 barcoding.
- These sites are highly expressed across most cell types.
- Barcoding information from these sites is recoverable via scRNA-seq platforms.
Conclusions:
- The identified endogenous sites offer a scalable solution for CRISPR/Cas9-based lineage tracing in zebrafish.
- This approach facilitates simultaneous characterization of cell type and lineage information.
- Enables advanced studies in developmental biology and systems biology.
