Arabidopsis thaliana
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA310776 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR3143654.fastq.gz | Fastqsanger.gz | |||
| SRR3143655.fastq.gz | Fastqsanger.gz | |||
| SRR3956083.fastq.gz | Fastqsanger.gz | |||
| SRR3956084.fastq.gz | Fastqsanger.gz | |||
| SRR3956085.fastq.gz | Fastqsanger.gz |
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Project description:microRNA-mediated ribosome stalling promotes secondary siRNA biogenesis in plants
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Project description:Environmental stress is detrimental to plants viability and requires an adequate reprogramming of cellular activities to maximize plant survival. We present a global analysis of the adaptive stress response of Arabidopsis thaliana to prolonged heat stress. We combine deep sequencing of RNA and ribosome protected fragments to provide genome wide map of adaptation to heat stress on at transcriptional and translational level. Our analysis shows that the genes with the highest upregulation upon heat stress are known heat-responsive gene, chaperons and other genes involved in protein folding control. Majority of these genes exhibits increase on both transcriptional and translational level. No translational inhibition or ribosome stalling was observed, which can be observed in the early thermal stress response, indicating that plants alter their cellular composition in order to adapt to the prolonged exposure to increased temperatures.
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Project description:We previously reported that ribosome stalling at AUG-stop sequences in the 5'-UTR plays a critical role in regulating the expression of Arabidopsis thaliana NIP5;1, which encodes a boron uptake transporter, in response to boron conditions in media. Here, we conducted ribosome profiling analysis to reveal the genome-wide regulation of translation in response to boron conditions in A. thaliana. We identified 460 translationally regulated genes. Transcripts with reduced translation efficiency were rich in upstream open reading frames (uORFs), highlighting the importance of uORF-mediated translational regulation. We found that 148 uORF instances had greater ribosome density under high boron conditions. Moreover, translationally downregulated transcripts were rich in minimum uORFs (AUG-stops), suggesting that AUG-stops play a global role in the boron response. Boron increased the ribosome occupancy of stop codons, indicating that this element is involved in global translational termination processes.
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Project description:High-throughput approaches for profiling the 5' ends of RNA degradation intermediates on a genome-wide scale are frequently applied in the validation of cleavage sites guided by microRNAs (miRNAs). However, the complexity of the RNA degradome beyond miRNA targets is currently largely unclear which limits the application of RNA degradome. Here, we provide multiple lines of evidence to show that the plant RNA degradome contains in vivo ribosome-protected mRNA fragments. We observed a 3-nt periodicity and a bias toward the translational frame in the global analysis of 5' truncated mRNA ends mapped to the coding sequence (CDS) of Arabidopsis (Arabidopsis thaliana), rice (Oryza sativa) and soybean (Glycine max). In addition, predominant 5' termini of RNA degradation intermediates separated by a length equal to a ribosome-protected mRNA fragment were evident in some conserved peptide upstream open reading frames (uORFs) of Arabidopsis and rice. Through the analysis of RNA degradome data, we uncovered novel uORFs and CDS regions potentially associated with stacked ribosomes in Arabidopsis. Furthermore, the analysis of RNA degradome data suggested that the binding of Arabidopsis ARGONAUTE7 to a non-cleavable target site of miR390 might directly hinder ribosome movement. This work demonstrates an alternative use of RNA degradome data in the study of ribosome stalling.
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