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Exhaustive profiling in Arabidopsis reveals abundant polysome-associated 24-nt small RNAs including hitherto undescribed AGO5-associated pseudogene-derived siRNAs (psiRNAs)

ABSTRACT: Exhaustive profiling in Arabidopsis reveals abundant polysome-associated 24-nt small RNAs including hitherto undescribed AGO5-associated pseudogene-derived siRNAs (psiRNAs)

PROVIDER: PRJNA389736 | ENA |

REPOSITORIES: ENA

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Arabidopsis thaliana

Project description:Exhaustive profiling in Arabidopsis reveals abundant polysome-associated 24-nt small RNAs including hitherto undescribed AGO5-associated pseudogene-derived siRNAs (psiRNAs) [RNA]

| PRJNA389738 | ENA

Arabidopsis thaliana

| PRJNA389737 | ENA

Exhaustive profiling in Arabidopsis reveals abundant polysome-associated 24-nt small RNAs including hitherto undescribed AGO5-associated pseudogene-derived siRNAs (psiRNAs)

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

2017-12-31 | GSE99828 | GEO

Exhaustive profiling in Arabidopsis reveals abundant polysome-associated 24-nt small RNAs including hitherto undescribed AGO5-associated pseudogene-derived siRNAs (psiRNAs) [RNA]

Project description:The present study was primarily aimed at expanding the scope of the previous analyses, which focused largely on AGO1-miRNA interactions with total polysomes and membrane-bound polysomes (MBPs), respectively. Our larger aim was to comprehensively analyze which, among the multiple AGO effector proteins and the numerous cellular sRNA classes of Arabidopsis, interact with the translational machinery.

2017-12-31 | GSE99826 | GEO

Exhaustive profiling in Arabidopsis reveals abundant polysome-associated 24-nt small RNAs including hitherto undescribed AGO5-associated pseudogene-derived siRNAs (psiRNAs) [sRNA]

Project description:The present study was primarily aimed at expanding the scope of the previous analyses, which focused largely on AGO1-miRNA interactions with total polysomes and MBPs, respectively. Our larger aim was to comprehensively analyze which, among the multiple AGO effector proteins and the numerous cellular sRNA classes of Arabidopsis, interact with the translational machinery.

2017-12-31 | GSE99827 | GEO

Extensive profiling in Arabidopsis reveals abundant polysome-associated 24-nt small RNAs including AGO5-dependent pseudogene-derived siRNAs.

Project description:In a reductionist perspective, plant silencing small (s)RNAs are often classified as mediating nuclear transcriptional gene silencing (TGS) or cytosolic posttranscriptional gene silencing (PTGS). Among the PTGS diagnostics is the association of AGOs and their sRNA cargos with the translation apparatus. In Arabidopsis, this is observed for AGO1 loaded with micro(mi)RNAs and, accordingly, translational-repression (TR) is one layer of plant miRNA action. Using AGO1:miRNA-mediated TR as a paradigm, we explored, with two unrelated polysome-isolation methods, which, among the ten Arabidopsis AGOs and numerous sRNA classes, interact with translation. We found that representatives of all three AGO-clades associate with polysomes, including the TGS-effector AGO4 and stereotypical 24-nt sRNAs that normally mediate TGS of transposons/repeats. Strikingly, approximately half of these annotated 24-nt siRNAs displayed unique matches in coding regions/introns of genes, and in pseudogenes, but not in transposons/repeats commonly found in their vicinity. Protein-coding gene-derived 24-nt sRNAs correlate with gene-body methylation. Those derived from pseudogenes belong to two main clusters defined by their parental-gene expression patterns, and are vastly enriched in AGO5, itself found on polysomes. Based on their tight expression pattern in developing and mature siliques, their biogenesis, and genomic/epigenomic features of their loci-of-origin, we discuss potential roles for these hitherto unknown polysome-enriched, pseudogene-derived siRNAs.

| S-EPMC6800511 | biostudies-literature

A pseudogene lncRNA at the interface of inflammation and anti-inflammatory therapeutics

Project description:Pseudogenes are thought to be inactive gene sequences, but recent evidence of extensive pseudogene transcription raised the question of potential function. Here we discover and characterize the sets of lncRNAs induced by inflammatory signaling via TNFα. TNFα regulates hundreds of lncRNAs, including 54 pseudogene lncRNAs, several of which show exquisitely selective expression in response to specific cytokines and microbial components in a NF-κB-dependent manner. Lethe, a pseudogene lncRNA, is selectively induced by proinflammatory cytokines via NF-κB or glucocorticoid receptor agonist, and functions in negative feedback signaling to NF-κB. Lethe interacts with NF-κB subunit RelA to inhibit RelA DNA binding and target gene activation. Lethe level decreases with organismal age, a physiological state associated with increased NF-κB activity. These findings suggest that expression of pseudogenes lncRNAs are actively regulated and constitute functional regulators of inflammatory signaling.

2013-08-05 | GSE47494 | GEO

A pseudogene lncRNA at the interface of inflammation and anti-inflammatory therapeutics

2013-08-05 | E-GEOD-47494 | biostudies-arrayexpress

Francisella noatunensis subsp orientalis FNO12 pseudogene validation

Project description:Due to the detection of mRNA expression for several protein CDS annotated as pseudogenes in the results of the microarray experiment, a shotgun proteomic approach was applied to verify actual protein translation for each pseudogene in the genome of FNO12.

2019-05-27 | PXD012449 | Pride

Arabidopsis AGO5 contributes to a POL II-based RNA silencing pathway directing epigenetic marks

Project description:To characterise the Arabidopsis AGO5 protein, we report the AGO5 associated sRNAs, ago5 mutant total sRNAs and digital gene indexing tags with altered abundance in the ago5 mutant. Examination of AGO5 associated sRNAs, population of total sRNAs in the ago5 mutant and characterisation of RNA transcripts with altered abundance in the ago5 mutant.

2014-07-27 | E-GEOD-30970 | biostudies-arrayexpress

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