Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

N6-methyladenosine mRNA methylomes in the MTA RNAi strawberry fruits and the controls

ABSTRACT: N6-methyladenosine mRNA methylomes in the MTA RNAi strawberry fruits and the controls

PROVIDER: PRJNA731153 | ENA |

REPOSITORIES: ENA

ACCESS DATA

Json Xml

Similar Datasets

N6-methyladenosine mRNA methylomes in the MTA RNAi strawberry fruits and the controls

Project description:For exploring the influence of the m6A methyltransferase gene MTA silencing in the global m6A mRNA methylomes of strawberry fruits, we performed m6A-seq in the MTA RNAi strawberry fruits (RNAi-MTA) and the controls with three independently biological replicates. Results showed that MTA silencing induces the m6A hypomethylation of thousands of transcripts, including those of ripening and ABA pathway genes.

2021-05-20 | GSE174703 | GEO

Transcriptomic studies in the development and ripening of strawberry fruits

Project description:Strawberry is an ideal model for studying the molecular biology of the development and ripening of non-climacteric fruits. By using a custom-made and high quality oligo microarray platform done with over 32000 probes including all of the genes actually described in the strawberry genome, we have analyzed the expression of genes during the development and ripening in the receptacles of these fruits.

2018-05-09 | GSE95300 | GEO

Transcriptomic studies in the development and ripening of strawberry fruits (Agilent)

2019-10-18 | GSE126220 | GEO

N6-methyladenosine RNA methylomes in woodland strawberry fruit at three different development stages.

Project description:N6-methyladenosine RNA methylomes in woodland strawberry fruit at three different development stages.

| PRJNA703676 | ENA

N6-methyladenosine RNA methylomes in woodland strawberry fruit at three different development stages.

Project description:For exploring whether mRNA m6A modification participates in the regulation of strawberry fruit ripening, we performed m6A-seq in woodland strawberry fruit at three different development stages, including the S6 stage (almost 15 days post-anthsis (DPA)), the RS1 stage (21 DPA), and the RS3 stage (27 DPA), with three biological replicates. mRNA methylome analysis reveals that m6A methylation prevalently distributes in the strawberry transcriptome and highly enrichs in the coding sequence, stop codon and 3’ untranslated region.

2021-05-17 | GSE167183 | GEO

RdDM is involved in epigenetic regulation of strawberry fruit ripening

Project description:DNA methylation is a conserved epigenetic mark that influences diverse biological processes in many eukaryotes. Recently, DNA methylation was proposed to regulate fleshy fruit ripening. Fleshy fruits can be distinguished by their ripening process as climacteric fruits, such as tomatoes, or non-climacteric fruits, such as strawberries. Tomatoes undergo a global decrease in DNA methylation during ripening, due to increased expression of a DNA demethylase gene. The dynamics and biological relevance of DNA methylation during ripening of non-climacteric fruits, or other climacteric fruits, are unknown. Here, we generated and characterized single-base resolution maps of the DNA methylome in strawberry fruit, from immature to ripe stages. We observed an overall loss of DNA methylation during strawberry fruit ripening. Thus, ripening-induced DNA hypomethylation occurs not only in climacteric fruit, but also in non-climacteric fruit. However, we discovered that the mechanisms underlying DNA hypomethylation during ripening of tomato and strawberry are distinct. Unlike in tomatoes, DNA demethylase genes were not up-regulated during ripening of strawberries. Instead, genes involved in RNA-directed DNA methylation were down-regulated during strawberry ripening. Further, ripening-induced DNA hypomethylation was associated with decreased siRNA levels, consistent with reduced RdDM activity. Therefore, we propose that DNA hypomethylation during strawberry ripening is caused by diminished RdDM activity. Finally, hundreds of ripening-related genes displayed altered expression that was associated with, and thus potentially regulated by, DNA hypomethylation during ripening. Our findings provide new insight into the DNA methylation dynamics during the ripening of non-climateric fruit and reveal a novel function of RdDM in regulating an important process in plant development.

2018-11-13 | GSE113084 | GEO

The NAC transcription factor FaRIF controls fruit ripening in strawberry

Project description:In contrast to climacteric fruits such as tomato, the knowledge on key regulatory genes controlling the ripening of strawberry, a non-climacteric fruit, is still limited. NAC transcription factors mediate different developmental processes in plants. Here, we identified and characterized FaRIF (Ripening Inducing Factor), a NAC transcription factor that is highly expressed and induced in strawberry receptacles during ripening. Functional analyses based on stable transgenic lines aimed at silencing FaRIF by RNA interference, either from a constitutive promoter or the ripe receptacle-specific EXP2 promoter, as well as overexpression lines showed that FaRIF controls critical ripening-related processes such as fruit softening and pigment and sugar accumulation. Physiological, metabolome and transcriptome analyses of receptacles of FaRIF-silenced and overexpression lines point to FaRIF as a key regulator of strawberry fruit ripening from early developmental stages, controlling abscisic acid (ABA) biosynthesis and signaling, cell wall degradation and modification, the phenylpropanoid pathway, volatiles production, and the balance of the aerobic/anaerobic metabolism. FaRIF is therefore a target to be modified/edited to control the quality of strawberry fruits.

2021-02-20 | GSE167107 | GEO

Comprehensive transcriptomic dataset for early stage fruit development in woodland strawberry Fragaria vesca

Project description:Fragaria vesca, a diploid woodland strawberry with a small and sequenced genome, is an excellent model for studying fruit development. The strawberry fruit is unique in that the edible flesh is actually enlarged receptacle tissue. The true fruit are the numerous dry achenes dotting the receptacleM-^Rs surface. Auxin produced from the achene is essential for the receptacle fruit set, a paradigm for studying crosstalk between hormone signaling and development. To investigate the molecular mechanism underlying strawberry fruit set, next-generation sequencing was employed to profile early-stage fruit development with five fruit tissue types and five developmental stages from floral anthesis to enlarged fruits. This two-dimensional data set provides a systems-level view of molecular events with precise spatial and temporal resolution.

2013-10-01 | E-MTAB-1902 | biostudies-arrayexpress

Gene expression profiling of sarcoma cells treated with mithramycin A (MTA), nano-encapsulated MTA or MTA-analogs

Project description:This study was designed to gain insight about the mechanisms involved in the anti-tumor effects of mithramycin A (MTA) and the MTA analog EC-8042 in sarcoma cells. In addition, we also studied whether this molecular features could be influenced by the nano-encapsulation of MTA.

2021-03-30 | GSE161616 | GEO

Transcriptomic studies in the development and ripening of strawberry fruits (Agilent)

Project description:Transcriptomic studies in the development and ripening of strawberry fruits (Agilent)

| PRJNA521350 | ENA