MIC-Drop-seq: scalable single-cell phenotyping of mutant vertebrate embryos

Area of Science:

• Developmental Biology
• Genomics
• Systems Biology

Background:

• Pooled perturbation screens are valuable for understanding cellular regulatory networks.
• Scaling these screens for whole-animal studies, especially in complex organisms, presents significant technical hurdles.

Purpose of the Study:

• To introduce MIC-Drop-seq, a novel technique enabling high-throughput genetic screening in zebrafish embryos.
• To demonstrate the utility of MIC-Drop-seq for dissecting gene regulatory networks and developmental processes at single-cell resolution.

Main Methods:

• MIC-Drop-seq combines CRISPR gene disruption with multiplexed single-cell RNA sequencing (scRNA-seq) in zebrafish embryos.
• The method allows simultaneous assessment of gene expression changes and cell abundance across numerous cell types following genetic perturbations.

Main Results:

• A single MIC-Drop-seq experiment identified phenotypes for 50 transcription factors across 74 cell types.
• The study confirmed known transcription factor roles and discovered new functions in brain and mesoderm development.
• Cell-extrinsic phenotypes were abundant, revealing widespread cell-to-cell communication in developmental regulation.

Conclusions:

• MIC-Drop-seq overcomes scalability challenges for whole-animal genetic screens.
• The technique provides insights into cell-extrinsic effects of gene perturbations, crucial for understanding developmental networks.
• MIC-Drop-seq is poised to accelerate the dissection of gene regulatory networks governing animal development.