ArticleNucleic acids research2025
A high-resolution view of RNA endonuclease cleavage in Bacillus subtilis.
Article in Nucleic acids research, 2025. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 16 papers.
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Who cites it
16 citing papers in PubMed.
- Long-range mRNA folding shapes expression and sequence of bacterial genes.Molecular cell · 2026Article
- High-resolution profiling of bacterial transcriptomes by SEnd-seq.The Biochemical journal · 2026Review
- Systems-level analysis predicts no autotrophy-linked protein-RNA interactions in Clostridium autoethanogenum.Nature communications · 2026Article
- Purine bias in bacterial genes is driven by runaway transcription.Nature microbiology · 2026Article
- Stress-induced ribosome degradation in Bacillus subtilis is mediated by the RNase Y-specificity complex.Nature communications · 2026Article
- Metastable Folding of Bacillus subtilis glmS Ribozyme Modulates Turnover by RNase J1.Journal of molecular biology · 2026Article
- The FsrA-Mediated Iron-Sparing Response Regulates the Biosynthesis of the Epipeptide EPE in Bacillus subtilis.Molecular microbiology · 2026Article
- Long-range mRNA folding shapes expression and sequence of bacterial genes.bioRxiv : the preprint server for biology · 2025Article
- c-di-GMP-Dependent Regulation of Motility bybioRxiv : the preprint server for biology · 2025Article
- Unconventional mRNA processing and degradation pathways for the polycistronic yrzI (spyTA) mRNA in Bacillus subtilis.FEBS letters · 2025Article
- Membrane Localization of RNase Y Is Important for Global Gene Expression inInternational journal of molecular sciences · 2024Article
- Critical factors for precise and efficient RNA cleavage by RNase Y in Staphylococcus aureus.PLoS genetics · 2024Article
- Interplay of two small RNAs fine-tunes hierarchical flagella gene expression in Campylobacter jejuni.Nature communications · 2024Article
- Methodologies for bacterial ribonuclease characterization using RNA-seq.FEMS microbiology reviews · 2023Review
- Article
- Formation of a stable RNase Y-RicT (YaaT) complex requires RicA (YmcA) and RicF (YlbF).bioRxiv : the preprint server for biology · 2023Article
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8 authors.
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Abstract
RNA endonucleases are the rate-limiting initiator of decay for many bacterial mRNAs. However, the positions of cleavage and their sequence determinants remain elusive even for the well-studied Bacillus subtilis. Here we present two complementary approaches-transcriptome-wide mapping of endoribonucleolytic activity and deep mutational scanning of RNA cleavage sites-that reveal distinct rules governing the specificity among B. subtilis endoribonucleases. Detection of RNA terminal nucleotides in both 5'- and 3'-exonuclease-deficient cells revealed >103 putative endonucleolytic cleavage sites with single-nucleotide resolution. We found a surprisingly weak consensus for RNase Y targets, a contrastingly strong primary sequence motif for EndoA targets, and long-range intramolecular secondary structures for RNase III targets. Deep mutational analysis of RNase Y cleavage sites showed that the specificity is governed by many disjointed sequence features. Our results highlight the delocalized nature of mRNA stability determinants and provide a strategy for elucidating endoribonuclease specificity in vivo.
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