Simultaneous lineage tracing and cell-type identification using CRISPR-Cas9-induced genetic scars

Area of Science:

• Developmental Biology
• Genomics
• Cell Biology

Background:

• Understanding cell differentiation from a single cell into a complex organism is a central goal in developmental biology.
• Single-cell RNA sequencing (scRNA-seq) is vital for cataloging cell types within tissues.
• A significant challenge lies in organizing these cell types into developmental lineage trees.

Purpose of the Study:

• To develop a method for simultaneous lineage tracing and transcriptome profiling in single cells.
• To reconstruct developmental lineage trees and understand cell origins.
• To provide a systematic approach for tracing cell types under various conditions.

Main Methods:

• LINNAEUS (lineage tracing by nuclease-activated editing of ubiquitous sequences) strategy.
• Combines scRNA-seq with computational analysis of lineage barcodes.
• Utilizes genome editing of transgenic reporter genes to generate barcodes.

Main Results:

• Successfully reconstructed developmental lineage trees in zebrafish larvae.
• Applied to heart, liver, pancreas, and telencephalon of adult fish.
• Demonstrated simultaneous lineage tracing and transcriptome profiling.

Conclusions:

• LINNAEUS offers a powerful tool for understanding cell development and lineage.
• Facilitates the tracing of origins for both novel and known cell types.
• Advances the study of developmental processes and cell fate determination.