ArticleNucleic acids research2022
Ubiquitous mRNA decay fragments in E. coli redefine the functional transcriptome.
Article in Nucleic acids research, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 26 papers.
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Who cites it
26 citing papers in PubMed.
- Long-range mRNA folding shapes expression and sequence of bacterial genes.Molecular cell · 2026Article
- Translation as a regulatory hub for secondary metabolism in Streptomyces spp.Essays in biochemistry · 2026Review
- Regulation of multiple paralogs of a small subunit ribosomal protein inRNA (New York, N.Y.) · 2026Article
- BR-bodies link RNA homeostasis to stress tolerance and intracellular fitness inbioRxiv : the preprint server for biology · 2026Article
- Dynamic partitioning shapes thebioRxiv : the preprint server for biology · 2026Article
- Identification of conserved RNA regulatory switches in living cells using RNA secondary structure ensemble mapping and covariation analysis.Nature biotechnology · 2026Article
- Developing the protein quality control system inSynthetic and systems biotechnology · 2026Article
- Structure of the 30S translation initiation complex coupled to paused RNA polymerase and its potential for riboregulation.Nature communications · 2025Article
- Long-range mRNA folding shapes expression and sequence of bacterial genes.bioRxiv : the preprint server for biology · 2025Article
- Analysis of 3'-seq data from multiplebioRxiv : the preprint server for biology · 2025Article
- A general RNA-templated RNA extension activity ofRNA (New York, N.Y.) · 2025Article
- A high-resolution view of RNA endonuclease cleavage in Bacillus subtilis.Nucleic acids research · 2025Article
- The membrane-targeting-sequence motif is required for exhibition of recessive resurrection in Escherichia coli RNase E.Nucleic acids research · 2025Article
- Improving polyketide biosynthesis by rescuing the translation of truncated mRNAs into functional polyketide synthase subunits.Nature communications · 2025Article
- Diverse intrinsic properties shape transcript stability and stabilization inNAR genomics and bioinformatics · 2024Article
- Cooperation of regulatory RNA and the RNA degradosome in transcript surveillance.Nucleic acids research · 2024Article
- Co-transcriptional gene regulation in eukaryotes and prokaryotes.Nature reviews. Molecular cell biology · 2024Review
- Article
- Differential roles of positive and negative supercoiling in organizing the E. coli genome.Nucleic acids research · 2024Article
- Molecular Time Capsules Enable Transcriptomic Recording in Living Cells.bioRxiv : the preprint server for biology · 2023Article
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4 authors.
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No grant is acknowledged in the PubMed record.
Abstract
Bacterial mRNAs have short life cycles, in which transcription is rapidly followed by translation and degradation within seconds to minutes. The resulting diversity of mRNA molecules across different life-cycle stages impacts their functionality but has remained unresolved. Here we quantitatively map the 3' status of cellular RNAs in Escherichia coli during steady-state growth and report a large fraction of molecules (median>60%) that are fragments of canonical full-length mRNAs. The majority of RNA fragments are decay intermediates, whereas nascent RNAs contribute to a smaller fraction. Despite the prevalence of decay intermediates in total cellular RNA, these intermediates are underrepresented in the pool of ribosome-associated transcripts and can thus distort quantifications and differential expression analyses for the abundance of full-length, functional mRNAs. The large heterogeneity within mRNA molecules in vivo highlights the importance in discerning functional transcripts and provides a lens for studying the dynamic life cycle of mRNAs.
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