ArticleThe Plant cell2012
The primary transcriptome of barley chloroplasts: numerous noncoding RNAs and the dominating role of the plastid-encoded RNA polymerase.
Article in The Plant cell, 2012. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 136 papers.
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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
136 citing papers in PubMed, 275 citations in OpenAlex.
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- Landscape of plastid DNA breaks in Arabidopsis during development and environmental stimulus.The Plant cell · 2026Article
- Comparative Chloroplast Genomics of Sugar Beet and Wild Relatives: Insights into Photosystem Gene Regulation and Stress Tolerance.Functional & integrative genomics · 2026Article
- The evolutionary path of widespread IR heteroplasmy of chloroplast genomes in the context of Rhodophyta phylogeny.Journal of molecular evolution · 2026Article
- Plastome evolution and phylogenomics of Glycine (Leguminosae: Papilionoideae).BMC plant biology · 2026Article
- A red/blue optoswitch for temporal control of chloroplast transcription and biogenesis in Arabidopsis.Nature communications · 2026Article
- Gene loss and positively selected genes in chloroplast genomes reveal adaptive evolution in Styracaceae.BMC plant biology · 2026Article
- The GT1 domain of RNase J ensures RNA quality control through dsRNA binding in Arabidopsis plastids.Nucleic acids research · 2026Article
- Identification of a Chlorophyll-Deficient Mutant in Maize Associated with Exogenous Vector Insertion.Plants (Basel, Switzerland) · 2026Article
- Membranous Interacting Partners of Phage-Type Plastid RNA Polymerase Have Limited Impact on Plastid Gene Expression During Chloroplast Development.Plant direct · 2026Article
- 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
- OsFLN2 gene knockout reduces leaf water status and photosynthetic performance of rice plants under water deficit.BMC plant biology · 2025Article
- Article
- Regreening mechanisms in cucumber: insights from a CsSIG2 mutation affecting chloroplast development.TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik · 2025Article
- OsPRDA1 Interacts With OsFSD2 To Promote Chloroplast Development by Regulating Chloroplast Gene Expression in Rice.Rice (New York, N.Y.) · 2025Article
- Comparative chloroplast genome analyses ofFrontiers in plant science · 2025Article
- Comparative analyses of chloroplast genomes inFrontiers in plant science · 2025Article
- Architecture of the spinach plastid-encoded RNA polymerase.Nature communications · 2024Article
76 more citing papers are in PubMed but not listed here.
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Authors and funding
6 authors at 2 institutions in 2 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Gene expression in plastids of higher plants is dependent on two different transcription machineries, a plastid-encoded bacterial-type RNA polymerase (PEP) and a nuclear-encoded phage-type RNA polymerase (NEP), which recognize distinct types of promoters. The division of labor between PEP and NEP during plastid development and in mature chloroplasts is unclear due to a lack of comprehensive information on promoter usage. Here, we present a thorough investigation into the distribution of PEP and NEP promoters within the plastid genome of barley (Hordeum vulgare). Using a novel differential RNA sequencing approach, which discriminates between primary and processed transcripts, we obtained a genome-wide map of transcription start sites in plastids of mature first leaves. PEP-lacking plastids of the albostrians mutant allowed for the unambiguous identification of NEP promoters. We observed that the chloroplast genome contains many more promoters than genes. According to our data, most genes (including genes coding for photosynthesis proteins) have both PEP and NEP promoters. We also detected numerous transcription start sites within operons, indicating transcriptional uncoupling of genes in polycistronic gene clusters. Moreover, we mapped many transcription start sites in intergenic regions and opposite to annotated genes, demonstrating the existence of numerous noncoding RNA candidates.
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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.