Ontology highlight
ABSTRACT:
PROVIDER: PRJNA852371 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR19836439_1.fastq.gz | Fastqsanger.gz | |||
| SRR19836439_2.fastq.gz | Fastqsanger.gz | |||
| SRR19836440_1.fastq.gz | Fastqsanger.gz | |||
| SRR19836440_2.fastq.gz | Fastqsanger.gz | |||
| SRR19836441_1.fastq.gz | Fastqsanger.gz |
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Project description:Plants generally possess a strong ability to regenerate organs; for example, in tissue culture, shoots can regenerate from callus, a clump of actively proliferating, undifferentiated cells. Processing of pre-mRNA and ribosomal RNAs is important for callus formation and shoot regeneration. However, our knowledge of the roles of RNA quality control via the nonsense-mediated mRNA decay (NMD) pathway in shoot regeneration is limited. Here, we examined the shoot regeneration phenotypes of the low-beta-amylase1 (lba1)/upstream frame shift1-1 (upf1-1) and upf3-1 mutants, in which the core NMD components UPF1 and UPF3 are defective. These mutants formed callus from hypocotyl explants normally, but this callus behaved abnormally during shoot regeneration: the mutant callus generated numerous adventitious root structures instead of adventitious shoots in an auxin-dependent manner. Quantitative RT-PCR and microarray analyses showed that the upf mutations had widespread effects during culture on shoot-induction medium. In particular, the expression patterns of early auxin response genes, including those encoding AUXIN/INDOLE ACETIC ACID (AUX/IAA) family members, were significantly affected in the upf mutants. Also, the upregulation of shoot apical meristem-related transcription factor genes, such as CUP-SHAPED COTYLEDON1 (CUC1) and CUC2, was inhibited in the mutants. Taken together, these results indicate that NMD-mediated transcriptomic regulation modulates the auxin response in plants and thus plays crucial roles in the early stages of shoot regeneration.
2019-09-01 | GSE134854 | GEO
Project description:The Arabidopsis Branching Enzyme 1 (BE1) gene encodes a putative glycoside hydrolase involved in carbohydrate metabolism. A partial loss-of-function mutation of the BE1 gene (be1-3 mutant) severely impaired adventitious shoot formation and somatic embryogenesis but not root formation in tissue culture. To gain a better understanding of the molecular mechanism underlying the in vitro plant regeneration defects caused by the BE1 gene mutation, we performed RNA sequencing analysis (RNA-seq) to examine the differential gene expression between WS and be1-3 mutant at dedifferentiation and redifferentiation stages.
2014-02-12 | E-MTAB-4394 | biostudies-arrayexpress
Project description:Adventitious root formation at the base of plant cuttings is an innate de novo organogenesis process that allows massive vegetative propagation of many economically and ecologically important species. The early molecular events following shoot excision are not well understood. Using whole-genome microarrays, we detected significant transcriptome remodeling during 48 hours following shoot removal in Populus softwood cuttings in the absence of exogenous auxin, with 27% and 36% of the gene models showing differential abundance between 0 and 6 hours, and 6 and 24 hours, respectively. During these two time intervals, gene networks involved in protein turnover, protein phosphorylation, molecular transport and translation were among the most significantly regulated. Transgenic lines expressing a constitutively active form of the Populus type-B response regulator PtRR13 (ΔDDKPtRR13) have a delayed rooting phenotype and cause misregulation of COV1, a negative regulator of vascularization; PDR9, an auxin efflux transporter; two AP2/ERF genes with sequence similarity to TINY1. Cytokinin action appeared to disrupt root development 24 hours after shoot excision, when root founder cells are hypothesized to be sensitive to the negative effects of cytokinin. Our results suggest that PtRR13 acts downstream of cytokinin to repress adventitious root formation in intact plants, and that reduced cytokinin signaling after shoot excision enables coordinated expression of ethylene, auxin and vascularization pathways leading to adventitious root development.
2009-03-27 | GSE15049 | GEO
Project description:De novo shoot regeneration is an essential step for massive propagation and genetic engineering of elite germplasm in forestry. Poplar that is a fast growth tree species have a very important ecologically and economically role around the world, especially in China. In this study, we found that PtWOX11 that is a homologue of AtWOX11 not only involved de novo root formation but also promote de novo shoot regeneration in poplar. We demonstrated that PtWOX11 can enhance callus regeneration competence and shoot regeneration during two-step de novo shoot regeneration. Furthermore, by using RNA-seq and qPCR, we uncovered that during callus induction stage PtWOX11 activates PtPLTs expression to promote callus formation and regeneration competence, and promote PtCUC2/3, PtWUSa and PtSTM transcription to fulfil shoot organogenesis during shoot regeneration stage. Overall, our data indicated that PtWOX11 play a new function and transcriptional regulation mechanism on de novo shoot regeneration in poplar.
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Project description:Effect of the presence of fruits on the expression of genes possibly involved in floral induction in the terminal meristem of spur bourse shoot. Investigation on mecanisms involved in Biennial Bearing in mature apple trees cultivar Royal Gala.
2016-03-02 | GSE64646 | GEO
Project description:Protein arginine methylation plays essential roles in diverse biological processes, but its role in regulating shoot regeneration remains elusive. In this study, we analyzed the function of the protein arginine methyltransferase AtPRMT5 during de novo shoot regeneration in Arabidopsis. AtPRMT5 encodes a type II PRMT that methylates proteins, including histones and RNA splicing factors. Mutation of AtPMRT5 decreased the frequency of shoot regeneration and number of shoots per callus in the atprmt5 mutant compared with those of the wild type. To understand the mechanism of AtPRMT5 regulation of shoot regeneration, we analyzed the transcript levels of wild type and the mutant atprmt5 calli during shoot regeneration by RNA-seq. Three biological repeats of wild type and the mutant atprmt5-1 calli were used for RNA sequencing. Total RNAs were isolated from the calli of wild type Col and the mutant atprmt5-1 cultured on cultured on shoot-induction medium. The RNA-seq llibraries were constructed with TruSeq Stranded mRNA Library Prep Kit and sequenced using the Illumina Hiseq 2500. The raw reads were aligned to the genome sequences of TAIR10 using Tophat software. The gene expression levels were measured in RPKM, and many critical genes regulated by AtPRMT5 were identified to be involved in shoot regeneration.
2017-06-18 | E-MTAB-5044 | biostudies-arrayexpress
Project description:48 apple trees from a segregating F1 population from a cross of 'Ottawa 3' x 'Robusta 5' were analyzed by microarray to identify gene expression differences between the individuals to correlate gene expression patterns with phenotypic traits segregating in the population 48 individual apple trees were assayed once each using RNA isolated from a single shoot tip from each tree. There were no biological or technical replicates in the experiment. There was no control sample, since all 48 were compared to each other.
2013-11-04 | E-GEOD-43268 | biostudies-arrayexpress
Project description:The capacity of plant regeneration in different ecotypes of Arabidopsis largely varies. However, the mechanism underlying this process remains exclusive. Here, we identified a critical thioredoxin gene DCC1 in determining natural variation for shoot regeneration in Arabidopsis. Functional loss of DCC1 resulted in the repression of shoot regeneration. DCC1 encodes a thioredoxin, which was localized in mitochondria. DCC1 directly interacted with CARBONIC ANHYDRASE 2 (CA2) to regulate the mitochondrial respiratory complex activity and mediate the Reactive Oxygen Species (ROS) level. Defects of DCC1 or CA2 caused the increased ROS level. To understand the regulatory mechanism of DCC1-mediated ROS in shoot regeneration, we analyzed the transcript levels of wild type Col-0 and the mutant dcc1 calli during shoot regeneration by RNA-seq. Three biological repeats of wild type Co-0 and the mutant dcc1 calli were used for RNA sequencing. Total RNAs were isolated from the calli of wild type Col-0 and the mutant dcc1 cultured on shoot-induction medium. The RNA-seq was performed using the Illumina Hiseq 2500. The raw reads were aligned to the genome sequences of TAIR10 using Tophat2 software. The gene expression levels were measured in FPKM, and many critical genes were identified to be involved in shoot regeneration.
2018-05-06 | E-MTAB-5236 | biostudies-arrayexpress
Project description:Detached Arabidopsis leaves can regenerate adventitious roots, providing a platform to study de novo root regeneration (DNRR). We performed time-lapse RNA-seq within 5 d revealed activation of gene networks in cell fate transition.
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