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Related Concept Videos

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Bacteria and archaea are susceptible to viral infections just like eukaryotes; therefore, they have developed a unique adaptive immune system to protect themselves. Clustered regularly interspaced short palindromic repeats and CRISPR-associated proteins (CRISPR-Cas) are present in more than 45% of known bacteria and 90% of known archaea.
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Updated: May 3, 2026

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Using CRISPR barcoding as a molecular clock to capture dynamic processes at single-cell resolution.

Yolanda Andres-Lopez1,2, Alice Santambrogio3,4, Ioannis Kafetzopoulos3,4

  • 1Instituto de Biología Molecular de Barcelona, Consejo Superior de Investigaciones Científicas (IBMB-CSIC), 08028 Barcelona, Spain.

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|May 1, 2026
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Summary
This summary is machine-generated.

Researchers developed scDynaBar, a new method using CRISPR-Cas9 dynamic barcoding and single-cell sequencing to track cellular events over time. This molecular clock approach reveals the transient nature of two-cell-like states in stem cells.

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Area of Science:

  • Single-cell biology
  • Molecular biology
  • Genetics

Background:

  • Biological processes are dynamic, but tracking temporal changes at the single-cell level is challenging.
  • Existing methods for capturing cellular dynamics are limited in scope and resolution.
  • Understanding dynamic cellular transitions is crucial for developmental biology and disease research.

Purpose of the Study:

  • To introduce scDynaBar, a novel method combining CRISPR-Cas9 dynamic barcoding with single-cell sequencing.
  • To establish a molecular clock within individual cells to record the timing of cellular events.
  • To demonstrate the utility of scDynaBar in tracking dynamic cellular transitions.

Main Methods:

  • CRISPR-Cas9 dynamic barcoding to generate time-dependent genetic barcodes.
  • Single-cell RNA sequencing to capture both transcriptome and barcode sequences.
  • Analysis of barcode sequence divergence to infer the timing of cellular events.
  • Application in mouse embryonic stem cells (mESCs) and a mouse gastruloid model.

Main Results:

  • scDynaBar successfully tracks temporal changes in biological systems.
  • Evidence for the transient nature of the two-cell (2C)-like state in mESCs was provided.
  • Consistent mutation rates of dynamic barcodes were observed across diverse cell types.
  • The method demonstrated applicability beyond mESCs, including in a mouse gastruloid model.

Conclusions:

  • scDynaBar offers a powerful new tool for studying single-cell dynamics and temporal processes.
  • The dynamic barcoding approach can serve as a molecular clock for recording cellular history.
  • This technology opens new avenues for investigating transient cellular states and developmental trajectories.
  • scDynaBar has broad applicability across various biological systems and research questions.