Arabidopsis thaliana
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA232638 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR1061592.fastq.gz | Fastqsanger.gz | |||
| SRR1061593.fastq.gz | Fastqsanger.gz | |||
| SRR1061594.fastq.gz | Fastqsanger.gz | |||
| SRR1061595.fastq.gz | Fastqsanger.gz |
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Project description:3' and 5' end modifications in plant microRNA post biogenesis: evidences from NGS of small RNAs
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Project description:Eukaryotic messenger RNAs (mRNAs) possess a 5’-end N7-methyl guanosine (m7G) cap that promotes their translation and stability. However, it was recently demonstrated that eukaryotic mRNAs can also carry a 5' end nicotinamide adenine dinucleotide (NAD+) cap that promotes mRNA decay mediated by the NAD+ decapping enzyme DXO1. However, the dynamic regulation of NAD+ capping in plant remains unknown. Here, we describe the global landscape of NAD+-capped RNAs in Arabidopsis thaliana, and demonstrate that DXO1 is responsible for removal of these 5’-end modifications and facilitates mRNA degradation in plant transcriptomes. We also reveal that in the absence of DXO1 NAD+-capped mRNAs are unstable and processed into smRNAs. Furthermore, we find that Abscisic Acid (ABA) remodel the landscape of RNA cap epitransciptome, and the mRNA lost their NAD+ cap contribute to their stability under ABA. Overall, our results support a link between ABA response and RNA NAD+ capping.
2020-11-23 | GSE142388 | GEO
Project description:Eukaryotic messenger RNAs (mRNAs) possess a 5’-end N7-methyl guanosine (m7G) cap that promotes their translation and stability. However, it was recently demonstrated that eukaryotic mRNAs can also carry a 5' end nicotinamide adenine dinucleotide (NAD+) cap that promotes mRNA decay mediated by the NAD+ decapping enzyme DXO1. However, the dynamic regulation of NAD+ capping in plant remains unknown. Here, we describe the global landscape of NAD+-capped RNAs in Arabidopsis thaliana, and demonstrate that DXO1 is responsible for removal of these 5’-end modifications and facilitates mRNA degradation in plant transcriptomes. We also reveal that in the absence of DXO1 NAD+-capped mRNAs are unstable and processed into smRNAs. Furthermore, we find that Abscisic Acid (ABA) remodel the landscape of RNA cap epitransciptome, and the mRNA lost their NAD+ cap contribute to their stability under ABA. Overall, our results support a link between ABA response and RNA NAD+ capping.
2020-11-23 | GSE142389 | GEO
Project description:Uridylation of diverse RNA species represents an emerging theme in post-transcriptional gene regulation. In the microRNA pathway, such modifications regulate small RNA biogenesis and stability in plants, worms and mammals. Here, we report the first uridylyltransferase that acts on small RNAs in Drosophila, which we refer to as Tailor. Tailor is the source for the majority of 3´ end-modifications in microRNAs and predominantly targets precursor-hairpins. Uridylation modulates the characteristic two-nucleotide 3´ overhangs of microRNA hairpins, which regulates processing by Dicer-1 and destabilizes RNA hairpins. Furthermore, Tailor preferentially uridylates mirtron-hairpins, thereby impeding the production of non-canonical microRNAs. Mirtron-selectivity is explained by unique primary sequence specificity of Tailor, selecting RNA substrates ending with a 3´ guanosine, a feature not previously observed for TUTases. In contrast to mirtrons, conserved Drosophila pre-miRNAs are significantly depleted in 3´ guanosine, thereby escaping regulatory uridylation. Our data support the hypothesis that evolutionary adaptation to pre-miRNA uridylation shapes the nucleotide composition of pre-miRNA 3´ ends. Hence, hairpin-uridylation may serve as a barrier for the de novo creation of miRNAs in Drosophila.
2015-10-19 | GSE67646 | GEO
Project description:Backgropund:In a major paradigm shift in the last decade, the knowledge about a whole class of non-coding RNAs known as miRNAs has emerged, which have proved these to be important regulators of a wide range of cellular processes by the way of modulation of gene expression. It is reported that some of these miRNAs are modified by addition or deletion of nucleotides at their ends, after biogenesis. However, the biogenesis and functions of these modifications are not well studied in eukaryotes, especially in plants. In this study, we examined the miRNA modifications in different tissues of the various plants, namely rice, tomato and Arabidopsis and identified some common features of such modifications. Results:We have analyzed different aspects of miRNA modifications in plants. To achieve this end, we developed a PERL script to find the modifications in the sequences using small RNA deep sequencing data. The modification occurs in both mature and passenger (star) strands, as well as at both the 5' and 3' ends of miRNAs. Interestingly, we found a position-specific nucleotide biased modification, as evident by increased number of modification at the 5' end with the presence of Cytosine (nucleotide 'C') at the 3âend of the miRNA sequence. The level of modifications is not strictly dependent on the abundance of miRNA. Our study showed that the modification events are independent of plant species, tissue and physiological conditions. Our analysis also indicates that the RNAi enzyme, namely, the RNA dependent RNA polymerase 6 (RDR6) may not have any role in Arabidopsis miRNA modifications. Some of these modified miRNAs are bound to AGO1, suggesting their possible roles in biological processes. Conclusions:This is a first report that reveals that 5' nucleotide additions are preferred for mature miRNA sequences with 3â terminal âCâ nucleotide. Our analysis also indicates that the miRNAs modifications involving addition of nucleotides to the 5â or 3â end are independent of RDR6 activity and are not restricted by plant species, physiological conditions and tissue types. The results also indicate that such modifications might be important for biological processes. small RNA profiles of Healthy and ToLCV infected tomato leaves were generated by deep sequencing using Illumina GAII.
2015-10-24 | E-GEOD-53253 | biostudies-arrayexpress
Project description:Backgropund:In a major paradigm shift in the last decade, the knowledge about a whole class of non-coding RNAs known as miRNAs has emerged, which have proved these to be important regulators of a wide range of cellular processes by the way of modulation of gene expression. It is reported that some of these miRNAs are modified by addition or deletion of nucleotides at their ends, after biogenesis. However, the biogenesis and functions of these modifications are not well studied in eukaryotes, especially in plants. In this study, we examined the miRNA modifications in different tissues of the various plants, namely rice, tomato and Arabidopsis and identified some common features of such modifications. Results:We have analyzed different aspects of miRNA modifications in plants. To achieve this end, we developed a PERL script to find the modifications in the sequences using small RNA deep sequencing data. The modification occurs in both mature and passenger (star) strands, as well as at both the 5' and 3' ends of miRNAs. Interestingly, we found a position-specific nucleotide biased modification, as evident by increased number of modification at the 5' end with the presence of Cytosine (nucleotide 'C') at the 3âend of the miRNA sequence. The level of modifications is not strictly dependent on the abundance of miRNA. Our study showed that the modification events are independent of plant species, tissue and physiological conditions. Our analysis also indicates that the RNAi enzyme, namely, the RNA dependent RNA polymerase 6 (RDR6) may not have any role in Arabidopsis miRNA modifications. Some of these modified miRNAs are bound to AGO1, suggesting their possible roles in biological processes. Conclusions:This is a first report that reveals that 5' nucleotide additions are preferred for mature miRNA sequences with 3â terminal âCâ nucleotide. Our analysis also indicates that the miRNAs modifications involving addition of nucleotides to the 5â or 3â end are independent of RDR6 activity and are not restricted by plant species, physiological conditions and tissue types. The results also indicate that such modifications might be important for biological processes. Total 14 samples were analyzed, each in a pair of control and heat stress.
2015-10-24 | E-GEOD-53252 | biostudies-arrayexpress
Project description:Backgropund:In a major paradigm shift in the last decade, the knowledge about a whole class of non-coding RNAs known as miRNAs has emerged, which have proved these to be important regulators of a wide range of cellular processes by the way of modulation of gene expression. It is reported that some of these miRNAs are modified by addition or deletion of nucleotides at their ends, after biogenesis. However, the biogenesis and functions of these modifications are not well studied in eukaryotes, especially in plants. In this study, we examined the miRNA modifications in different tissues of the various plants, namely rice, tomato and Arabidopsis and identified some common features of such modifications. Results:We have analyzed different aspects of miRNA modifications in plants. To achieve this end, we developed a PERL script to find the modifications in the sequences using small RNA deep sequencing data. The modification occurs in both mature and passenger (star) strands, as well as at both the 5' and 3' ends of miRNAs. Interestingly, we found a position-specific nucleotide biased modification, as evident by increased number of modification at the 5' end with the presence of Cytosine (nucleotide 'C') at the 3âend of the miRNA sequence. The level of modifications is not strictly dependent on the abundance of miRNA. Our study showed that the modification events are independent of plant species, tissue and physiological conditions. Our analysis also indicates that the RNAi enzyme, namely, the RNA dependent RNA polymerase 6 (RDR6) may not have any role in Arabidopsis miRNA modifications. Some of these modified miRNAs are bound to AGO1, suggesting their possible roles in biological processes. Conclusions:This is a first report that reveals that 5' nucleotide additions are preferred for mature miRNA sequences with 3â terminal âCâ nucleotide. Our analysis also indicates that the miRNAs modifications involving addition of nucleotides to the 5â or 3â end are independent of RDR6 activity and are not restricted by plant species, physiological conditions and tissue types. The results also indicate that such modifications might be important for biological processes. small RNA profiles of wild type and RDR6 (-) of Arabidopsis plants were generated using deep sequencing data.
2015-10-24 | E-GEOD-53687 | biostudies-arrayexpress
Project description:Ribosome biogenesis is a major cellular processes involving a large inventory of proteinaceous and RNA cofactors. Recent bioinformatics approaches discovered a large but not complete overlap of the inventory between yeast, mammals and plants. We re-inspected the complexity of ribosome biogenesis factors (RBFs) by assigning co-orthologs to each protein family in the A. thaliana and S. lycopersicum genomes. We realized that about 25% of all analyzed RBFs in the two plant genomes are encoded by more than one gene. The majority is expressed in leaves and anthers of tomato as determined by next generation sequencing (NGS). For the analysis of NGS data we developed a software pipeline M-bM-^@M-^XCRACPipeM-bM-^@M-^Y. This pipeline is designed to be very flexible with respect to genome selection and experimental set up. The NGS analysis revealed the expression of 24.538 genes in tomato leaves and of 22.893 genes in anthers. The observed expression of RBFs was confirmed by qRT-PCR for a randomly chosen sub-set of genes. Further, analysis of the expression profile of selected RBFs during male gametophyte development revealed a differential expression in the different developmental stages for the majority of genes. Based on our analysis we conclude that RBFs described in yeast but not present in plant genomes as concluded from previous orthology analysis are in parts replaced by other RBFs for which multiple genes have been identified in here. In addition, the obtained complexity for some RBFs accounts for a tissue and developmental specific regulation of ribosome biogenesis as well. 2 samples
2014-08-01 | E-GEOD-56610 | biostudies-arrayexpress