MitoScribe single-cell molecular recorder logs graded signaling dynamics into mitochondrial DNA

Area of Science:

• Molecular Biology
• Genetics
• Cell Biology

Background:

• Genetically encoded DNA recorders capture transient biological events as genomic mutations.
• Existing DNA-based recorders have limited capacity for quantifying signal magnitude within single cells.

Purpose of the Study:

• To introduce MitoScribe, a mitochondrial DNA (mtDNA)-based platform for high-capacity recording of biological signals.
• To enable sensitive, non-destructive, and durable measurement of molecular signals within individual cells.

Main Methods:

• Utilized mitochondrial DNA (mtDNA) base editors (DdCBEs) to introduce neutral single-nucleotide substitutions into mtDNA.
• Leveraged the high copy number of mtDNA per cell for signal amplification and recording.
• Integrated MitoScribe with single-cell RNA sequencing and mitochondrial transcript enrichment.

Main Results:

• MitoScribe demonstrated reproducible, sensitive, and high-throughput recording of molecular signals like hypoxia and various signaling pathways.
• Enabled multiplexed recording of independent signals and coincidence detection of overlapping signals.
• Reconstructed single-cell signaling dynamics and linked early differentiation heterogeneity to later cell states in human iPSC differentiation.

Conclusions:

• MitoScribe offers a scalable platform for high-resolution molecular recording in complex cellular environments.
• Provides a powerful tool for studying cellular signaling dynamics and heterogeneity.
• Facilitates deeper understanding of cell fate decisions and biological processes.