ArticleDNA research : an international journal for rapid publication of reports on genes and genomes2009
Cluster analysis and comparison of various chloroplast transcriptomes and genes in Arabidopsis thaliana.
Article in DNA research : an international journal for rapid publication of reports on genes and genomes, 2009. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 21 papers.
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Who cites it
21 citing papers in PubMed.
- Sequence dynamics and plastome evolution: decoding the complete chloroplast genome of Oenothera drummondii and comparative analysis within Oenothera (Onagraceae).Functional & integrative genomics · 2025Article
- Response of the organellar and nuclear (post)transcriptomes of Arabidopsis to drought.Frontiers in plant science · 2023Article
- Ascorbate peroxidase postcold regulation of chloroplast NADPH dehydrogenase activity controls cold memory.Plant physiology · 2022Article
- Comparative Analyses of 3,654 Plastid Genomes Unravel Insights Into Evolutionary Dynamics and Phylogenetic Discordance of Green Plants.Frontiers in plant science · 2022Article
- Review
- The Chloroplast RNA Binding Protein CP31A Has a Preference for mRNAs Encoding the Subunits of the Chloroplast NAD(P)H Dehydrogenase Complex and Is Required for Their Accumulation.International journal of molecular sciences · 2020Article
- PUMPKIN, the Sole Plastid UMP Kinase, Associates with Group II Introns and Alters Their Metabolism.Plant physiology · 2019Article
- RNA-stabilization factors in chloroplasts of vascular plants.Essays in biochemistry · 2018Review
- Support vector machine classifier for prediction of the metastasis of colorectal cancer.International journal of molecular medicine · 2018Article
- Cryptochrome 2 extensively regulates transcription of the chloroplast genome in tomato.FEBS open bio · 2017Article
- Organellar Gene Expression and Acclimation of Plants to Environmental Stress.Frontiers in plant science · 2017Review
- The Coordination of Gene Expression within Photosynthesis Pathway for Acclimation of C4 Energy Crop Miscanthus lutarioriparius.Frontiers in plant science · 2016Article
- HIGH CHLOROPHYLL FLUORESCENCE145 Binds to and Stabilizes the psaA 5' UTR via a Newly Defined Repeat Motif in Embryophyta.The Plant cell · 2015Article
- PsbN is required for assembly of the photosystem II reaction center in Nicotiana tabacum.The Plant cell · 2014Article
- Pattern dynamics in adaxial-abaxial specific gene expression are modulated by a plastid retrograde signal during Arabidopsis thaliana leaf development.PLoS genetics · 2013Article
- Arabidopsis chloroplast RNA binding proteins CP31A and CP29A associate with large transcript pools and confer cold stress tolerance by influencing multiple chloroplast RNA processing steps.The Plant cell · 2012Article
- RHON1 is a novel ribonucleic acid-binding protein that supports RNase E function in the Arabidopsis chloroplast.Nucleic acids research · 2012Article
- A tiling microarray for global analysis of chloroplast genome expression in cucumber and other plants.Plant methods · 2011Article
- Intracompartmental and intercompartmental transcriptional networks coordinate the expression of genes for organellar functions.Plant physiology · 2011Article
- Recruitment of a ribosomal release factor for light- and stress-dependent regulation of petB transcript stability in Arabidopsis chloroplasts.The Plant cell · 2011Article
Corrections and comments
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3 authors.
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Abstract
Chloroplast RNA metabolism is integrated into wider gene regulatory networks. To explore how, we performed a chloroplast genome-wide expression analysis on numerous nuclear Arabidopsis mutants affected in diverse chloroplast functions and wild-type plants subjected to various stresses and conditions. On the basis of clustering analysis, plastid genes could be divided into two oppositely regulated clusters, largely congruent with known targets of nucleus- and plastid-encoded RNA polymerases, respectively. Further eight sub-clusters contained co-transcribed and functionally tightly associated genes. The chloroplast transcriptomes could also be classified into two major groups comprising mutants preferentially affected in general plastid gene expression and other chloroplast functions, respectively. Deviations from characteristic expression profiles of transcriptomes served to identify novel mutants impaired in accumulation and/or processing of specific plastid RNAs. Expression profiles were useful to distinguish albino mutants affected in plastid gene expression from those with defects in other plastid functions. Remarkably, biotic and abiotic stressors did not define transcriptionally determined clusters indicating that post-transcriptional regulation of plastid gene expression becomes more important under changing environmental conditions. Overall, the identification of sets of co-regulated genes provides insights into the integration of plastid gene expression into common pathways that ensures a coordinated response.
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