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A mouse model with high clonal barcode diversity for joint lineage, transcriptomic, and epigenomic profiling in
Li Li1, Sarah Bowling1, Sean E McGeary2
1Stem Cell Program, Boston Children's Hospital, Boston, MA, USA; Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA, USA.
Cell
|October 18, 2023
Summary
We developed DARLIN, a new mouse model for tracking cell lineages. This tool enables high-resolution analysis of cell development and reveals that cellular memory is linked to DNA methylation.
Area of Science:
- Developmental Biology
- Genomics
- Stem Cell Biology
Background:
- Cellular lineage tracing is crucial for understanding tissue development and homeostasis.
- Existing lineage-recording mouse models lack the barcode diversity and single-cell resolution needed for complex tissues.
- Profiling large tissues requires advanced lineage-recording tools with high capacity.
Purpose of the Study:
- To develop an inducible Cas9 barcoding mouse line with massive lineage barcode diversity.
- To enable high-resolution lineage tracing in tissues with millions of cells.
- To investigate hematopoietic stem cell (HSC) fate bias, migration, and the molecular basis of cellular clonal memory.
Main Methods:
- Development of DARLIN (Diverse Array of Random barcoding LINeage) mouse line using inducible Cas9, terminal deoxynucleotidyl transferase (TdT), and 30 CRISPR target sites.
- Application of DARLIN for lineage tracing across various tissues, achieving barcode detection in ~70% of profiled single cells.
- Establishment of a protocol for joint transcriptomic and epigenomic single-cell measurements with DARLIN.
Main Results:
- DARLIN generates extensive lineage barcodes, facilitating deep lineage profiling.
- Analysis of developing HSCs using DARLIN revealed novel insights into fate bias and migration patterns.
- Cellular clonal memory was found to correlate with genome-wide DNA methylation, independent of gene expression or chromatin accessibility.
Conclusions:
- DARLIN significantly advances the capability for high-resolution lineage tracing in complex biological systems.
- The findings provide new understanding of HSC behavior and the epigenetic basis of cellular memory.
- DARLIN is poised to become an essential tool for studying lineage relationships and molecular signatures in diverse physiological contexts.
