ArticleNature communications2018
SMRT-Cappable-seq reveals complex operon variants in bacteria.
Article in Nature communications, 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 72 papers.
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Who cites it
72 citing papers in PubMed, 111 citations in OpenAlex.
- Cross-domain signal grammars of transcription termination.Advanced biotechnology · 2026Review
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- A transcription unit based systems biology study onFrontiers in microbiology · 2026Article
- How Klebsiella pneumoniae controls its virulence.PLoS pathogens · 2025Review
- Analysis of 3'-seq data from multiplebioRxiv : the preprint server for biology · 2025Article
- RIBOSS detects novel translational events by combining long- and short-read transcriptome and translatome profiling.Briefings in bioinformatics · 2025Article
- BacTermFinder: a comprehensive and general bacterial terminator finder using a CNN ensemble.NAR genomics and bioinformatics · 2025Article
- Cappable-seq RNA-sequencing data sets ofMicrobiology resource announcements · 2025Article
- An optimized protocol for quality control of gene therapy vectors using nanopore direct RNA sequencing.Genome research · 2024Article
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- Signal recognition particle RNA is critical for genetic competence and virulence ofJournal of bacteriology · 2024Article
- Analysis of bacterial transcriptome and epitranscriptome using nanopore direct RNA sequencing.Nucleic acids research · 2024Article
- Transformers and large language models in healthcare: A review.Artificial intelligence in medicine · 2024Review
- Co-transcriptional gene regulation in eukaryotes and prokaryotes.Nature reviews. Molecular cell biology · 2024Review
- Synthetic genomes unveil the effects of synonymous recoding.bioRxiv : the preprint server for biology · 2024Article
- The read-through transcription-mediated autoactivation circuit for virulence regulator expression drives robust type III secretion system 2 expression in Vibrio parahaemolyticus.PLoS pathogens · 2024Article
- Exploring the transcriptional landscape of phage-host interactions using novel high-throughput approaches.Current opinion in microbiology · 2024Review
12 more citing papers are in PubMed but not listed here.
Corrections and comments
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Authors and funding
4 authors at 2 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Current methods for genome-wide analysis of gene expression require fragmentation of original transcripts into small fragments for short-read sequencing. In bacteria, the resulting fragmented information hides operon complexity. Additionally, in vivo processing of transcripts confounds the accurate identification of the 5' and 3' ends of operons. Here we develop a methodology called SMRT-Cappable-seq that combines the isolation of un-fragmented primary transcripts with single-molecule long read sequencing. Applied to E. coli, this technology results in an accurate definition of the transcriptome with 34% of known operons from RegulonDB being extended by at least one gene. Furthermore, 40% of transcription termination sites have read-through that alters the gene content of the operons. As a result, most of the bacterial genes are present in multiple operon variants reminiscent of eukaryotic splicing. By providing such granularity in the operon structure, this study represents an important resource for the study of prokaryotic gene network and regulation.
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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.