Arabidopsis thaliana
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA389787 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR6333610.fastq.gz | Fastqsanger.gz | |||
| SRR6333611.fastq.gz | Fastqsanger.gz | |||
| SRR6333602.fastq.gz | Fastqsanger.gz | |||
| SRR6333612.fastq.gz | Fastqsanger.gz | |||
| SRR6333603.fastq.gz | Fastqsanger.gz |
Items per page: 5 1 - 5 of 18 |
Similar Datasets
Project description:The characteristic leaf shapes we see in all plants are in good part outcome of the combined action of several transcription factor networks that translate into cell division activity during the early development of the organ. We show here that wild-type leaves have distinct transcriptomic profiles in center and marginal regions. Certain transcripts are enriched in margins, including those of CINCINNATA-like TCPs, and members of the NGATHA (NGA) and STYLISH (STY) gene families. We study in detail the contribution of miR319 regulated TCP (Teosinte branched, Cycloidea, PCF1/2) transcription factors to the development of the center and marginal regions of Arabidopsis leaves. We compare in molecular analyses wildtype, a tcp2 tcp4 mutant that has enlarged flat leaves and a tcp2 tcp3 tcp4 tcp10 mutant with strongly crinkled leaves. The different leaf domains of the tcp mutants show changed expression patterns for many photosynthesis related genes, indicating delayed differentiation, especially in the marginal parts of the organ. At the same time, we found an upregulation of cyclin genes and other genes that are known to participate in cell division, specifically in the marginal regions of tcp2 tcp3 tcp4 tcp10. Using GUS reporter constructs we confirmed extended mitotic activity in the tcp2 tcp3 tcp4 tcp10 leaf which persisted in small defined foci in the margins when the mitotic activity had already ceased in wild-type leaves. Our results describe the role of miR319-regulated TCP transcription factors in the coordination of activities in different leaf domains during the organs development.
2017-11-20 | GSE99854 | GEO
Project description:TCP transcription factors from the CYC2-class are involved in the development of monosymmetric flowers in all core eudicot species analysed so far. In Antirrhinum majus, the CYC2/TCP transcription factor CYCLOIDEA (CYC) is the molecular key regulator driving the development of flower monosymmetry (Luo D, Carpenter R, Vincent C, Copsey L, Coen E: Origin of floral asymmetry in Antirrhinum. Nature 1996, 383:794-799). In the Brassicaceae Iberis amara, a stronger expression of the CYC2 gene IaTCP1 in the small adaxial petals likely leads to the reduced petal size in comparison to large abaxial petals, with hardly any IaTCP1 expression. This results in the formation of the monosymmetric Iberis flower (Busch A, Zachgo S: Control of corolla monosymmetry in the Brassicaceae Iberis amara. PNAS 2007, 104:16714-16719). In contrast, the orthologous TCP/CYC2 transcription factor TCP1 from Arabidopsis thaliana, which forms equally sized and shaped petal pairs, only shows an early and transient expression in the adaxial area of floral primordia. This implies that monosymmetry in the Brassicaceae evolved through a heterochronic expression shift of the TCP/CYC2 key regulator gene IaTCP1. Transgenic Arabidopsis plants overexpressing IaTCP1 and TCP1 develop smaller petals whereas transgenic plants overexpressing CYC from Antirrhinum majus produce larger flowers. In any case, petal size is affected. To compare the effects of the three CYC2 TCP transcription factors on downstream (regulatory) networks in Arabidopsis thaliana, a microarray analysis was conducted.
2014-10-14 | GSE62213 | GEO
Project description:Leaf size and flatness directly affect photosynthesis and are closely related to agricultural yield. The final leaf size and shape are coordinately determined by cell proliferation, differentiation, and expansion during leaf development. Lettuce (Lactuca sativa L.) is one of the most important leafy vegetables worldwide, and lettuce leaves vary in shape and size. However, the molecular mechanisms of leaf development in lettuce are largely unknown. In this study, we showed that the lettuce APETALA2 (LsAP2) gene regulates leaf morphology. LsAP2 encodes a transcriptional repressor that contains the conserved EAR motif, which mediates interactions with the TOPLESS/TOPLESS-RELATED (TPL/TPR) corepressors. Overexpression of LsAP2 led to small and crinkly leaves, and many bulges were seen on the surface of the leaf blade. LsAP2 physically interacted with the CINCINNATA (CIN)-like TEOSINTE BRANCHED1/CYCLOIDEA/PROLIFERATING CELL FACTOR (TCP) transcription factors and inhibited their transcriptional activation activity. RNA sequencing analysis showed that LsAP2 affected the expression of auxin- and polarity-related genes. In addition, LsAP2 directly repressed the abaxial identity gene KANADI2 (LsKAN2). Together, these results indicate that LsAP2 regulates leaf morphology by inhibiting CIN-like TCP transcription factors and repressing LsKAN2, and our work provides insights into the regulatory mechanisms of leaf development in lettuce.
2021-03-29 | GSE168886 | GEO
Project description:TCP transcription factors from the CYC2-class are involved in the development of monosymmetric flowers in all core eudicot species analysed so far. In Antirrhinum majus, the CYC2/TCP transcription factor CYCLOIDEA (CYC) is the molecular key regulator driving the development of flower monosymmetry (Luo D, Carpenter R, Vincent C, Copsey L, Coen E: Origin of floral asymmetry in Antirrhinum. Nature 1996, 383:794-799). In the Brassicaceae Iberis amara, a stronger expression of the CYC2 gene IaTCP1 in the small adaxial petals likely leads to the reduced petal size in comparison to large abaxial petals, with hardly any IaTCP1 expression. This results in the formation of the monosymmetric Iberis flower (Busch A, Zachgo S: Control of corolla monosymmetry in the Brassicaceae Iberis amara. PNAS 2007, 104:16714-16719). In contrast, the orthologous TCP/CYC2 transcription factor TCP1 from Arabidopsis thaliana, which forms equally sized and shaped petal pairs, only shows an early and transient expression in the adaxial area of floral primordia. This implies that monosymmetry in the Brassicaceae evolved through a heterochronic expression shift of the TCP/CYC2 key regulator gene IaTCP1. Transgenic Arabidopsis plants overexpressing IaTCP1 and TCP1 develop smaller petals whereas transgenic plants overexpressing CYC from Antirrhinum majus produce larger flowers. In any case, petal size is affected. To compare the effects of the three CYC2 TCP transcription factors on downstream (regulatory) networks in Arabidopsis thaliana, a microarray analysis was conducted. The coding sequences of the TCP/CYC2 transcription factors IaTCP1, TCP1 and CYC were cloned into the pBAR vector (GenBank: AJ251014), resulting in the constructs #0522 (IaTCP1), #0569 (TCP1) and #0577 (CYC). In pBAR, all genes are under the control of the CaMV35S-promoter. Arabidopsis plants were transformed (via floral dip) with respective constructs and also with the empty vector (pBar). Transgenic plants (T1) with petal size deviation from the control (plants transformed with the empty vector and wild type) were selfed and resulting T2 lines with petal size deviations from control were selected. Inflorescence buds from secondary inflorescences were harvested from transgenic T2 plants that formed smaller (#0255 or #0569) or larger (#0577) petals in the main inflorescence. Total RNA was isolated and sent to the Integrated Functional Genomics Service at the University of Münster, Germany, which carried out probe preparation, hybridization and statistical analysis of the data. Differential gene expression was always determined from a comparison of gene expression from #0522, #0569 and #0577, respectively, against the control (#pBar; inflorescence gene expression in plants transformed with an empty vector).
2014-10-14 | E-GEOD-62213 | biostudies-arrayexpress
Project description:TCP (TEOSINTE BRANCHED1/CYCLOIDEA/PCF1) transcription factors control developmental processes in plants. We identified direct target genes of the Arabidopsis class I TCP20 protein in leaf development based on a glucocorticoid receptor induction assay and genome-wide expression studies. For this, we tagged TCP20 with a glucucorticoid receptor (GR) domain and transformed the resulting TCP20-GR construct into tcp20 knockout plants. Induction of these and wild type controls was done with Dexamethasone and Cycloheximide. Plants were harvested 8 h after induction, uninduced plants were taken as control.
2011-08-09 | GSE29012 | GEO
Project description:Mutations in the CINCINNATA gene in Antirrhinum and its orthologues in Arabidopsis cause negative surface curvature in leaves due to excess marginal growth. CIN-like genes code for TCP transcription factors and are expressed in a broad zone of a growing leaf somewhat distal to the proliferation zone. Although a few TCP targets are known, the role of CIN-like TCP genes in regulating leaf curvature has remained unclear. We have compared the global transcription profile of wild type and cincinnata mutant to identify its targets. By combining DNA-protein interaction, chromatin immunoprecipitation and RNA in situ hybridization, we show that CIN maintains surface flatness by regulating signaling or level of major plant hormones. CIN promotes cytokinin signaling directly and GA level indirectly, in accelerating maturity in leaf cells along the tip-to-base direction. In addition, CIN suppresses auxin signaling more at the margin than centre by establishing a margin-to-medial expression gradient of a homologue of the auxin suppressor IAA3. Our results uncover an underlying mechanism in a developing leaf that controls maturity of leaf and its surface curvature. Considering the conservation of CIN-like genes and their function in leaf morphogenesis in multiple plant species, it is likely that such mechanism is evolutionarily conserved.
2013-05-01 | GSE40621 | GEO
Project description:Leaves are flat determinate organs derived from indeterminate shoot apical meristems. The presence of a specific leaf meristem is debated, as anatomical features typical of meristems are not present in leaves. Here we demonstrate that multiple NGATHA (NGA) and CINCINNATA-class-TCP (CIN-TCP) transcription factors act redundantly to suppress activity of a leaf margin meristem in Arabidopsis thaliana, and that their absence confers persistent marginal growth of leaves, cotyledons and floral organs. The marginal meristem is activated by the juxtaposition of adaxial and abaxial domains and maintained by WOX homeobox transcription factors, but other margin elaboration genes are dispensable for its maintenance. This genetic framework parallels the morphogenetic program of shoot apical meristems and may represent a relic from an ancestral shoot system from which seed plant leaves evolved.
2016-10-03 | GSE78693 | GEO
Project description:Detection of genes acting downsteram of ectopically expressed TCP/CYC2 transcription factors in Arabidopsis thaliana
| PRJNA263483 | ENA
Project description:TCP (TEOSINTE BRANCHED1/CYCLOIDEA/PCF1) transcription factors control developmental processes in plants. We identified direct target genes of the Arabidopsis class I TCP20 protein in leaf development based on a glucocorticoid receptor induction assay and genome-wide expression studies. For this, we tagged TCP20 with a glucucorticoid receptor (GR) domain and transformed the resulting TCP20-GR construct into tcp20 knockout plants. Induction of these and wild type controls was done with Dexamethasone and Cycloheximide. Plants were harvested 8 h after induction, uninduced plants were taken as control. In sum, 8 samples, each pools of 30 seedlings. Wild type and TCP20-GR plants at induction times t=0 and t=8, in two biological replicates.
2011-08-08 | E-GEOD-29012 | biostudies-arrayexpress