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Heterogeneous ribonucleoprotein interactions and impeded translational elongation in the respiratory tissue of SARS-CoV-2 pathology

ABSTRACT: Heterogeneous ribonucleoprotein interactions and impeded translational elongation in the respiratory tissue of SARS-CoV-2 pathology

PROVIDER: PRJNA918676 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR22989500_1.fastq.gz	Fastqsanger.gz
	SRR22989500_2.fastq.gz	Fastqsanger.gz
	SRR22989501_1.fastq.gz	Fastqsanger.gz
	SRR22989501_2.fastq.gz	Fastqsanger.gz
	SRR22989502_1.fastq.gz	Fastqsanger.gz

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Heterogeneous ribonucleoprotein interactions and impeded translational elongation in the respiratory tissue of SARS-CoV-2 pathology (Ribo-Seq)

Project description:Heterogeneous ribonucleoprotein interactions and impeded translational elongation in the respiratory tissue of SARS-CoV-2 pathology (Ribo-Seq)

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Heterogeneous ribonucleoprotein interactions and impeded translational elongation in the respiratory tissue of SARS-CoV-2 pathology (RNA-Seq)

Project description:Heterogeneous ribonucleoprotein interactions and impeded translational elongation in the respiratory tissue of SARS-CoV-2 pathology (RNA-Seq)

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Heterogeneous ribonucleoprotein interactions and impeded translational elongation in the respiratory tissue of SARS-CoV-2 pathology (RNA-Seq)

Project description:Translational regulation in in vivo tissue environments during viral pathogenesis has hardly been scrutinized due to the lack of tissue translatomes upon viral infection despite a number of the translatome studies on virus-infected cells cultured in vitro. We constructed the first temporal profile of lung translatomes during SARS-CoV-2 pathogenesis by applying ribosome profiling (Ribo-seq) to a severe COVID-19 mouse model. Unexpectedly, we observed gradual accumulations of non-canonical Ribo-seq reads representing hitherto-unidentified ribonucleoproteins (RNPs) that are likely involved in impeded translational elongation in the infected tissues. Contemporarily developing ribosome heterogeneity with prominently deviated 5S rRNP association supported the malfunction of elongating ribosomes. The analyses of canonical Riboseq reads (ribosome footprints) highlighted two obstructive characteristics to host gene expression: attenuated translation for transcriptionally up-regulated genes including immune response genes and ribosome stalling on codons within transmembrane domain-coding regions. Our study elucidates hidden molecular features of gene regulation in vivo underlying SARS-CoV-2 pathogenesis.

2023-12-01 | GSE222251 | GEO

Heterogeneous ribonucleoprotein interactions and impeded translational elongation in the respiratory tissue of SARS-CoV-2 pathology (Ribo-Seq)

2023-12-01 | GSE222249 | GEO

Heterogeneous ribonucleoprotein interactions and impeded translational elongation in the respiratory tissue of SARS-CoV-2 pathology

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

2023-12-01 | GSE222252 | GEO

Deficiency of the Heterogeneous Nuclear Ribonucleoprotein U locus leads to delayed hindbrain neurogenesis

Project description:Deficiency of the Heterogeneous Nuclear Ribonucleoprotein U locus leads to delayed hindbrain neurogenesis

| PRJNA952545 | ENA

Muscle Developmental Defects in Heterogeneous Nuclear Ribonucleoprotein A1 Knockout Mice

Project description:Transcriptome analysis of total RNA samples from heart tissue of knockout mice Alternative splicing is the main mechanism to increase protein diversity from an mRNA. Heterogeneous ribonucleoprotein (hnRNP) family members are vital regulators of alternative splicing. The hnRNP A1 is the most well-known protein in this family, but its role in embryonic development is not well understood. We generated hnRNP A1 knockout mice to study the function of hnRNP A1 in vivo. The hnRNP A1-depleted mice showed embryonic lethality because of muscle developmental defects. In a previous study, cellular hnRNP A2/B1 was reported to be capable of compensating for the expression of hnRNP A1. However, this phenomenon did not occur in the hnRNP A1 heterozygous mice in vivo. We demonstrated that hnRNP A1 regulated muscle-related genes expression and alternative splicing. In summary, our data demonstrated that hnRNP A1 plays a critical role in embryonic muscle development. Understanding the effects of hnRNP A1 in vivo may help to define the function of hnRNP A1 in alternative splicing.

2016-12-05 | GSE79076 | GEO

The Heterogeneous Nuclear Ribonucleoprotein U (HNRNPU) is the Safeguard of Neural Stem Cell Viability

Project description:The Heterogeneous Nuclear Ribonucleoprotein U (HNRNPU) is the Safeguard of Neural Stem Cell Viability

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Deficiency of the Heterogeneous Nuclear Ribonucleoprotein U locus leads to delayed hindbrain neurogenesis

Project description:Genetic variants affecting Heterogeneous Nuclear Ribonucleoprotein U (HNRNPU) have been identified in several neurodevelopmental disorders (NDDs). HNRNPU is widely expressed in the human brain and shows the highest postnatal expression in the cerebellum. Recent studies have investigated the role of HNRNPU in cerebral cortical development, but the effects of HNRNPU deficiency on cerebellar development remain unknown. Here, we describe the molecular and cellular outcomes of HNRNPU locus deficiency during in vitro neural differentiation of patient-derived and isogenic neuroepithelial stem cells with a hindbrain profile. We demonstrate that HNRNPU deficiency leads to chromatin remodeling of A/B compartments, and transcriptional rewiring, partly by impacting exon inclusion during mRNA processing. Genomic regions affected by the chromatin restructuring and host genes of exon usage differences show a strong enrichment for genes implicated in epilepsies, intellectual disability, and autism. Lastly, we show that at the cellular level. HNRNPU downregulation leads to altered neurogenesis and an increased fraction of neural progenitors in the maturing neuronal population. We conclude that, HNRNPU locus is involved in delayed commitment of neural progenitors to neuronal maturation in cell types with hindbrain profile.

2023-10-02 | GSE229004 | GEO

Heterogeneous nuclear ribonucleoprotein C1/C2 links transcriptional and splicing actions of 1,25-dihydroxyvitamin D

Project description:Heterogeneous nuclear ribonucleoprotein C1/C2 (hnRNPC1/C2) functions as an RNA splicing regulator through co-transcriptional association with nascent mRNA. HnRNPC1/C2 can also bind to double-stranded DNA as a vitamin D response element-binding protein (VDRE-BP), thereby regulating transcriptional activity of the vitamin D receptor (VDR) bound to 1,25-dihydroxyvitamin D (1,25(OH)2D). In this way hnRNPC1/C2 may act as a coupling factor for 1,25(OH)2D-directed transcription and RNA splicing. Studies using MG63 osteoblastic cells confirmed that 1,25(OH)2D-VDR mediated induction of the gene for the enzyme 24-hydroxylase (CYP24A1), involved CYP24A1-specific chromatin and RNA immunoprecipitation of hnRNPC1/C2. Furthermore, small interfering (siRNA) knockdown of hnRNPC1/C2 in MG63 cells and was associated with dysregulated expression of CYP24A1 and an alternatively spliced form of CYP24A1 (CYP24A1-variant 2). Genome-wide analysis of RNA expression and alternative splicing indicated that dual role of hnRNPC1/C2 in directing 1,25(OH)2D-mediated gene expression is not restricted to the classical VDR-target CYP24A1. Knockdown of hnRNPC1/C2 resulted in 3500 differentially expressed genes (DEG), and treatment with 1,25(OH)2D 324 DEG. A further 87 DEG were only observed in 1,25(OH)2D-treated cells in hnRNPC1/C2 knockdown cells. HnRNPC1/C2 knockdown or 1,25(OH)2D treatment also induced alternative splicing (AS) (5039 and 310 AS events respectively). Combined hnRNPC1/C2 knockdown and 1,25(OH)2D treatment resulted in significant overlap between DEG and AS genes, but this was not observed for 1,25(OH)2D treatment alone. These data indicate that hnRNPC1/C2 can act to couple transcriptional and splicing responses to 1,25(OH)2D by binding to both DNA and RNA. Similar mechanisms may also exist for other members of the hnRNP and steroid receptor family.

2016-12-06 | GSE63086 | GEO

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