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Functional RNA dynamics are progressively governed by RNA destabilization during the adaptation to chronic hypoxia

ABSTRACT: Functional RNA dynamics are progressively governed by RNA destabilization during the adaptation to chronic hypoxia

PROVIDER: PRJNA822350 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR18583413.fastq.gz	Fastqsanger.gz
	SRR18583414.fastq.gz	Fastqsanger.gz
	SRR18583415.fastq.gz	Fastqsanger.gz
	SRR18583416.fastq.gz	Fastqsanger.gz
	SRR18583417.fastq.gz	Fastqsanger.gz

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Functional RNA Dynamics Are Progressively Governed by RNA Destabilization during the Adaptation to Chronic Hypoxia.

Project description: Not available

| S-EPMC9144826 | biostudies-literature

Functional RNA dynamics are progressively governed by RNA destabilization during the adaptation to chronic hypoxia

Project description:Previous studies towards reduced oxygen availability mostly focused on changes in total mRNA expression neglecting underlying transcriptional and post-transcriptional events. Therefore, we generated a comprehensive overview of hypoxia-induced changes in total mRNA expression, global de novo transcription, and mRNA stability in monocytic THP-1 cells. Since hypoxic epi-sodes often persist for prolonged periods, we further compared adaptations to acute and chronic hypoxia. While total mRNA changes correlated well with enhanced transcription during short term hypoxia, mRNA destabilization gained importance under chronic conditions. Reduced mRNA stability not only added to compensatory attenuation of immune responses, but most no-tably to the reduction of nuclear-encoded mRNAs associated with various mitochondrial func-tions. These changes may prevent the futile production of new mitochondria under conditions where mitochondria cannot exert their full metabolic function and are indeed actively removed by mitophagy. The post-transcriptional mode of regulation might further allow for rapid recov-ery of mitochondrial capacities upon reoxygenation. Our results provide a comprehensive re-source of functional mRNA expression dynamics and underlying transcriptional and post-transcriptional regulatory principles during the adaptation to hypoxia. Furthermore, we specifically uncover mitochondrial functions controlled by RNA stability regulation in the con-text of hypoxia.

2022-06-01 | GSE199947 | GEO

Induction of a transcriptional adaptation response by RNA destabilization events [dst278]

Project description:Transcriptional adaptation (TA) is a cellular process whereby mRNA-destabilizing mutations lead to the transcriptional upregulation of so-called adapting genes. The nature of the TA-triggering factor(s) remains unclear, namely whether an mRNA-borne premature termination codon (PTC) or the subsequent mRNA degradation process, and/or its products, elicits TA. Here, we first established two perturbations leading to mRNA destabilization for mouse Actg1: a Cas9-induced mutation that leads to a PTC, and Cas13d-mediated mRNA cleavage. We find that both perturbations are effective in degrading Actg1 mRNA and upregulating Actg2. Notably, increased chromatin accessibility at the Actg2 locus was observed only in the Cas9-induced mutant allele but not in the Cas13d-targeted cells, suggesting that chromatin remodeling is not required for Actg2 upregulation. We further show that ribozyme-mediated Actg1 pre-mRNA cleavage also leads to a robust upregulation of Actg2. Together, these data highlight the critical role of RNA destabilization events as a trigger for TA.

2025-03-17 | GSE282000 | GEO

Induction of a transcriptional adaptation response by RNA destabilization events [dst278]

Project description:Induction of a transcriptional adaptation response by RNA destabilization events [dst278]

| PRJNA1186596 | ENA

Induction of a transcriptional adaptation response by RNA destabilization events [dst175]

Project description:Induction of a transcriptional adaptation response by RNA destabilization events [dst175]

| PRJNA1207915 | ENA

Progressively overloaded single-cell RNA-seq with cell hashing

Project description:Progressively overloaded single-cell RNA-seq with cell hashing

| PRJNA753770 | ENA

Circular RNA expression in ALS is progressively deregulated and tissue-dependent

Project description:Circular RNA expression in ALS is progressively deregulated and tissue-dependent

| PRJNA1223873 | ENA

Progressively overloaded single-cell RNA-seq with cell hashing

Project description:Barcode-based multiplexing methods can be used to increase throughput and reduce batch effects in large single-cell genomics studies. To evaluate methods for demultiplexing barcode-multiplexed data, we generated a dataset by labeling samples separately with barcode-tagged antibodies, mixing those samples, and progressively overloading a droplet-based scRNA-seq system.

2021-12-01 | GSE181862 | GEO

mRNA destabilization by BTG1 and BTG2 maintains T cell quiescence [RNA-seq]

Project description:mRNA destabilization by BTG1 and BTG2 maintains T cell quiescence [RNA-seq]

| PRJNA517726 | ENA

Pervasive TTP binding but selective target mRNA destabilization in the macrophage transcriptome [RNA-Seq]

Project description:Precise control of mRNA decay is fundamental for robust yet not exaggerated inflammatory responses to pathogens. Parameters determining the specificity and extent of mRNA degradation within the entire inflammation-associated transcriptome remain incompletely understood. Using transcriptome-wide high resolution occupancy assessment of the mRNA-destabilizing protein TTP, a major inflammation-limiting factor, we qualitatively and quantitatively characterize TTP binding positions and functionally relate them to TTP-dependent mRNA decay in immunostimulated macrophages. We identify pervasive TTP binding with incompletely penetrant linkage to mRNA destabilization. A necessary but not sufficient feature of TTP-mediated mRNA destabilization is binding to 3â untranslated regions (UTRs). Mapping of binding positions of the mRNA-stabilizing protein HuR in activated macrophages revealed that TTP and HuR binding sites in 3â UTRs occur mostly in different transcripts implicating only a limited co-regulation of inflammatory mRNAs by these proteins. Remarkably, we identify robust and widespread TTP binding to introns of stable transcripts. Nuclear TTP is associated with spliced-out introns and maintained in the nucleus throughout the inflammatory response. Our study establishes a functional annotation of binding positions dictating TTP-dependent mRNA decay in immunostimulated macrophages. The findings allow navigating the transcriptome-wide landscape of RNA elements controlling inflammation. RNA-Seq of RNA isolated from murine bone marrow derived macrophages (WT or TTP-deficient) stimulated for 6 h with LPS

2016-05-17 | E-GEOD-63467 | biostudies-arrayexpress

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