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Effective extraction of polyribosomes exposes gene expression strategies in primary astrocytes

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

ORGANISM(S): Mus musculus

PROVIDER: GSE216583 | GEO | 2023/02/09

REPOSITORIES: GEO

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Effective extraction of polyribosomes exposes gene expression strategies in primary astrocytes.

Project description:Regulation of mRNA translation in astrocytes gains a growing interest. However, until now, successful ribosome profiling of primary astrocytes has not been reported. Here, we optimized the standard 'polysome profiling' method and generated an effective protocol for polyribosome extraction, which enabled genome-wide assessment of mRNA translation dynamics along the process of astrocyte activation. Transcriptome (RNAseq) and translatome (Riboseq) data generated at 0, 24 and 48 h after cytokines treatment, revealed dynamic genome-wide changes in the expression level of ∼12 000 genes. The data clarify whether a change in protein synthesis rate results from a change in mRNA level or translation efficiency per se. It exhibit different expression strategies, based on changes in mRNA abundance and/or translation efficiency, which are specifically assigned to gene subsets depending on their function. Moreover, the study raises an important take-home message related to the possible presence of 'difficult to extract' polyribosome sub-groups, in all cell types, thus illuminating the impact of ribosomes extraction methodology on experiments addressing translation regulation.

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Effective extraction of polyribosomes from primary astrocytes exposes strategies of gene expression regulation [Heavy_complex_RNAseq]

Project description:We optimized a polysome profiling protocol considering the unique morphology and ribosomal distribution of astrocytes. This ‘astrocyte-optimized’ protocol was then used to study primary astrocytes treated with proinflammatory cytokines, enabeling Riboseq analysis for measurment of the transcriptome, translatome, and translation efficiency with a coverage of over 12,000 genes. We found several regulation strategies of gene expression in astrocytes executed as part of an extensive inflamatory response. Enhanced translation efficiency was one of these strategies, used specifically for genes related to oxidative phosphorylation, and ribosomal proteins.

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Effective extraction of polyribosomes from primary astrocytes exposes strategies of gene expression regulation [RNAseq_Riboseq]

Project description:We optimized a standard polysome profiling protocol considering the unique morphology and ribosomal distribution of astrocytes. This ‘astrocyte-optimized’ protocol was then used to study primary astrocytes treated with proinflammatory cytokines, enabeling Ribo-seq analysis for measurment of the transcriptome, translatome, and translation efficiency with a coverage of over 12,000 genes. We found several regulation strategies of gene expression executed as part of an extensive inflamatory response. Enhanced translation efficiency was one of these strategies, used specifically for genes related to oxidative phosphorylation, and ribosomal proteins.

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Effective extraction of polyribosomes exposes gene expression strategies in primary astrocytes

Project description:Effective extraction of polyribosomes exposes gene expression strategies in primary astrocytes

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Effective extraction of polyribosomes from primary astrocytes exposes strategies of gene expression regulation [Heavy_complex_RNAseq]

Project description:Effective extraction of polyribosomes from primary astrocytes exposes strategies of gene expression regulation [Heavy_complex_RNAseq]

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Effective extraction of polyribosomes from primary astrocytes exposes strategies of gene expression regulation [RNAseq_Riboseq]

Project description:Effective extraction of polyribosomes from primary astrocytes exposes strategies of gene expression regulation [RNAseq_Riboseq]

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