ArticleNature communications2022
Massively parallel characterization of engineered transcript isoforms using direct RNA sequencing.
Article in Nature communications, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 21 papers.
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Who cites it
21 citing papers in PubMed.
- Cross-domain signal grammars of transcription termination.Advanced biotechnology · 2026Review
- Nanopore direct RNA sequencing and the epitranscriptome: Advances in mapping native RNA landscapes.iMeta · 2026Review
- Evaluation of synthetic post-transcription regulatory sequences reveals design principle to enhance mRNA stability and translation efficiency.Synthetic and systems biotechnology · 2026Article
- Tunable gene expression in zebrafish using RiboSCALE.bioRxiv : the preprint server for biology · 2026Article
- Analysis and control of untemplated DNA polymerase activity for guided synthesis of kilobase-scale DNA sequences.Nature communications · 2026Article
- The Japan-UK Synthetic Biology Conference, Spring 2025: Strengthening Global Links to Engineer Biology.ACS synthetic biology · 2025Article
- Characterization of bacterial intrinsic transcription terminators identified with TERMITe-a novel method for comprehensive analysis of Term-seq data.Nucleic acids research · 2025Article
- AND Logic Based on Suppressor tRNAs Enables Stringent Control of Sliding Base Editors inACS synthetic biology · 2024Article
- CryptKeeper: a negative design tool for reducing unintentional gene expression in bacteria.bioRxiv : the preprint server for biology · 2024Article
- Measuring the burden of hundreds of BioBricks defines an evolutionary limit on constructability in synthetic biology.Nature communications · 2024Article
- Transfer learning for cross-context prediction of protein expression from 5'UTR sequence.Nucleic acids research · 2024Article
- Characterization of bacterial intrinsic transcription terminators identified with TERMITe - a novel method for comprehensive analysis of Term-seq data.bioRxiv : the preprint server for biology · 2024Article
- Engineering is evolution: a perspective on design processes to engineer biology.Nature communications · 2024Article
- Nanoporous Amorphous Carbon Monolayer Derived from Fullerene Film.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2024Article
- CryptKeeper: a negative design tool for reducing unintentional gene expression in bacteria.Synthetic biology (Oxford, England) · 2024Article
- Data hazards in synthetic biology.Synthetic biology (Oxford, England) · 2024Review
- Effective design and inference for cell sorting and sequencing based massively parallel reporter assays.Bioinformatics (Oxford, England) · 2023Article
- Accuracy and data efficiency in deep learning models of protein expression.Nature communications · 2022Article
- Hypermutation of specific genomic loci of Pseudomonas putida for continuous evolution of target genes.Microbial biotechnology · 2022Article
- Development of ONT-cappable-seq to unravel the transcriptional landscape ofComputational and structural biotechnology journal · 2022Article
Corrections and comments
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Authors and funding
2 authors.
Funding
Abstract
Transcriptional terminators signal where transcribing RNA polymerases (RNAPs) should halt and disassociate from DNA. However, because termination is stochastic, two different forms of transcript could be produced: one ending at the terminator and the other reading through. An ability to control the abundance of these transcript isoforms would offer bioengineers a mechanism to regulate multi-gene constructs at the level of transcription. Here, we explore this possibility by repurposing terminators as 'transcriptional valves' that can tune the proportion of RNAP read-through. Using one-pot combinatorial DNA assembly, we iteratively construct 1780 transcriptional valves for T7 RNAP and show how nanopore-based direct RNA sequencing (dRNA-seq) can be used to characterize entire libraries of valves simultaneously at a nucleotide resolution in vitro and unravel genetic design principles to tune and insulate termination. Finally, we engineer valves for multiplexed regulation of CRISPR guide RNAs. This work provides new avenues for controlling transcription and demonstrates the benefits of long-read sequencing for exploring complex sequence-function landscapes.
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