Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

Transcriptome analysis of genes regulated by CUP-SHAPED COTYLEDON1 (CUC1) transcription factor in Arabidopsis thaliana

ABSTRACT: Samples 1 & 2: Comparison of gene expression between wild type (ecotype Ler) and 35S:CUC1, in which CUP-SHAPED COTYLEDON1, a master regulator of the shoot meristem and boundary establishment, is constitutively expressed under the cauliflower mosaic virus 35S promoter. Samples 3 & 4: Comparison of gene expression between stm-1 (ecotype Ler) and stm-1 35S:CUC1 RNA was isolated from cotyledons of 5-day-old (for Ler vs 35S:CUC1) or 10-day-old (for stm vs 35S:CUC1stm) seedlings. Two independent biological replicates were analyzed for each comparison.

ORGANISM(S): Arabidopsis thaliana

SUBMITTER: Mitsuhiro Aida

PROVIDER: E-GEOD-27482 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Publications

CUP-SHAPED COTYLEDON1 transcription factor activates the expression of LSH4 and LSH3, two members of the ALOG gene family, in shoot organ boundary cells.

Takeda Seiji S Hanano Keiko K Kariya Ayano A Shimizu Satoko S Zhao Li L Matsui Minami M Tasaka Masao M Aida Mitsuhiro M

The Plant journal : for cell and molecular biology 20110412 6

The establishment of organ boundaries is a fundamental process for proper morphogenesis in multicellular organisms. In plants, the shoot meristem repetitively forms organ primordia from its periphery, and boundary cells are generated between them to separate their cellular fates. The genes CUP-SHAPED COTYLEDON1 (CUC1) and CUC2, which encode plant-specific NAC transcription factors, play central roles in establishment of the shoot organ boundaries in Arabidopsis thaliana. Here we show that CUC1 p ...[more]

PMID: 21435050

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Project description:Arabidopsis ecotypes of Sha and Ler showed differences in tolerance to salinity stress. A previous study indicated that a premature stop codon resulting in a truncated Response to ABA and Salt 1 (RAS1) protein in Sha contributes to the increased salt tolerance relative to Ler ecotype. Sha exhibited higher germination rates and longer roots on MS plate, presumably due to the decreased ABA sensitivity in Sha. More Sha plants also survived in soil after salt treatment with relatively lower electrolyte leakage when compared to Ler. Transcriptome analysis revealed that expression levels of many genes were changed between Sha and Ler ecotypes and by salt treatments. About 500 transcripts were commonly changed by at least one salinity effect and one ecotype effect, and 171 of them were co-regulated by all four comparisons. Transcripts involved in redox, secondary metabolism, auxin metabolism, photosynthesis, cell wall, and protein synthesis were mainly down-regulated by salinity effects, while transposable element genes, microRNA and antisense sequences, histone superfamily genes, and biotic stress related genes were significantly changed by Sha ecotype effects and only slightly by salinity. Several metabolic pathways such as stress, TCA, hormone/lipid/secondary metabolism, redox, development, and GO terms involved in stress, oxidation, and defense response were enriched by both salinity and ecotype effects. Ninety-five highly inducible genes were identified as candidates of RAS1 target genes and the functions involved hormone metabolism, biotic stress, RNA, DNA synthesis, protein metabolism, cell, and microRNA metabolism. All these results indicated that the Sha ecotype was possibly preconditioned to abiotic stress relative to Ler through regulation of signaling pathways and stress responsive gene expression. These comparative transcriptomic and analytical results also confirm the complexity of ABA responses and salt stress tolerance mechanisms, and they suggest additional targets for improving tolerance.

Dataset Information

Transcriptome analysis of genes regulated by CUP-SHAPED COTYLEDON1 (CUC1) transcription factor in Arabidopsis thaliana

Publications

CUP-SHAPED COTYLEDON1 transcription factor activates the expression of LSH4 and LSH3, two members of the ALOG gene family, in shoot organ boundary cells.

Similar Datasets

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