ArticleNucleic acids research2012
Short non-coding RNA fragments accumulating in chloroplasts: footprints of RNA binding proteins?
Article in Nucleic acids research, 2012. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 68 papers.
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Who cites it
68 citing papers in PubMed.
- Expanding the palette of cis-elements to tune the expression of chloroplast transgenes in tobacco.The Plant journal : for cell and molecular biology · 2026Article
- Pentatricopeptide repeat proteins in crops: Advances in functional mechanisms and breeding applications.Journal of integrative plant biology · 2026Review
- Bundle sheath cell-specific expression of chloroplast genes encoding subunits of the NADH dehydrogenase-like complex in maize.The Plant journal : for cell and molecular biology · 2025Article
- High Conservation of Translation-Enabling RNA Editing Sites in Hyper-editing Ferns Implies They Are Not Selectively Neutral.Molecular biology and evolution · 2025Article
- Pentatricopeptide repeat proteins in plants: Cellular functions, action mechanisms, and potential applications.Plant communications · 2025Review
- The chloroplast RNA-binding protein CP29A supportsProceedings of the National Academy of Sciences of the United States of America · 2025Article
- Applications of Synthetic Pentatricopeptide Repeat Proteins.Plant & cell physiology · 2024Review
- The Use of Nanopore Sequencing to Analyze the Chloroplast Transcriptome Part II: Bioinformatic Analyzes and Virtual RNA Blots.Methods in molecular biology (Clifton, N.J.) · 2024Article
- Interplay of endonucleolytic and exonucleolytic processing in the 3'-end formation of a mitochondrial nad2 RNA precursor in Arabidopsis.Nucleic acids research · 2023Article
- Plant organellar RNA maturation.The Plant cell · 2023Review
- A CRR2-Dependent sRNA Sequence Supports Papillomavirus Vaccine Expression in Tobacco Chloroplasts.Metabolites · 2023Article
- Progress, challenge and prospect of plant plastome annotation.Frontiers in plant science · 2023Review
- Plant mitochondrial RNA editing factors can perform targeted C-to-U editing of nuclear transcripts in human cells.Nucleic acids research · 2022Article
- Pentatricopeptide repeat protein MITOCHONDRIAL STABILITY FACTOR 3 ensures mitochondrial RNA stability and embryogenesis.Plant physiology · 2022Article
- Natural Selection Shapes Maintenance of Orthologous sRNAs in Divergent Host-Restricted Bacterial Genomes.Molecular biology and evolution · 2021Article
- In vivo stabilization of endogenous chloroplast RNAs by customized artificial pentatricopeptide repeat proteins.Nucleic acids research · 2021Article
- Arabidopsis Mitochondrial Transcription Termination Factor mTERF2 Promotes Splicing of Group IIB Introns.Cells · 2021Article
- Noncoding RNA: An Insight into Chloroplast and Mitochondrial Gene Expressions.Life (Basel, Switzerland) · 2021Review
- The Arabidopsis mTERF-repeat MDA1 protein plays a dual function in transcription and stabilization of specific chloroplast transcripts within the psbE and ndhH operons.The New phytologist · 2020Article
- The OPR Protein MTHI1 Controls the Expression of Two Different Subunits of ATP Synthase CFo inThe Plant cell · 2020Article
8 more citing papers are in PubMed but not listed here.
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Authors and funding
2 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Chloroplast RNA metabolism is controlled and excecuted by hundreds of nuclear-encoded, chloroplast-localized RNA binding proteins. Contrary to the nucleo-cytosolic compartment or bacteria, there is little evidence for non-coding RNAs that play a role as riboregulators of chloroplasts. We mined deep-sequencing datasets to identify short (16-28 nt) RNAs in the chloroplast genome and found 50 abundant small RNAs (sRNAs) represented by multiple, in some cases, thousands of sequencing reads, whereas reads are in general absent from the surrounding sequence space. Other than sRNAs representing the most highly abundant mRNAs, tRNAs and rRNAs, most sRNAs are located in non-coding regions and many are found a short distance upstream of start codons. By transcript end mapping we show that the 5' and 3' termini of chloroplast RNAs coincide with the ends of sRNAs. Sequences of sRNAs identified in Arabidopsis are conserved between different angiosperm species and in several cases, we identified putative orthologs in rice deep sequencing datasets. Recently, it was suggested that small chloroplast RNA fragments could result from the protective action of pentatricopeptide repeat (PPR) proteins against exonucleases, i.e. footprints of RNA binding proteins. Our data support this scenario on a transcriptome-wide level and suggest that a large number of sRNAs are in fact remnants of PPR protein targets.
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