Detection of genes acting downsteram of ectopically expressed TCP/CYC2 transcription factors in Arabidopsis thaliana
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ABSTRACT:
ORGANISM(S): Arabidopsis thaliana
PROVIDER: GSE62213 | GEO | 2014/10/14
SECONDARY ACCESSION(S): PRJNA263483
REPOSITORIES: GEO
Similar Datasets
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:During the process of flower opening, most petals move downward in the direction of pedicel (i.e., epinastic movement). In most Delphinium flowers, however, their two lateral petals display a very peculiar movement, the mirrored helical rotation. Such a distinctive petal movement requires the twist of the stalk. However, in some lineages, their lateral petals also exhibit asymmetric bending that increases the degree of mirrored helical rotation, facilitating the formation of a 3D final shape. Notably, the petal asymmetric bending is a novel trait that has not been noticed yet so that its morphological nature, developmental process and molecular mechanisms remain largely unknown. Here, by using D. anthriscifolium as a model, we determined that the petal asymmetric bending was caused by localized expansion of cell width, accompanied with specialized arrangement of surface ornamentation, on the adaxial epidermis. Digital gene analyses, gene expression and functional studies revealed that a class I homeodomain-leucine zipper family transcription factor gene, DeanLATE MERISTEM IDENTITY1 (DeanLMI1), contributes to the petal asymmetric bending; knockdown of it led to the formation of explanate 2D petals. Specifically, DeanLMI1 promotes cell expansion in width and influences the arrangement of surface ornamentation, through regulating the auxin distribution, on the localized adaxial epidermis. These results not only provide a comprehensive portrait of petal asymmetric bending for the first time, but also shed some new insight into the mechanisms of flower opening and helical movement in plants.
2023-12-11 | GSE249849 | GEO
Project description:Water deficit stress (WDS) is a crucial factor that causes the inhibition of petal expansion and abnormal flower opening in rose. The regulatory mechanisms of petal expansion by WDS at transcriptional level were investigated by analysis expression profiles under WDS. Analysis used total RNA samples of petals taken from flowers treated by WDS comparison to those from control flowers. Transcriptome dynamics during treatment time responsive to WDS.
2013-01-09 | E-GEOD-33217 | biostudies-arrayexpress
Project description:Background: Vicia sativa (the common vetch) possesses a predominant zygomorphic flower and belongs to the subfamily Papilionoideae, which is related to Arabidopsis thaliana in the eurosid II clade of the core eudicots. Each vetch flower consists of 21 concentrically arranged organs: the outermost five sepals, then five petals and ten stamens, and a single carpel in the center. Methodology/Principal Findings: We explored the floral transcriptome to examine a genome-scale genetic model of the zygomorphic flower of vetch. mRNA was obtained from an equal mixture of six floral organs, leaves and roots. De novo assembly of the vetch transcriptome using Illumina paired-end technology produced 71,553 unigenes with an average length of 511 bp. We then compared the expression changes in the 71,553 unigenes in the eight independent organs through RNA-Seq Quantification analysis. We predominantly analyzed gene expression patterns specific to each floral organ and combinations of floral organs that corresponded to the traditional ABC model domains. Comparative analyses were performed in the floral transcriptomes of vetch and Arabidopsis, and genomes of vetch and Medicago truncatula. Conclusions/Significance: Our comparative analysis of vetch and Arabidopsis showed that the vetch flowers conform to a strict ABC model. We analyzed the evolution and expression of the TCP gene family in vetch at a whole-genome level, and several unigenes specific to three different vetch petals, which might offer some clues toward elucidating the molecular mechanisms underlying floral zygomorphy. Our results provide the first insights into the genome-scale molecular regulatory network that controls the evolution and development of the zygomorphic flower in Papilionoideae. Examination of the transcriptomic changes in the six floral organs, leaves and roots in common vetch.
2013-03-26 | E-GEOD-35437 | biostudies-arrayexpress
Project description:In Antirrhinum, the equivalent mutant to the Arabidopsis cuc1 cuc2 double is called cup. We have cloned CUP and shown that it encodes a NAC-domain transcription factor homologous to CUC1 and CUC2. Yeast two-hybrid analysis shows that CUP interacts with TIC, an Antirrhinum TCP transcription factor. Moving back to Arabidopsis, the closest homologues to TIC encode TCP factors TCP13 and TCP14 which, we have now shown, also interact in two-hybrid experiments with CUC1 and CUC2. We have identified insertions in both TCP13 and TCP14. CUP, CUC1 and CUC2 play a role in the establishment of boundaries between lateral organs. As evolutionarily conserved interactors, we expect TCP13 and TCP14 to act in the same process. Homozygous tcp13 mutant flowers show mixed cell identity (mci) with the boundaries of organ identity out of register with those of physical organ development. tcp 14 mutants show a very weak phenotype, but the double heterozygote is identical to the tcp13 homozygote. The double homozygote is underway at the moment and this application takes into account the time required to generate these plants.The aim of this microarray experiment is to identify targets of TCP13 and TCP14. We propose to compare expression levels in WT, tcp13, tcp14, tcp13/+ tcp14/+, and tcp13 tcp14 plants. Although we initially propose only duplicate experiments for each mutant, requiring a total of 10 chips, the experimental material will serve as internal replicates, since we expect to see different degrees of inactivation/activation of at least a core of conserved genes. The fact that all of the mutant combinations observed so far produce flowers with the appropriate cell types present, but in a different position, suggests that, unlike in homeotic mutants, very similar sets of floral genes will be present in each sample. This gives us hope that we might find a smaller number of genes with altered expression. Our tissue samples will be wild type and mutant inflorescences and, as such, will contain a variety of flowers at different stages of development. By taking a large number of flowers and buds we hope to overcome any sampling errors. Although we have requested 10 chips - for duplicate analyses of WT, both single mutants, the heterozygote and the double mutant - it remains a formal possibility that the double homozygote is inviable, or produces no inflorescence. In this unlikely eventuality we would only submit 8 of the 10 samples.
2022-11-21 | E-NASC-19 | biostudies-arrayexpress
Project description:In Antirrhinum, the equivalent mutant to the Arabidopsis cuc1 cuc2 double is called cup. We have cloned CUP and shown that it encodes a NAC-domain transcription factor homologous to CUC1 and CUC2. Yeast two-hybrid analysis shows that CUP interacts with TIC, an Antirrhinum TCP transcription factor. Moving back to Arabidopsis, the closest homologues to TIC encode TCP factors TCP13 and TCP14 which, we have now shown, also interact in two-hybrid experiments with CUC1 and CUC2. We have identified insertions in both TCP13 and TCP14. CUP, CUC1 and CUC2 play a role in the establishment of boundaries between lateral organs. As evolutionarily conserved interactors, we expect TCP13 and TCP14 to act in the same process. Homozygous tcp13 mutant flowers show mixed cell identity (mci) with the boundaries of organ identity out of register with those of physical organ development. tcp 14 mutants show a very weak phenotype, but the double heterozygote is identical to the tcp13 homozygote. The double homozygote is underway at the moment and this application takes into account the time required to generate these plants.The aim of this microarray experiment is to identify targets of TCP13 and TCP14. We propose to compare expression levels in WT, tcp13, tcp14, tcp13/+ tcp14/+, and tcp13 tcp14 plants. Although we initially propose only duplicate experiments for each mutant, requiring a total of 10 chips, the experimental material will serve as internal replicates, since we expect to see different degrees of inactivation/activation of at least a core of conserved genes. The fact that all of the mutant combinations observed so far produce flowers with the appropriate cell types present, but in a different position, suggests that, unlike in homeotic mutants, very similar sets of floral genes will be present in each sample. This gives us hope that we might find a smaller number of genes with altered expression. Our tissue samples will be wild type and mutant inflorescences and, as such, will contain a variety of flowers at different stages of development. By taking a large number of flowers and buds we hope to overcome any sampling errors. Although we have requested 10 chips - for duplicate analyses of WT, both single mutants, the heterozygote and the double mutant - it remains a formal possibility that the double homozygote is inviable, or produces no inflorescence. In this unlikely eventuality we would only submit 8 of the 10 samples. Experiment Overall Design: Number of plants pooled:10
2008-06-14 | E-GEOD-6149 | biostudies-arrayexpress
Project description:Background: Vicia sativa (the common vetch) possesses a predominant zygomorphic flower and belongs to the subfamily Papilionoideae, which is related to Arabidopsis thaliana in the eurosid II clade of the core eudicots. Each vetch flower consists of 21 concentrically arranged organs: the outermost five sepals, then five petals and ten stamens, and a single carpel in the center. Methodology/Principal Findings: We explored the floral transcriptome to examine a genome-scale genetic model of the zygomorphic flower of vetch. mRNA was obtained from an equal mixture of six floral organs, leaves and roots. De novo assembly of the vetch transcriptome using Illumina paired-end technology produced 71,553 unigenes with an average length of 511 bp. We then compared the expression changes in the 71,553 unigenes in the eight independent organs through RNA-Seq Quantification analysis. We predominantly analyzed gene expression patterns specific to each floral organ and combinations of floral organs that corresponded to the traditional ABC model domains. Comparative analyses were performed in the floral transcriptomes of vetch and Arabidopsis, and genomes of vetch and Medicago truncatula. Conclusions/Significance: Our comparative analysis of vetch and Arabidopsis showed that the vetch flowers conform to a strict ABC model. We analyzed the evolution and expression of the TCP gene family in vetch at a whole-genome level, and several unigenes specific to three different vetch petals, which might offer some clues toward elucidating the molecular mechanisms underlying floral zygomorphy. Our results provide the first insights into the genome-scale molecular regulatory network that controls the evolution and development of the zygomorphic flower in Papilionoideae.
2013-03-26 | GSE35437 | GEO
Project description:In Antirrhinum, the equivalent mutant to the Arabidopsis cuc1 cuc2 double is called cup. We have cloned CUP and shown that it encodes a NAC-domain transcription factor homologous to CUC1 and CUC2. Yeast two-hybrid analysis shows that CUP interacts with TIC, an Antirrhinum TCP transcription factor. Moving back to Arabidopsis, the closest homologues to TIC encode TCP factors TCP13 and TCP14 which, we have now shown, also interact in two-hybrid experiments with CUC1 and CUC2. We have identified insertions in both TCP13 and TCP14. CUP, CUC1 and CUC2 play a role in the establishment of boundaries between lateral organs. As evolutionarily conserved interactors, we expect TCP13 and TCP14 to act in the same process. Homozygous tcp13 mutant flowers show mixed cell identity (mci) with the boundaries of organ identity out of register with those of physical organ development. tcp 14 mutants show a very weak phenotype, but the double heterozygote is identical to the tcp13 homozygote. The double homozygote is underway at the moment and this application takes into account the time required to generate these plants.The aim of this microarray experiment is to identify targets of TCP13 and TCP14. We propose to compare expression levels in WT, tcp13, tcp14, tcp13/+ tcp14/+, and tcp13 tcp14 plants. Although we initially propose only duplicate experiments for each mutant, requiring a total of 10 chips, the experimental material will serve as internal replicates, since we expect to see different degrees of inactivation/activation of at least a core of conserved genes. The fact that all of the mutant combinations observed so far produce flowers with the appropriate cell types present, but in a different position, suggests that, unlike in homeotic mutants, very similar sets of floral genes will be present in each sample. This gives us hope that we might find a smaller number of genes with altered expression. Our tissue samples will be wild type and mutant inflorescences and, as such, will contain a variety of flowers at different stages of development. By taking a large number of flowers and buds we hope to overcome any sampling errors. Although we have requested 10 chips - for duplicate analyses of WT, both single mutants, the heterozygote and the double mutant - it remains a formal possibility that the double homozygote is inviable, or produces no inflorescence. In this unlikely eventuality we would only submit 8 of the 10 samples. Keywords: genetic_modification_design
2007-01-22 | GSE6149 | GEO
Project description:Investigation of gene expression level changes in snapdragon petals and sepals during flower development The flower developmental stages analyzed in this study are representative of distinct developmental events: (i) preanthesis, (ii) anthesis, (iii) maturation and (iv) presenescence and are further described in the accompanying article. A 24 chip study using total RNA recovered from samples of petal and sepal tissue of Antirrhinum majus cv. Maryland True Pink harvested at four different stages of flower development, namely (i) preanthesis (three days before flower opening=d-3), (ii) anthesis (day of flower opening=d1), (iii) maturation (four days after flower opening=d4) and (iv) presenescence (seven days after flower opening=d7). Three separate samples were extracted per tissue and developmental stages. Each chip measures the expression level of 11,959 ESTs from Antirrhinum majus cv. Maryland True Pink with up to six 60-mer probes per target.
2012-06-06 | E-GEOD-36356 | biostudies-arrayexpress
Project description:Investigation of genome-wide gene expression in sepals, petals, stamens, staminodia and carpels in pre-anthesis Aquilegia flowers. One goal was to identify transcriptional signatures associated with petaloidy by comparing gene expression in petals and petaloid sepals. Other goals were to study the evolutionary origin and ecological function of staminodia by comparing a) expression patterns in stamens, staminodia and carpels, b) identifying transcriptional regulators expressed in staminodia and c) using gene set enrichment analysis to identify biological processes operating in staminodia. A 15 chip study using total RNA from the five floral tissues from three replicate natural populations with each sample representing tissue pooled from 60 flowers.
2010-05-18 | E-GEOD-19432 | biostudies-arrayexpress