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
| Autor: | Amber M. Hotto, Benoît Castandet, Arnaud Germain, David B. Stern |
|---|---|
| Přispěvatelé: | Boyce Thompson Institute [Ithaca], Institut des Sciences des Plantes de Paris-Saclay (IPS2 (UMR_9213 / UMR_1403)), Institut National de la Recherche Agronomique (INRA)-Université Paris-Sud - Paris 11 (UP11)-Université Paris Diderot - Paris 7 (UPD7)-Université d'Évry-Val-d'Essonne (UEVE)-Centre National de la Recherche Scientifique (CNRS), United States Department of Energy (DOE) DE-FG02-10ER20015LabEx Saclay Plant Sciences-SPS ANR-10-LABX-0040SPS |
| Jazyk: | angličtina |
| Rok vydání: | 2019 |
| Předmět: |
0106 biological sciences
Small RNA Chloroplasts Polynucleotide Phosphorylase DNA Plant Noncoding Rnas Arabidopsis RNA-binding protein Computational biology Biology Pentatricopeptide Repeat Protein 01 natural sciences Protein Structure Secondary Transcriptome Genomic Imprinting 03 medical and health sciences Transcription (biology) Genetics Coding region Deprivation Response [SDV.BBM]Life Sciences [q-bio]/Biochemistry Molecular Biology Polynucleotide phosphorylase Gene-expression RNA and RNA-Protein Complexes 030304 developmental biology 0303 health sciences Arabidopsis Proteins Psbn Gene Intron High-Throughput Nucleotide Sequencing RNA-Binding Proteins RNA Promoter Sequence Analysis DNA Plastid Sigma-factor Plants Genetically Modified biology.organism_classification Messenger-rna Transcription Initiation Site Coding Region 010606 plant biology & botany |
| Zdroj: | Nucleic Acids Research Nucleic Acids Research, Oxford University Press, 2019, 47 (22), pp.11889-11905. ⟨10.1093/nar/gkz1059⟩ Nucleic Acids Research, 2019, 47 (22), pp.11889-11905. ⟨10.1093/nar/gkz1059⟩ |
| ISSN: | 0305-1048 1362-4962 |
| DOI: | 10.1093/nar/gkz1059⟩ |
| Popis: | 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. UsingArabidopsis thalianaas a model, we catalogued >215 primary 5’ ends corresponding to transcription start sites (TSS), as well as 1,628 processed 5’ ends and 1,299 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 forpnp1-1, a mutant lacking the processing enzyme polynucleotide phosphorylase. Nearly 2,000 termini were altered inpnp1-1, 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. |
| Databáze: | OpenAIRE |
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