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Cell-type-specific profiling of loaded miRNAs from Caenorhabditis elegans reveals spatial and temporal flexibility in Argonaute loading [RNA-seq]

ABSTRACT: Cell-type-specific profiling of loaded miRNAs from Caenorhabditis elegans reveals spatial and temporal flexibility in Argonaute loading [RNA-seq]

PROVIDER: PRJNA659145 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR12506931.fastq.gz	Fastqsanger.gz
	SRR12506931_1.fastq.gz	Fastqsanger.gz
	SRR12506931_2.fastq.gz	Fastqsanger.gz
	SRR12506932.fastq.gz	Fastqsanger.gz
	SRR12506932_1.fastq.gz	Fastqsanger.gz

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Cell-type-specific profiling of loaded miRNAs from Caenorhabditis elegans reveals spatial and temporal flexibility in Argonaute loading [miRNA-seq]

Project description:We aimed to characterize the cell-type specific loading patterns of miRNAs in c.elegans. We expressed cell-type specific HA-epitope tagged versions of Argonaute-like 1 (ALG-1) and ALG-2 from three major tissue types i.e. intestine, nervous system and body wall mucle. We found that most miRNAs display highly cell-type specific loading patterns. ALG-1 is more ubiquitously loaded whereas ALG-2 is eniriched for miRNA loading within the nervous system. Addtionally we show that there is flexibility in ALG loading which changes during the aging process.

2020-08-25 | GSE156716 | GEO

Cell-type-specific profiling of loaded miRNAs from Caenorhabditis elegans reveals spatial and temporal flexibility in Argonaute loading

Project description:Cell-type-specific profiling of loaded miRNAs from Caenorhabditis elegans reveals spatial and temporal flexibility in Argonaute loading

| PRJNA658897 | ENA

Cell-type-specific profiling of loaded miRNAs from Caenorhabditis elegans reveals spatial and temporal flexibility in Argonaute loading [miRNA-seq]

Project description:Cell-type-specific profiling of loaded miRNAs from Caenorhabditis elegans reveals spatial and temporal flexibility in Argonaute loading [miRNA-seq]

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Hierarchical rules for Argonaute loading in Drosophila

Project description:Drosophila Argonaute-1 and Argonaute-2 differ in function and small RNA content. AGO2 binds to siRNAs, whereas AGO1 is almost exclusively occupied by microRNAs. microRNA duplexes are intrinsically asymmetric, with one strand, the miR strand, preferentially entering AGO1 to recognize and regulate the expression of target mRNAs. The other strand, miR*, has been viewed as a by-product of microRNA biogenesis. Here, we show that miR*s are often loaded as functional species into AGO2. This indicates that each microRNA precursor can potentially produce two mature small RNA strands that are differentially sorted within the RNAi pathway. miR* biogenesis depends upon the canonical microRNA pathway, but loading into AGO2 is mediated by factors traditionally dedicated to siRNAs. By inferring and validating hierarchical rules that predict differential AGO loading, we find that intrinsic determinants, including structural and thermodynamic properties of the processed duplex, regulate the fate of each RNA strand within the RNAi pathway. These were independently processed and sequenced using the Illumina GAII platform. In total, five libraries were analyzed.

2009-11-15 | E-GEOD-17734 | biostudies-arrayexpress

Cell-type-specific profiling of loaded miRNAs from Caenorhabditis elegans reveals spatial and temporal flexibility in Argonaute loading.

Project description:Multicellularity has coincided with the evolution of microRNAs (miRNAs), small regulatory RNAs that are integrated into cellular differentiation and homeostatic gene-regulatory networks. However, the regulatory mechanisms underpinning miRNA activity have remained largely obscured because of the precise, and thus difficult to access, cellular contexts under which they operate. To resolve these, we have generated a genome-wide map of active miRNAs in Caenorhabditis elegans by revealing cell-type-specific patterns of miRNAs loaded into Argonaute (AGO) silencing complexes. Epitope-labelled AGO proteins were selectively expressed and immunoprecipitated from three distinct tissue types and associated miRNAs sequenced. In addition to providing information on biological function, we define adaptable miRNA:AGO interactions with single-cell-type and AGO-specific resolution. We demonstrate spatial and temporal dynamicism, flexibility of miRNA loading, and suggest miRNA regulatory mechanisms via AGO selectivity in different tissues and during ageing. Additionally, we resolve widespread changes in AGO-regulated gene expression by analysing translatomes specifically in neurons.

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Cell-type-specific profiling of loaded miRNAs from Caenorhabditis elegans reveals spatial and temporal flexibility in Argonaute loading

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

2020-08-25 | GSE156721 | GEO

Cell-type-specific profiling of loaded miRNAs from Caenorhabditis elegans reveals spatial and temporal flexibility in Argonaute loading [RNA-seq]

Project description:We report the the 'translatome' of the nervous system in c.elegans by immunoprecipitating FLAG- epitope tagged RPL-18 expressed under a nervous system specific promoter. In addition we compared this to the nervous system specific 'translatome' in an alg-2 mutant background. As such we were able to determine the specifc effects of ALG-2 on the nervous sytem gene expression landscape.

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Transcription profiling of human dermal fibroblasts after 3 hours of cyclic mechanical loading compared with ni loading - collagen 1 hydrogel dynamic loading tests

Project description:Cell viability and global gene expression was anayzed from collagen 1 hydrogel scaffolds following 3 hours of cyclic mechanical loading and compared with non-loaded scaffolds. Experiment Overall Design: 6 samples are analyzed (2 sets in triplicate). The first set is the Loaded condition in which Collagen 1 hydrogels seeded with Human dermal fibroblasts underwent cyclic loading of 0.1Hz for 180 minutes at 37 degrees Celsius. The second set is the control Unloaded condition in which the Collagen 1 hydrogels seeded with Human dermal fibroblasts are incubated at 37 degrees Celsius with no loading.

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