Barcoding Notch signaling in the developing brain

Area of Science:

• Developmental Biology
• Genetics
• Neuroscience

Background:

• Developmental signaling pathways guide cell fate determination and behavior.
• Existing fluorescent reporters lack scalability and molecular resolution for cell types.
• Understanding transient signaling dynamics is crucial for mapping developmental processes.

Purpose of the Study:

• To introduce SABER-seq, a novel CRISPR-Cas molecular recorder for capturing transient developmental signals.
• To demonstrate SABER-seq's capability in recording Notch signaling in developing zebrafish brains.
• To enable high-resolution mapping of cell lineages based on historical signaling activity.

Main Methods:

• SABER-seq utilizes a CRISPR-Cas system with a signaling sensor and a barcode recorder.
• The sensor activates Cas9 in a Notch-dependent, inducible manner.
• Mutations are permanently stored in the genome, allowing later analysis via single-cell transcriptomics.

Main Results:

• SABER-seq successfully recorded Notch signaling dynamics in the developing zebrafish brain.
• Combined with a brain atlas, SABER-seq identified cell types originating from Notch-active progenitors.
• Rare instances of differential Notch activity in progenitors were detected in mature neuronal subtypes.

Conclusions:

• SABER-seq provides a scalable, high-resolution platform for mapping developmental signaling.
• This technology allows for the deconstruction of transient signaling events at later developmental stages.
• SABER-seq enhances our ability to trace cell lineage and understand signaling's role in differentiation.