ArticleThe Plant journal : for cell and molecular biology2022
High-resolution map of plastid-encoded RNA polymerase binding patterns demonstrates a major role of transcription in chloroplast gene expression.
Article in The Plant journal : for cell and molecular biology, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 12 papers.
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Who cites it
12 citing papers in PubMed, 23 citations in OpenAlex.
- Landscape of plastid DNA breaks in Arabidopsis during development and environmental stimulus.The Plant cell · 2026Article
- Recombination and Retroprocessing in Broomrapes Reveal RNA-Mediated Gene Transfer Mechanism and a Generalizable Model for Mitochondrial Evolution in Heterotrophic Plants.Genome biology and evolution · 2026Article
- Membranous Interacting Partners of Phage-Type Plastid RNA Polymerase Have Limited Impact on Plastid Gene Expression During Chloroplast Development.Plant direct · 2026Article
- Regreening mechanisms in cucumber: insights from a CsSIG2 mutation affecting chloroplast development.TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik · 2025Article
- Membrane protein provision controls prothylakoid biogenesis in tobacco etioplasts.The Plant cell · 2024Article
- PAP1 and PAP7 are required for association of plastid-encoded RNA polymerase with DNA.Plant molecular biology · 2024Article
- Membrane association of active genes organizes the chloroplast nucleoid structure.Proceedings of the National Academy of Sciences of the United States of America · 2024Article
- Chloroplast gene expression: Recent advances and perspectives.Plant communications · 2023Review
- Correlated retrograde and developmental regulons implicate multiple retrograde signals as coordinators of chloroplast development in maize.The Plant cell · 2022Article
- RNA biology takes root in plant systems.Plant direct · 2022Article
- Organellar transcripts dominate the cellular mRNA pool across plants of varying ploidy levels.Proceedings of the National Academy of Sciences of the United States of America · 2022Article
- "Omics" insights into plastid behavior toward improved carotenoid accumulation.Frontiers in plant science · 2022Review
Corrections and comments
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Authors and funding
5 authors at 2 institutions in 2 countries.
Funding
Abstract
Plastids contain their own genomes, which are transcribed by two types of RNA polymerases. One of those enzymes is a bacterial-type, multi-subunit polymerase encoded by the plastid genome. The plastid-encoded RNA polymerase (PEP) is required for efficient expression of genes encoding proteins involved in photosynthesis. Despite the importance of PEP, its DNA binding locations have not been studied on the genome-wide scale at high resolution. We established a highly specific approach to detect the genome-wide pattern of PEP binding to chloroplast DNA using plastid chromatin immunoprecipitation-sequencing (ptChIP-seq). We found that in mature Arabidopsis thaliana chloroplasts, PEP has a complex DNA binding pattern with preferential association at genes encoding rRNA, tRNA, and a subset of photosynthetic proteins. Sigma factors SIG2 and SIG6 strongly impact PEP binding to a subset of tRNA genes and have more moderate effects on PEP binding throughout the rest of the genome. PEP binding is commonly enriched on gene promoters, around transcription start sites. Finally, the levels of PEP binding to DNA are correlated with levels of RNA accumulation, which demonstrates the impact of PEP on chloroplast gene expression. Presented data are available through a publicly available Plastid Genome Visualization Tool (Plavisto) at https://plavisto.mcdb.lsa.umich.edu/.
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