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Systematic analysis of gene expression profiles controlled by hnRNP Q and hnRNP R, two closely related human heterogeneous nuclear ribonucleoproteins.

ABSTRACT: Systematic analysis of gene expression profiles controlled by hnRNP Q and hnRNP R, two closely related human heterogeneous nuclear ribonucleoproteins.

PROVIDER: PRJNA465747 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR7132480.fastq.gz	Fastqsanger.gz
	SRR7132490.fastq.gz	Fastqsanger.gz
	SRR7132481.fastq.gz	Fastqsanger.gz
	SRR7132491.fastq.gz	Fastqsanger.gz
	SRR7132482.fastq.gz	Fastqsanger.gz

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Differential RNA Interactions with Heterogeneous Nuclear Ribonucleoproteins During Vesicular Stomatitis Virus Infection

Project description:Heterogeneous nuclear ribonucleoproteins (hnRNPs) are involved in many processes in RNA metabolism. In addition to their functions in the nucleus, hnRNPs can function in the replication of RNA viruses in the cytoplasm. In vesicular stomatitis virus (VSV)-infected cells, several hnRNPs relocalize from the nucleus to the cytoplasm. This raises the question of whether these hnRNPs are relocalized together with their host nuclear RNAs or whether they associate with new RNAs in the cytoplasm. hnRNP A1, hnRNP C1/C2, and hnRNP K were immunoprecipitated from mock- or VSV-infected cells, and RNAs were analyzed by high content RNA sequencing. Each hnRNP displayed a loss of interaction with cellular transcripts in favor of viral mRNAs. hnRNP A1 was preferentially associated with VSV phosphoprotein (P) mRNA; hnRNP C1/C2 was preferentially associated with VSV glycoprotein (G) mRNA, and hnRNP K bound viral transcripts in rank of abundance.

2016-06-04 | GSE82226 | GEO

Systematic analysis of gene expression profiles controlled by hnRNP Q and hnRNP R, two closely related human heterogeneous nuclear ribonucleoproteins.

Project description:hnRNPQ and the highly related hnRNPR regulate expression of genes related with neuronal and immune functions

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Differential RNA Interactions with Heterogeneous Nuclear Ribonucleoproteins During Vesicular Stomatitis Virus Infection

Project description:Differential RNA Interactions with Heterogeneous Nuclear Ribonucleoproteins During Vesicular Stomatitis Virus Infection

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Collaborative interactions of heterogenous ribonucleoproteins contribute to transcriptional regulation of sterol metabolism

Project description:Heterogeneous nuclear ribonucleoproteins (hnRNPs) are a group of functionally versatile proteins that play critical roles in the biogenesis, cellular localization and transport of RNA. Although several lines of evidence link hnRNP abnormalities to neurodegenerative diseases and cancer their contribution to metabolic control remains unexplored. Here, we outline a role for hnRNPs in regulatory circuits controlling sterol homoeostasis. Specifically, we find that tissue-selective loss of the conserved hnRNP RALY enriches for metabolic pathways arguing that hnRNPs can discriminately influence regulated gene expression programs. Liver-specific deletion of RALY alters hepatic lipid content and serum cholesterol level. In vivo interrogation of chromatin architecture and genome-wide RALY binding pattern reveal insights into its cooperative interactions and mode of action in regulating cholesterogenesis. Interestingly, we find that RALY binds the promoter region of the master metabolic regulator Srebp2 and show that it directly interacts with coactivator NFY to influence cholesterogenic gene expression. Our work offers new insights into mechanisms orchestrating selective promoter activation in metabolic control and a model by which hnRNPs can impact metabolic health and disease states.

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Alternative splicing controlled by heterogeneous nuclear ribonucleoprotein L (hnRNP L) regulates development, proliferation and migration of thymic pre-T cells

Project description:The regulation of post-transcriptional modifications of pre-mRNA by alternative splicing is important for cellular function, development and immunity The receptor tyrosine phosphatase CD45, which is expressed on all hematopoietic cells, is known for its role in the development and activation of T cells. To investigate the role of hnRNP L further, we have generated conditional hnRNP L knockout mice carrying floxed alleles and the T-cell specific Lck-Cre recombinase transgene. The Lck-Cre transgene is active in DN3, DN4 as well as in DP and SP cells. We found that deletion of hnRNP L results in a decreased thymic cellularity caused by a partial block at the transition stage between DN4 and DP cells. In addition, hnRNP L-/- thymocytes express aberrant levels of the CD45RA splice isoform and show high levels of phosphorylated Lck at the activator tyrosine Y394 but lacking phosphorylation of the inhibitory tyrosine Y505. This is indicative of an increased basal Lck activation and correlated with a higher proliferation rate of DN4 cells in hnRNP L-/- mice. Deletion of hnRNP L also blocked egress of SP cells to peripheral lymphoid organs and the migration of SP thymocytes in response to the chemokines CCL21 and SDF-1a. Since we found that actin polymerization was also compromised in hnRNP L-/- SP cells, we propose that a defect in the signal transduction cascade downstream of the chemokine receptors CCR7 and CXCR4 caused by the absence of hnRNP L is responsible for this phenotype. Our results indicate that hnRNPL regulates pre-T cell development and migration by regulating CD45 pre-mRNA splicing and chemokine receptor signaling. RNA-seq from Thymocytes from WT mice compared to KO (hnRNP L) mice

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Alternative splicing controlled by heterogeneous nuclear ribonucleoprotein L (hnRNP L) regulates development, proliferation and migration of thymic pre-T cells

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Expression signatures of human HeLa cells with RNAi targetting A1 hnRNP, FUS, H hnRNP and p68-DDX5

Project description:Transcription profiling of human HeLa cells (cervical cancer cell line) transfected with a plasmid expressing shRNAs cloned into the pSuper expression vector compared to emprty vector negative controls for transfection. Four different RNA interference treatments targetted: A1 hnRNP (HNRNPA1, Heterogeneous nuclear ribonucleoprotein A1); FUS (fusion gene, involved in t(12;16) in malignant liposarcoma); H hnRNP (HNRNPH1); and p68 helicase (DDX5, DEAD (Asp-Glu-Ala-Asp) box polypeptide 5). Keywords: genetic modification

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Heterogeneous nuclear ribonucleoproteins (hnRNPs) in cellular processes: Focus on hnRNP E1's multifunctional regulatory roles.

Project description: Not available

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Aurora B phosphorylates hnRNP U/SAF-A to facilitate XIST RNA removal from the inactive X chromosome during mitosis

Project description:We show that Aurora-B phosphorylates heterogeneous nuclear ribonucleoprotein U (hnRNP U) in the SAP domain to dissociate hnRNP U from chromatin during mitosis. We use RNA-seq to show that hnRNP U associates with hundreds of mRNAs and lncRNAs during interphase and mitosis.

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