ArticleNucleic acids research2019
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.
Article in Nucleic acids research, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 17 papers.
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Who cites it
17 citing papers in PubMed.
- A poly(A)-independent PacBio strategy for organellar transcriptome profiling.Plant physiology · 2026Article
- Landscape of plastid DNA breaks in Arabidopsis during development and environmental stimulus.The Plant cell · 2026Article
- The GT1 domain of RNase J ensures RNA quality control through dsRNA binding in Arabidopsis plastids.Nucleic acids research · 2026Article
- The chloroplast RNA-binding protein CP29A supportsProceedings of the National Academy of Sciences of the United States of America · 2025Article
- The landscape of Arabidopsis tRNA aminoacylation.The Plant journal : for cell and molecular biology · 2024Article
- 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
- The Use of Nanopore Sequencing to Analyze the Chloroplast Transcriptome Part I: Library Preparation.Methods in molecular biology (Clifton, N.J.) · 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
- High-resolution map of plastid-encoded RNA polymerase binding patterns demonstrates a major role of transcription in chloroplast gene expression.The Plant journal : for cell and molecular biology · 2022Article
- Full Length Transcriptome Highlights the Coordination of Plastid Transcript Processing.International journal of molecular sciences · 2021Article
- In vivo stabilization of endogenous chloroplast RNAs by customized artificial pentatricopeptide repeat proteins.Nucleic acids research · 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
- 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
- Organellar and Secretory Ribonucleases: Major Players in Plant RNA Homeostasis.Plant physiology · 2020Article
- Plant Ribonuclease J: An Essential Player in Maintaining Chloroplast RNA Quality Control for Gene Expression.Plants (Basel, Switzerland) · 2020Review
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4 authors.
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Abstract
Chloroplast transcription requires numerous quality control steps to generate the complex but selective mixture of accumulating RNAs. To gain insight into how this RNA diversity is achieved and regulated, we systematically mapped transcript ends by developing a protocol called Terminome-seq. Using Arabidopsis thaliana as a model, we catalogued >215 primary 5' ends corresponding to transcription start sites (TSS), as well as 1628 processed 5' ends and 1299 3' ends. While most termini were found in intergenic regions, numerous abundant termini were also found within coding regions and introns, including several major TSS at unexpected locations. A consistent feature was the clustering of both 5' and 3' ends, contrasting with the prevailing description of discrete 5' termini, suggesting an imprecision of the transcription and/or RNA processing machinery. Numerous termini correlated with the extremities of small RNA footprints or predicted stem-loop structures, in agreement with the model of passive RNA protection. Terminome-seq was also implemented for pnp1-1, a mutant lacking the processing enzyme polynucleotide phosphorylase. Nearly 2000 termini were altered in pnp1-1, revealing a dominant role in shaping the transcriptome. In summary, Terminome-seq permits precise delineation of the roles and regulation of the many factors involved in organellar transcriptome quality control.
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