ArticleNature biotechnology2023
RNA recording in single bacterial cells using reprogrammed tracrRNAs.
Article in Nature biotechnology, 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 16 papers, 1 of them a synthesis that pooled it.
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Who cites it
16 citing papers in PubMed, 1 synthesis or guideline pooled it, 24 citations in OpenAlex.
- Engineering CRISPR guide RNAs for programmable RNA sensors.Biochemical Society transactions · 2023Pooled it
- Bacterial small regulatory RNAs.Nature reviews. Microbiology · 2026Review
- Bacterial surface display enables lysis-independent joint host-pathogen single-cell profiling.bioRxiv : the preprint server for biology · 2026Article
- Guide RNA reprogramming facilitates minimized tracrRNA-dependent off-target and versatile CRISPR/Cas9 engineering.Nature communications · 2026Article
- Programming Next-Generation Synthetic Biosensors by Genetic Circuit Design.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2026Review
- Bacteria as living biosensors for DNA.Nature reviews bioengineering · 2026Article
- Conditional guide RNA deactivation by mRNA and small molecule triggers in Saccharomyces cerevisiae.New biotechnology · 2025Article
- CRISPR beyond: harnessing compact RNA-guided endonucleases for enhanced genome editing.Science China. Life sciences · 2024Review
- Engineered transcription-associated Cas9 targeting in eukaryotic cells.Nature communications · 2024Article
- Toward DNA-Based Recording of Biological Processes.International journal of molecular sciences · 2024Review
- Engineered transcription-associated Cas9 targeting in eukaryotic cells.bioRxiv : the preprint server for biology · 2024Article
- TracrRNA reprogramming enables direct PAM-independent detection of RNA with diverse DNA-targeting Cas12 nucleases.Nature communications · 2024Article
- Repurposing Type I-A CRISPR-Cas3 for a robust diagnosis of human papillomavirus (HPV).Communications biology · 2024Article
- Accelerating Genetic Sensor Development, Scale-up, and Deployment Using Synthetic Biology.Biodesign research · 2024Article
- Molecular Time Capsules Enable Transcriptomic Recording in Living Cells.bioRxiv : the preprint server for biology · 2023Article
- Untangling Cellular Host-Pathogen Encounters at Infection Bottlenecks.Infection and immunity · 2023Review
Corrections and comments
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Authors and funding
9 authors at 2 institutions in 1 country.
Funding
Abstract
Capturing an individual cell's transcriptional history is a challenge exacerbated by the functional heterogeneity of cellular communities. Here, we leverage reprogrammed tracrRNAs (Rptrs) to record selected cellular transcripts as stored DNA edits in single living bacterial cells. Rptrs are designed to base pair with sensed transcripts, converting them into guide RNAs. The guide RNAs then direct a Cas9 base editor to target an introduced DNA target. The extent of base editing can then be read in the future by sequencing. We use this approach, called TIGER (transcribed RNAs inferred by genetically encoded records), to record heterologous and endogenous transcripts in individual bacterial cells. TIGER can quantify relative expression, distinguish single-nucleotide differences, record multiple transcripts simultaneously and read out single-cell phenomena. We further apply TIGER to record metabolic bet hedging and antibiotic resistance mobilization in Escherichia coli as well as host cell invasion by Salmonella. Through RNA recording, TIGER connects current cellular states with past transcriptional states to decipher complex cellular responses in single cells.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.