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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

ORGANISM(S): Arabidopsis thaliana

PROVIDER: GSE27482 | GEO | 2011/03/31

SECONDARY ACCESSION(S): PRJNA138589

REPOSITORIES: GEO

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

Project description: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.

2011-03-30 | E-GEOD-27482 | biostudies-arrayexpress

Mature Arabidopsis leaves: RAP2.6L overexpressing vs wild-type (Ws)

Project description:Transcriptional profiling of Arabidopsis thaliana, comparing control wild-type (ecotype Wassilewskija, Ws) leaves with leaves from transgenic plants overexpressing the transcription factor RAP2.6L under control of the cauliflower mosaic virus 35S promoter (RAP2.6L-OX; this line was originally described in Krishnaswamy et al (2010)).

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Arabidopsis thaliana

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

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Arabidopsis thaliana embryos: wild type vs cuc1 cuc2 double mutant

Project description:Transcriptional profiling of Arabidopsis embryos comparing cuc1-1 cuc2-1 mutant (test) and wild type Ler (reference). Goal was to screen genes regulated by CUC1 and CUC2 transcription factors, which are required for shoot meristem formation and cotyledon separation.

2020-03-19 | GSE147149 | GEO

cuc2-identification-Dynamic and specificity of CUP-SHAPED COTYLEDON transcription factors during leaf development

Project description:ngs2014_39_leafnet2-cuc2-identification-Identification of CUC2 targets-10-days old 35S::CUC2-GR Arabidopsis transgenic line grown in liquid culture have been treated for 6 hours with DEXAMETHASONE 10µM or Mock.

2022-05-18 | GSE184530 | GEO

Effect of ChCUC1 induction on gene expression in Cardamine hirsuta leaf development

Project description:Here we investigate the function of CUC1(CUP-SHAPED COTYLEDON1) in the diversification of leaf forms between simple-leaved Arabidopsis thaliana and compound-leaved Cardamine hirsuta. CUC transcription factors are conserved regulators in leaf margin dissection and leaflet formation. ChCUC1, ChCUC2 and ChCUC3 function redundantly and are required for the leaflet formation in C. hirsuta. Recently we discovered that ChCUC1 has species species-specific expression in young leaves of C.hirsuta. Moreover, interspecies gene transfer of ChCUC1 allele into A.thaliana is sufficient to increase leaf complexity. On this basis, we hypothesize that redeployment of ChCUC1 in leaves contributes to the formation of leaflets instead of serrations. However, the mechanism underlying ChCUC1 regulating cell division, cell polarity, cytoskeleton and thus leaf marginal patterning remains elusive. To this end, we make use of chromatin immunoprecipitation sequencing(ChIP-seq), transcriptomic, comparative genetics and advanced imaging approaches to identify the downstream regulating genes of ChCUC1.

2024-05-31 | GSE241051 | GEO

Quantitative Proteomic Analysis of ER Stress Response Reveals both Common and Specific Features in Two Contrasting Ecotypes of Arabidopsis

Project description:Accumulation of unfolded/misfolded proteins in endoplasmic reticulum (ER) elicits a well conserved response called the Unfolded Protein Response (UPR), which triggers the up-regulation of downstream genes involved in protein folding, vesicle trafficking, and ER-Associated Degradation (ERAD). Although the dynamic transcriptomic responses and underlying major transcriptional regulators in ER stress response in plants have been well established, the proteome changes induced by ER stress have not been reported in plants. In the current study, we found that the Arabidopsis Ler ecotype is more sensitive to ER stress than the Col ecotype. Quantitative mass spectrometry analysis with Tandem Mass Tag (TMT) isobaric labeling showed that totally 7439 and 7035 proteins were identified from Col and Ler seedlings, with 88 and 113 differentially regulated (FC>1.3 or <0.7, P<0.05) proteins by ER stress in Col and Ler, respectively. Among them, 40 proteins were commonly up-regulated in Col and Ler, of which 10 were not up-regulated in bzip28 bzip60 double mutant (Col background) plants. Of the 19 specifically up-regulated proteins in Col comparing to that in Ler, components in ERAD, N-glycosylation, vesicle trafficking and molecular chaperones were represented. Quantitative RT-PCR showed that genes encoding 7 out of 19 proteins were not up-regulated (FC>1.3 or <0.7, P<0.05) by ER stress in both ecotypes while genes encoding 12 out of 19 proteins were up-regulated by ER stress with no obvious differences in fold change between Col and Ler. Our results experimentally demonstrated the robust ER stress response at proteome level in plants and revealed differentially regulated proteins that may contribute to differed ER stress sensitivity between Col and Ler ecotypes in Arabidopsis.

2021-09-09 | PXD022630 | Pride

Tobacco mosaic virus infection alters phloem associated translatomes in Arabidopsis thaliana

Project description:In this study we used vascular specific promoters and a translating ribosome affinity purification strategy to identify phloem-associated translatome responses to infection by tobacco mosaic virus (TMV) in the systemic host Arabidopsis thaliana ecotype Shahdara. Three different promoter:FLAG-RPL18 lines were used. These included two phloem specific promoters (pSUC2 and pSULTR2;2) as well as the more ubiquitously expressed cauliflower mosaic virus 35S promoter (p35S). Immunopurification of ribosome-mRNA complexes was accomplished by the method described in Reynoso et al. (Plant Functional Genomics: Methods and Protocols, 185-207; 2015). The dataset includes samples from the leaves of 5-week-old plants inoculated with TMV (1 mg/mL) or mock inoculated with sterile water.

2017-07-17 | GSE97662 | GEO

Transcript profiling of different Arabidopsis thaliana ecotypes in response to Tobacco etch potyvirus infection

Project description:We have used a strain of Tobacco etch potyvirus (TEV) experimentally adapted to Arabidopsis thaliana ecotype Ler-0 to infect a set of seven A. thaliana plant ecotypes(Col-0, Ei-2, Wt-1, ler-0, Oy-0, St-0). Each ecotype was inoculated with the same amount of the virus. Using commercial microarrays containing probes Arabidopsis thaliana ssp. Col-0 plant transcripts, we explored the effect of viral infection in the plant transcriptome

2012-07-04 | GSE37269 | GEO

Gene expression profiling of the intact dermal sheath cup of human hair follicle

Project description:The dermal sheath cup is the peribulbar component of the hair follicle dermal sheath, and has hair inductive potential similar to the dermal papilla. To characterize it in comparison with other mesenchymal follicle tissuesparts, we performed gene expression profiling of intact dermal sheath cups, which were separated from hair follicles by microdissection. Gene expression profiles of the dermal sheath cup, dermal papilla and upper dermal sheath were compared. We identified a dermal sheath cup signature composed of 32 upregulated genes, which included extracellular matrix components and BMP binding mollecules, while dermal papilla signature included a number of dermal papilla signature genes which had already reported. Analyses of upstream regulators showed that TGF- b1 is a putative regulator of these genes. These results suggest some of molecular mechanism that contributes to human dermal sheath cup properties, which could be useful for hair follicle bioengineering.

2020-02-22 | GSE95219 | GEO

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