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Cell layer specific AGO1-loaded sRNA from dcl234 triple mutant; Cell layer specific and polysome associated RNA from Col0 and hyl1 mutant roots.

ABSTRACT: This SuperSeries is composed of the SubSeries listed below.

ORGANISM(S): Arabidopsis thaliana

PROVIDER: GSE104117 | GEO | 2019/04/24

REPOSITORIES: GEO

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Cell layer specific and polysome associated RNA from Arabidopsis thaliana Col0 and hyl1 mutant roots.

Project description:microRNAs (miRNA’s) regulation target gene expression, often transcription factors and as such control entire transcriptional networks. This control is important for various developmental transitions and stress responses in a wide range of eukaryotic organisms. While miRNA-mediated gene regulation has been investigated over time (temporal) and in whole organs or tissues in multiple different organisms highlighting their importance, there has been a distinct lack of focus on spatial resolution of miRNA biology. Here we present at cell-type specific resolution, miRNA loading and miRNA action within the Arabidopsis root. Our results for the first time demonstrate the multiple novel modes of miRNA action and illustrate the widespread nature of miRNA movement, at a genome scale within a complex eukaryotic organ.

2019-04-24 | GSE104116 | GEO

Cell layer specific AGO1-loaded sRNA from dcl234 triple mutant Cell layer specific and polysome associated RNA from Col0 and hyl1 mutant roots.

Project description:Cell layer specific AGO1-loaded sRNA from dcl234 triple mutant Cell layer specific and polysome associated RNA from Col0 and hyl1 mutant roots.

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Cell layer specific AGO1-loaded sRNA from Arabidopsis thaliana dcl234 triple mutant

2019-04-24 | GSE104115 | GEO

Cell layer specific and polysome associated RNA from Arabidopsis thaliana Col0 and hyl1 mutant roots.

Project description:Cell layer specific and polysome associated RNA from Arabidopsis thaliana Col0 and hyl1 mutant roots.

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Cell layer specific AGO1-loaded sRNA from Arabidopsis thaliana dcl234 triple mutant

Project description:Cell layer specific AGO1-loaded sRNA from Arabidopsis thaliana dcl234 triple mutant

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Root cell layer specific AGO1-bound sRNA and total sRNA from Arabidopsis ktn1 mutant

Project description:We profiled total sRNA and root cell layer specific AGO1-bound sRNA in ktn1 mutant to study the role of KTN1 in miRNA non-cell autonomous activiy in Arabidopsis.

2022-03-21 | GSE168805 | GEO

Root cell layer specific AGO1-bound sRNA and total sRNA from Arabidopsis ktn1 mutant

Project description:Root cell layer specific AGO1-bound sRNA and total sRNA from Arabidopsis ktn1 mutant

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Novel functional small RNAs are selectively loaded onto mammalian Ago1.

Project description:Argonaute (Ago) proteins function in RNA silencing as components of the RNA-induced silencing complex (RISC). In lower organisms, the small interfering RNA and miRNA pathways diverge due in part to sorting mechanisms that direct distinct small RNA (sRNA) duplexes onto specific Ago-RISCs. However, such sorting mechanisms appear to be lost in mammals. miRNAs appear not to distinguish among Ago1-4. To determine the effect of viral infection on the sorting system, we compared the content of deep-sequenced RNA extracted from immunoprecipitation experiments with the Ago1 and Ago2 proteins using Epstein-Barr virus (EBV)-infected cells. Consistent with previous observations, sequence tags derived from miRNA loci in EBV and humans globally associate in approximately equivalent amounts with Ago1 and Ago2. Interestingly, additional sRNAs, which have not been registered as miRNAs, were associated with Ago1. Among them, some unique sequence tags derived from tandem loci in the human genome associate exclusively with Ago1 but not, or rarely, with Ago2. This is supported by the observation that the expression of the unique sRNAs in the cells is highly dependent on Ago1 proteins. When we knocked down Ago1, the expression of the Ago1-specific sRNAs decreased dramatically. Most importantly, the Ago1-specific sRNAs bound to mRNAs and regulated target genes and were dramatically upregulated, depending on the EBV life cycle. Therefore, even in mammals, the sorting mechanism in the Ago1-4 family is functional. Moreover, the existence of Ago1-specific sRNAs implies vital roles in some aspects of mammalian biology.

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Expression data in Arabidopsis ago1-25 and hyl1-2 mutants.

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Differential sRNA regulation in leaves and roots of sugarcane under water depletion.

Project description:Plants have developed multiple regulatory mechanisms to respond and adapt to stress. Drought stress is one of the major constraints to agricultural productivity worldwide and recent reports have highlighted the importance of plant sRNA in the response and adaptation to water availability. In order to increase our understanding of the roles of sRNA in response to water depletion, cultivars of sugarcane were submitted to treatment of ceasing drip irrigation for 24 hours. Deep sequencing analysis was carried out to identify the sRNA regulated in leaves and roots of sugarcane cultivars with different drought sensitivities. The pool of sRNA selected allowed the analysis of different sRNA classes (miRNA and siRNA). Twenty-eight and 36 families of conserved miRNA were identified in leaf and root libraries, respectively. Dynamic regulation of miRNA was observed and the expression profiles of eight miRNA were verified in leaf samples from three biological replicates by stem-loop qRT-PCR assay using the cultivars: SP90-1638--sensitive cultivar--and SP83-2847 and SP83-5073--tolerant cultivars. Altered miRNA regulation was correlated with changes in mRNA levels of specific targets. Two leaf libraries from individual sugarcane cultivars with contrasting drought-tolerance properties were also analyzed. An enrichment of 22-nt sRNA species was observed in leaf libraries. 22-nt miRNA triggered siRNA production by cleavage of their targets in response to water depletion. A number of genes of the sRNA biogenesis pathway were down-regulated in tolerant genotypes and up-regulated in sensitive in response to water depletion treatment. Our analysis contributes to increase the knowledge on the roles of sRNA in sugarcane submitted to water depletion.

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