ArticleG3 (Bethesda, Md.)2011
Unexpected Diversity of Chloroplast Noncoding RNAs as Revealed by Deep Sequencing of the Arabidopsis Transcriptome.
Article in G3 (Bethesda, Md.), 2011. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 40 papers.
What it found
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
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Who cites it
40 citing papers in PubMed, 97 citations in OpenAlex.
- Comparative genomics uncovers organellar genome structural divergence in Caryophyllales and reveals widespread non-coding transcription in Bougainvillea glabra organellar.BMC genomics · 2025Article
- The landscape of Arabidopsis tRNA aminoacylation.The Plant journal : for cell and molecular biology · 2024Article
- DiffSegR: an RNA-seq data driven method for differential expression analysis using changepoint detection.NAR genomics and bioinformatics · 2023Article
- Chloroplast gene expression: Recent advances and perspectives.Plant communications · 2023Review
- Plant organellar RNA maturation.The Plant cell · 2023Review
- Review
- Does IR-loss promote plastome structural variation and sequence evolution?Frontiers in plant science · 2022Article
- Pervasive transcription of the mitochondrial genome inRNA biology · 2021Article
- Inverse regulation of light harvesting and photoprotection is mediated by a 3'-end-derived sRNA in cyanobacteria.The Plant cell · 2021Article
- Noncoding RNA: An Insight into Chloroplast and Mitochondrial Gene Expressions.Life (Basel, Switzerland) · 2021Review
- Tight association of genome rearrangements with gene expression in conifer plastomes.BMC plant biology · 2021Article
- Organellar and Secretory Ribonucleases: Major Players in Plant RNA Homeostasis.Plant physiology · 2020Article
- Chloroplast-to-nucleus retrograde signalling controls intercellular trafficking via plasmodesmata formation.Philosophical transactions of the Royal Society of London. Series B, Biological sciences · 2020Article
- Plant Ribonuclease J: An Essential Player in Maintaining Chloroplast RNA Quality Control for Gene Expression.Plants (Basel, Switzerland) · 2020Review
- A Single Cell but Many Different Transcripts: A Journey into the World of Long Non-Coding RNAs.International journal of molecular sciences · 2020Review
- Variation in plastid genomes in the gynodioecious species Silene vulgaris.BMC plant biology · 2019Article
- Systematic sequencing of chloroplast transcript termini from Arabidopsis thaliana reveals >200 transcription initiation sites and the extensive imprints of RNA-binding proteins and secondary structures.Nucleic acids research · 2019Article
- Multifarious Evolutionary Pathways of a Nuclear RNA Editing Factor: Disjunctions in Coevolution of DOT4 and Its Chloroplast Target rpoC1eU488SL.Genome biology and evolution · 2019Article
- Article
- RNase E and the High-Fidelity Orchestration of RNA Metabolism.Microbiology spectrum · 2018Review
Corrections and comments
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Authors and funding
5 authors at 3 institutions in 2 countries.
Funding
Abstract
Noncoding RNAs (ncRNA) are widely expressed in both prokaryotes and eukaryotes. Eukaryotic ncRNAs are commonly micro- and small-interfering RNAs (18-25 nt) involved in posttranscriptional gene silencing, whereas prokaryotic ncRNAs vary in size and are involved in various aspects of gene regulation. Given the prokaryotic origin of organelles, the presence of ncRNAs might be expected; however, the full spectrum of organellar ncRNAs has not been determined systematically. Here, strand-specific RNA-Seq analysis was used to identify 107 candidate ncRNAs from Arabidopsis thaliana chloroplasts, primarily encoded opposite protein-coding and tRNA genes. Forty-eight ncRNAs were shown to accumulate by RNA gel blot as discrete transcripts in wild-type (WT) plants and/or the pnp1-1 mutant, which lacks the chloroplast ribonuclease polynucleotide phosphorylase (cpPNPase). Ninety-eight percent of the ncRNAs detected by RNA gel blot had different transcript patterns between WT and pnp1-1, suggesting cpPNPase has a significant role in chloroplast ncRNA biogenesis and accumulation. Analysis of materials deficient for other major chloroplast ribonucleases, RNase R, RNase E, and RNase J, showed differential effects on ncRNA accumulation and/or form, suggesting specificity in RNase-ncRNA interactions. 5' end mapping demonstrates that some ncRNAs are transcribed from dedicated promoters, whereas others result from transcriptional read-through. Finally, correlations between accumulation of some ncRNAs and the symmetrically transcribed sense RNA are consistent with a role in RNA stability. Overall, our data suggest that this extensive population of ncRNAs has the potential to underpin a previously underappreciated regulatory mode in the chloroplast.
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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.