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High‐resolution map of plastid‐encoded RNA polymerase binding patterns demonstrates a major role of transcription in chloroplast gene expression
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 involv...
Autores principales: | , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
John Wiley and Sons Inc.
2022
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9540123/ https://www.ncbi.nlm.nih.gov/pubmed/35765883 http://dx.doi.org/10.1111/tpj.15882 |
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author | Palomar, V. Miguel Jaksich, Sarah Fujii, Sho Kuciński, Jan Wierzbicki, Andrzej T. |
author_facet | Palomar, V. Miguel Jaksich, Sarah Fujii, Sho Kuciński, Jan Wierzbicki, Andrzej T. |
author_sort | Palomar, V. Miguel |
collection | PubMed |
description | 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/. |
format | Online Article Text |
id | pubmed-9540123 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2022 |
publisher | John Wiley and Sons Inc. |
record_format | MEDLINE/PubMed |
spelling | pubmed-95401232022-10-14 High‐resolution map of plastid‐encoded RNA polymerase binding patterns demonstrates a major role of transcription in chloroplast gene expression Palomar, V. Miguel Jaksich, Sarah Fujii, Sho Kuciński, Jan Wierzbicki, Andrzej T. Plant J Original Articles 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/. John Wiley and Sons Inc. 2022-07-13 2022-08 /pmc/articles/PMC9540123/ /pubmed/35765883 http://dx.doi.org/10.1111/tpj.15882 Text en © 2022 The Authors. The Plant Journal published by Society for Experimental Biology and John Wiley & Sons Ltd. https://creativecommons.org/licenses/by-nc/4.0/This is an open access article under the terms of the http://creativecommons.org/licenses/by-nc/4.0/ (https://creativecommons.org/licenses/by-nc/4.0/) License, which permits use, distribution and reproduction in any medium, provided the original work is properly cited and is not used for commercial purposes. |
spellingShingle | Original Articles Palomar, V. Miguel Jaksich, Sarah Fujii, Sho Kuciński, Jan Wierzbicki, Andrzej T. High‐resolution map of plastid‐encoded RNA polymerase binding patterns demonstrates a major role of transcription in chloroplast gene expression |
title | High‐resolution map of plastid‐encoded RNA polymerase binding patterns demonstrates a major role of transcription in chloroplast gene expression |
title_full | High‐resolution map of plastid‐encoded RNA polymerase binding patterns demonstrates a major role of transcription in chloroplast gene expression |
title_fullStr | High‐resolution map of plastid‐encoded RNA polymerase binding patterns demonstrates a major role of transcription in chloroplast gene expression |
title_full_unstemmed | High‐resolution map of plastid‐encoded RNA polymerase binding patterns demonstrates a major role of transcription in chloroplast gene expression |
title_short | High‐resolution map of plastid‐encoded RNA polymerase binding patterns demonstrates a major role of transcription in chloroplast gene expression |
title_sort | high‐resolution map of plastid‐encoded rna polymerase binding patterns demonstrates a major role of transcription in chloroplast gene expression |
topic | Original Articles |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9540123/ https://www.ncbi.nlm.nih.gov/pubmed/35765883 http://dx.doi.org/10.1111/tpj.15882 |
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