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Cuc2-identification-Dynamic and specificity of CUP-SHAPED COTYLEDON transcription factors during leaf development

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

PROVIDER: PRJNA764928 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR15993003_1.fastq.gz	Fastqsanger.gz
	SRR15993003_2.fastq.gz	Fastqsanger.gz
	SRR15993004_1.fastq.gz	Fastqsanger.gz
	SRR15993004_2.fastq.gz	Fastqsanger.gz
	SRR15993005_1.fastq.gz	Fastqsanger.gz

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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

identification of target genes regulated by cuc2 in a.thaliana shoot apical meristem.-Morphodynamics in Plants: from gene to shape.

Project description:au13-03_cuc2 - identification of target genes regulated by cuc2 in a.thaliana shoot apical meristem. - Identification of genes specifically targeted by the CUC2 transcription factor that defines the margins of the floral meristem of Arabidopsis thaliana. - identify genes specifically targeted by CUP-SHAPED COTYLEDON 2 (CUC2), a transcription factor required for embryonic shoot meristem formation and specification of the organ boundary in A.thaliana

2018-12-01 | GSE121953 | GEO

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

2011-03-31 | GSE27482 | GEO

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

GhSBI1, a CUP-SHAPED COTYLEDON 2 homologue, modulates branch internode elongation in cotton.

Project description:Branch length is an important plant architecture trait in cotton (Gossypium) breeding. Development of cultivars with short branch has been proposed as a main object to enhance cotton yield potential, because they are suitable for high planting density. Here, we report the molecular cloning and characterization of a semi-dominant quantitative trait locus, Short Branch Internode 1(GhSBI1), which encodes a NAC transcription factor homologous to CUP-SHAPED COTYLEDON 2 (CUC2) and is regulated by microRNA ghr-miR164. We demonstrate that a point mutation found in sbi1 mutants perturbs ghr-miR164-directed regulation of GhSBI1, resulting in an increased expression level of GhSBI1. The sbi1 mutant was sensitive to exogenous gibberellic acid (GA) treatments. Overexpression of GhSBI1 inhibited branch internode elongation and led to the decreased levels of bioactive GAs. In addition, gene knockout analysis showed that GhSBI1 is required for the maintenance of the boundaries of multiple tissues in cotton. Transcriptome analysis revealed that overexpression of GhSBI1 affects the expression of plant hormone signalling-, axillary meristems initiation-, and abiotic stress response-related genes. GhSBI1 interacted with GAIs, the DELLA repressors of GA signalling. GhSBI1 represses expression of GA signalling- and cell elongation-related genes by directly targeting their promoters. Our work thus provides new insights into the molecular mechanisms for branch length and paves the way for the development of elite cultivars with suitable plant architecture in cotton.

| S-EPMC11500989 | biostudies-literature

Cotyledon tomentosa

Project description:Cotyledon tomentosa overview

| PRJNA725303 | ENA

REF6 recognizes specific DNA sequence to regulate H3K27me3 demethylation and organ boundary formation

Project description:RELATIVE OF EARLY FLOWERING 6 (REF6, also known as JMJ12) counteracts Polycomb mediated gene silencing through demethylating histone H3 lysine 27 trimethylation (H3K27me3) in Arabidopsis. Genome-wide analysis has demonstrated that REF6 dependent H3K37me3 demethylation occurs on hundreds of genes. However, how these genes are selectively subjected to H3K27me3 demethylation remains elusive. Here we show that a tandem array of four Cys2-His2 zinc finger domains (C2H2-ZF) at REF6 C-terminus are essential for REF6 function. Mechanistically, we find that C2H2-ZF cluster can directly recognize a specific DNA sequence motif, and is essential for binding of REF6 to its targets. In addition, we demonstrate that CUP-SHAPED COTYLEDON 1 (CUC1) and CUC3 harbor such sequence motif and are direct targets of REF6; while their close homolog, CUC2, without such binding motif is not bound by REF6. Furthermore, REF6 is essential for proper H3K27me3 level at CUC1 locus, CUC1 activation and cotyledon separation. Collectively, our study reveals not only a novel mechanism of H3K27me3 demethylase genome targeting to counteract Polycomb silencing, but also a new function of H3K27me3 demethylation in organ boundary formation.

2016-03-22 | GSE65329 | GEO

Insights from ANA-grade angiosperms into the early evolution of CUP-SHAPED COTYLEDON genes.

Project description:Background and aimsThe closely related NAC family genes NO APICAL MERISTEM (NAM) and CUP-SHAPED COTYLEDON3 (CUC3) regulate the formation of boundaries within and between plant organs. NAM is post-transcriptionally regulated by miR164, whereas CUC3 is not. To gain insight into the evolution of NAM and CUC3 in the angiosperms, we analysed orthologous genes in early-diverging ANA-grade angiosperms and gymnosperms.MethodsWe obtained NAM- and CUC3-like sequences from diverse angiosperms and gymnosperms by a combination of reverse transcriptase PCR, cDNA library screening and database searching, and then investigated their phylogenetic relationships by performing maximum-likelihood reconstructions. We also studied the spatial expression patterns of NAM, CUC3 and MIR164 orthologues in female reproductive tissues of Amborella trichopoda, the probable sister to all other flowering plants.Key resultsSeparate NAM and CUC3 orthologues were found in early-diverging angiosperms, but not in gymnosperms, which contained putative orthologues of the entire NAM + CUC3 clade that possessed sites of regulation by miR164. Multiple paralogues of NAM or CUC3 genes were noted in certain taxa, including Brassicaceae. Expression of NAM, CUC3 and MIR164 orthologues from Am. trichopoda was found to co-localize in ovules at the developmental boundary between the chalaza and nucellus.ConclusionsThe NAM and CUC3 lineages were generated by duplication, and CUC3 was subsequently lost regulation by miR164, prior to the last common ancestor of the extant angiosperms. However, the paralogous NAM clade genes CUC1 and CUC2 were generated by a more recent duplication, near the base of Brassicaceae. The function of NAM and CUC3 in defining a developmental boundary in the ovule appears to have been conserved since the last common ancestor of the flowering plants, as does the post-transcriptional regulation in ovule tissues of NAM by miR164.

| S-EPMC3108802 | biostudies-literature

Cotyledon tomentosa

Project description:Cotyledon tomentosa chloroplast genome

| PRJNA724941 | ENA

Interactions of CUP-SHAPED COTYLEDON and SPATULA genes control carpel margin development in Arabidopsis thaliana.

Project description:A characteristic feature of flowering plants is the fusion of carpels, which results in the formation of an enclosed gynoecium. In Arabidopsis thaliana, the gynoecium is formed by the fusion of two carpels along their margins, which also act as a meristematic site for the formation of internal structures such as ovules, the septum and transmitting tract. How gene interactions coordinate the fusion and differentiation of the marginal structures during gynoecium development is largely unknown. It was previously shown that the SPATULA (SPT) gene is required for carpel fusion, whereas overexpression of the CUP-SHAPED COTYLEDON genes CUC1 and CUC2 prevents it. Here we provide evidence that SPT promotes carpel fusion in the apical gynoecium partly through the negative regulation of CUC1 and CUC2 expression. In spt, transcripts of both CUC genes accumulated ectopically, and addition of cuc1 and cuc2 mutations to spt suppressed the split phenotype of carpels specifically along their lateral margins. In the basal gynoecium, on the other hand, all three genes promoted the formation of margin-derived structures, as revealed by the synergistic interactions of spt with each of the cuc mutations. Our results suggest that differential interactions among SPT, CUC1 and CUC2 direct the formation of domain-specific structures of the Arabidopsis gynoecium.

| S-EPMC3367164 | biostudies-literature

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