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Metabolic labeling of RNAs uncovers hidden features and dynamics of the Arabidopsis thaliana transcriptome

ABSTRACT: Metabolic labeling of RNAs uncovers hidden features and dynamics of the Arabidopsis thaliana transcriptome

PROVIDER: PRJNA485744 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR7688900.fastq.gz	Fastqsanger.gz
	SRR7688910.fastq.gz	Fastqsanger.gz
	SRR7688950.fastq.gz	Fastqsanger.gz
	SRR7688901.fastq.gz	Fastqsanger.gz
	SRR7688911.fastq.gz	Fastqsanger.gz

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Metabolic labeling of RNAs uncovers hidden features and dynamics of the Arabidopsis thaliana transcriptome [ERIC]

Project description:Metabolic labeling of RNAs uncovers hidden features and dynamics of the Arabidopsis thaliana transcriptome [ERIC]

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Metabolic labeling of RNAs uncovers hidden features and dynamics of the Arabidopsis thaliana transcriptome [NEU]

Project description:Metabolic labeling of RNAs uncovers hidden features and dynamics of the Arabidopsis thaliana transcriptome [NEU]

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Metabolic labeling of RNAs uncovers hidden features and dynamics of the Arabidopsis thaliana transcriptome [NEU]

Project description:We present and propose the application of 5-Ethynyl uridine for metabolic labeling of RNAs in plants, which allows the isolation of neo-synthesized RNAs from intact plants. This system provides the possibility to investigate neo-synthesized RNAs from living plant cells. Neu-RNAseq can be applied for the detection of splicing variants, especially RNAs containing retained introns and alternative 5’ and 3’ splice sites. A subset of unspliced RNAs identified by Neu-Seq is subjected for elimination by the NMD pathway, but the majority of the RNA splicing variants detected in Neu-Seq libraries will be further processed into mature mRNAs.

2018-10-31 | GSE118458 | GEO

Metabolic labeling of RNAs uncovers hidden features and dynamics of the Arabidopsis thaliana transcriptome [ERIC]

Project description:We provide evidence that 5-EU metabolic labeling of Arabidopsis RNAs can be used for pulse-chase experiments, which allowed us to determine Arabidopsis RNA half-lives genome-wide without chemical inhibition of transcription. Similar to BRIC-Seq, we performed 5-EU IP chase (ERIC)-Seq in seedlings of A. thaliana. Hierarchical clustering of gene expression values allowed us to define at least five clusters of mRNAs that exhibited distinct degradation kinetics. To determine the RNA half-lives of each group, we applied an exponential decay model and a locally weighted scatterplot smoothing (LOWESS) and calculated the time where the concentration was halved. It became obvious that the half-lives determined by ERIC-Seq are much shorter than the ones determined after treatment with cordycepin or actinomycin D, respectively. We found that genes belonging to cluster A exhibiting the shortest half-lives are enriched in genes transcribed into non-coding RNAs, stress-related genes, genes involved in hormonal pathways and the metabolism of polyamines, which are also involved in stress responses. On the contrary, genes from cluster E, which have the longest half-lives, are specifically enriched in genes responsible for mitochondrial and plastic functions as well as primary metabolism (such as the TCA cycle)

2018-10-31 | GSE118461 | GEO

Metabolic labeling of RNAs uncovers hidden features and dynamics of the Arabidopsis thaliana transcriptome

Project description:This SuperSeries is composed of the SubSeries listed below.

2018-10-31 | GSE118462 | GEO

Hidden features of NAD-RNA epitranscriptome in Drosophila life cycle

Project description:Hidden features of NAD-RNA epitranscriptome in Drosophila life cycle

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Hidden features of NAD-RNA epitranscriptome in Drosophila life cycle

Project description:Nicotinamide adenine dinucleotide (NAD), a nucleotide-containing metabolite, can be incorporated into the RNA 5’-terminus to result in NAD-capped RNA (NAD-RNA). Since NAD has been heightened as one of the most essential metabolites in cells, its attachment to RNA might indicate a yet-to-be discovered mechanism at the epitranscriptomic level. Here, we design a highly-sensitive method, DO-seq, to capture NAD-RNAs. Using Drosophila, we identify thousands of previously unexplored NAD-RNAs and their dynamics in the fly life cycle, from embryo to adult. We show the evidence that chromosomal clustering might be the structural basis by which co-expression can couple with NAD capping on physically and functionally-linked genes. Furthermore, we note that NAD capping of cuticle genes seems to inversely correlate with gene expression. Combined, we propose NAD-RNA epitranscriptome as a hidden layer of regulation that profoundly impacts biological processes. DO-seq empowers the identification of NAD-capped RNAs, facilitating functional investigation into this modification.

2023-12-21 | GSE228505 | GEO

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