Zea mays
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA1196818 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:Maize RNA Polymerase D1 (RPD1), the largest subunit of RNA polymerase IV (Pol IV), is required for normal plant development, repression of transposable elements (TEs), and for the regulation of specific alleles associated with TEs. Here, we define the nascent transcriptomes of rpd1 mutant and wild-type (WT) seedlings using global run-on sequencing (GRO-seq) to identify the broader targets of RPD1-based transcriptional regulation. Surprisingly, although TE-like sequences comprise >85% of the maize genome, most TEs are not transcribed at the seedling stage, even in rpd1 mutants. Profile comparisons identify the global set of genes and TEs whose transcription is altered in the absence of RPD1, in some cases in antisense orientation. These results indicate that maize Pol IV specifies Pol II-based transcriptional regulation for certain regions of the maize genome.
2015-02-04 | GSE54166 | GEO
Project description:Maize RNA Polymerase D1 (RPD1), the largest subunit of RNA polymerase IV (Pol IV), is required for normal plant development, repression of transposable elements (TEs), and for the regulation of specific alleles associated with TEs. Here, we define the nascent transcriptomes of rpd1 mutant and wild-type (WT) seedlings using global run-on sequencing (GRO-seq) to identify the broader targets of RPD1-based transcriptional regulation. Surprisingly, although TE-like sequences comprise >85% of the maize genome, most TEs are not transcribed at the seedling stage, even in rpd1 mutants. Profile comparisons identify the global set of genes and TEs whose transcription is altered in the absence of RPD1, in some cases in antisense orientation. These results indicate that maize Pol IV specifies Pol II-based transcriptional regulation for certain regions of the maize genome. Nuclei isolated from 10 wild-type and 10 rpd1 mutant seedlings were pooled and used to make two global run-on sequencing libraries.
2015-02-04 | E-GEOD-54166 | biostudies-arrayexpress
Project description:Maize seedling transcriptome responses to six abiotic perturbations (heat, cold, darkness, desiccation, salt, UV-B) and 2 controls were analyzed Keywords: comparitive transcriptome profiling
2008-06-01 | GSE9453 | GEO
Project description:To understand the transcriptome changes during drought tolerance in maize, the drought-tolerant line Han21 and drought-sensitive line Ye478, which show substantial differences in drought tolerance at the seedling stage, were selected for this study. Using the GeneChip Maize Genome Arrays, we applied genome-wide gene expression analysis to the two genotypes under gradual drought stress and re-watering. We identified 2172 common regulated transcripts in both lines under drought stress, with 1084 common up-regulated transcripts and 1088 common down-regulated transcripts. Among the 2172 transcripts, 58 potential protein kinases and 117 potential transcription factors were identified. The potential components of the ABA signaling pathway were identified from the common regulated transcripts. We also identified 940 differentially regulated transcripts between the two lines. Among the 940 transcripts, the differential expression levels of 29 transporters and 15 cell wall-related transcripts may contribute to the different tolerances of the two lines. Additionally, we found that the drought-responsive genes in the tolerant Han21 line recovered more quickly when the seedlings were re-watered, and 311 transcripts in the tolerant Han21 line were exclusively up-regulated at the re-watering stage compared to the control and stress conditions. Our study provides a global characterization of two maize inbred lines during drought stress and re-watering and will be valuable for further study of the molecular mechanisms of drought tolerance in maize.
2010-06-03 | GSE16567 | GEO
Project description:A multi-omics approach has revealed both common and distinctive cellular and molecular signatures of inflammation and immune dysregulation that characterize distinct phenotypes of human RAG deficiency.
2024-12-10 | GSE274284 | GEO
Project description:To understand the transcriptome changes during drought tolerance in maize, the drought-tolerant line Han21 and drought-sensitive line Ye478, which show substantial differences in drought tolerance at the seedling stage, were selected for this study. Using the GeneChip Maize Genome Arrays, we applied genome-wide gene expression analysis to the two genotypes under gradual drought stress and re-watering. We identified 2172 common regulated transcripts in both lines under drought stress, with 1084 common up-regulated transcripts and 1088 common down-regulated transcripts. Among the 2172 transcripts, 58 potential protein kinases and 117 potential transcription factors were identified. The potential components of the ABA signaling pathway were identified from the common regulated transcripts. We also identified 940 differentially regulated transcripts between the two lines. Among the 940 transcripts, the differential expression levels of 29 transporters and 15 cell wall-related transcripts may contribute to the different tolerances of the two lines. Additionally, we found that the drought-responsive genes in the tolerant Han21 line recovered more quickly when the seedlings were re-watered, and 311 transcripts in the tolerant Han21 line were exclusively up-regulated at the re-watering stage compared to the control and stress conditions. Our study provides a global characterization of two maize inbred lines during drought stress and re-watering and will be valuable for further study of the molecular mechanisms of drought tolerance in maize. In two independent experiments, we generate maize gene expression profiles during drought stress and re-watering through comparing genome-wide expression patterns of drought stress treatment and re-watering treatment by using 17,555 Affymetrix maize whole genome array.
2010-06-16 | E-GEOD-16567 | biostudies-arrayexpress
Project description:Here, in order to study maize drought stress responses at the molecular level, we have employed omics strategy to perform transcriptome and proteome profiling of drought contrasting maize lines at the various stages. We conducted a comparative analysis of different maize varieties at various stages after drought treatment. In addition, we evaluated some physiological responses of these maize lines under drought stress, and the results of this study provide further insights into the drought stress tolerance signatures in maize.
2019-09-23 | PXD015533 |
Project description:Chilling is a major stress to plants of subtropical and tropical origins including maize. To reveal molecular mechanisms underlying chilling tolerance and chilling survival, we investigated maize transcriptome responses to chilling stress in differentiated leaves and roots as well as in crowns with meristem activity for survival. Chilling stress on maize shoots and roots is found to each contribute to seedling lethality in maize. Comparison of maize lines with different chilling tolerance capacity reveals that chilling survival in maize is highly associated with upregulation in leaves and crowns of abscisic acid response pathway, transcriptional regulators and cold response as well as downregulation of heat response in crowns. Comparison of chilling treatment on whole and part of the plants reveals that response to distal-chilling is very distinct from, and sometimes opposite to, response to local- or whole-plant chilling in both leaves and roots, suggesting a communication between shoots and roots in environmental perception. In sum, this study details chilling responses in leaves, roots and crowns and reveals potential chilling survival mechanism in maize, which lays ground for further understanding survival and tolerance mechanisms under low but non-freezing temperatures in tropical and subtropical plants.
2023-07-14 | GSE167881 | GEO
Project description:Single-peptide DNA-dependent RNA polymerase homologous to multi-subunit RNA polymerase
| PRJNA319983 | ENA