Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Genome-wide maps of SBNO2 target transcripts and RNA-seq of SBNO2 deficient cells

ABSTRACT: DExD/H box helicases are ATPases that govern key biochemical events of host RNA metabolism including unwinding or annealing RNA, facilitating the formation or remodeling of ribonucleoprotein complexes, and controlling transcriptional or translational RNA pools essential for normal human neurodevelopment1-6. Some helicases also recognize foreign RNAs of infectious agents during immune responses but how they govern host genes essential for immunity is unknown. Here we describe a previously undiscovered genetic immunodysregulatory syndrome, due to Strawberry Notch Homolog 2 (SBNO2) deficiency, that highlights a new function of these helicases in binding to nascent transcripts of host cytokine and immune response genes near the transcription start site and increasing their expression.

ORGANISM(S): Homo sapiens

PROVIDER: GSE187784 | GEO | 2023/10/26

REPOSITORIES: GEO

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
		Other

Items per page:

1 - 1 of 1

Similar Datasets

Transcription profiling by array of cerebella from Sbno2-/- mice

Project description:This study sought to investigate the role of Strawberry notch homolog 2 (Sbno2), an interleukin-6 (IL-6)-regulated gene whose function is largely unknown, in the central nervous system through the use of a novel mouse model with germline deletion of Sbno2 (Sbno2-/-). In particular, to understand its role in IL-6-mediated neurological disease, these mice were crossed with the GFAP-IL6 transgenic mice, which chronically produces IL-6 from in astrocytes at pathophysiological levels.

2022-05-25 | E-MTAB-11169 | biostudies-arrayexpress

Evolutionary and Functional Insights into the Ski2-like helicase Family in Archaea: A Comparison of Thermococcales ASH-Ski2 and Hel308 Activities

Project description:RNA helicases perform essential housekeeping and regulatory functions in all domains of life by binding and unwinding RNA molecules. The Ski2-like proteins are primordial helicases that play an active role in eukaryotic RNA homeostasis pathways, with multiple homologs having specialized functions. The significance of the expansion and diversity of Ski2-like proteins in Archaea, the third domain of life, has not yet been established. Here, by studying the phylogenetic diversity of Ski2-like helicases among archaeal genomes and the enzymatic activities of those in Thermococcales, we provide further evidence of the function of this protein family in archaeal metabolism of nucleic acids. We show that, in the course of evolution, ASH-Ski2 and Hel308-Ski2, the two main groups of Ski2-like proteins, have diverged in their biological functions. Whereas Hel308 has been shown to mainly act on DNA, we show that ASH-Ski2, previously described to be associated with the 5′-3′ aRNaseJ exonuclease, acts on RNA by supporting an efficient annealing activity, but also an RNA unwinding with a 3′-5′ polarity. To gain insights into the function of Ski2, we also analyse the transcriptome of Thermococcus barophilus ASH-Ski2 mutant strain and provide evidence of the importance of ASH-Ski2 in cellular metabolism pathways related to translation.

2024-03-04 | GSE229955 | GEO

Proteomic analysis of Mason-Pfizer monkey virus virions

Project description:To accomplish their replication cycle, retroviruses rely heavily on a wide variety of cellular proteins and enzymes, such as helicases. Among these, the DExD-box and DEAH/RHA-box helicases were identified to play crucial roles in their nucleic acid metabolism. This study explores the Betaretrovirus Mason-Pfizer monkey virus (M-PMV), which uniquely encodes a G-patch motif - a feature shared with several endogenous retroviruses. Typically found in eukaryotic RNA-binding proteins, G-patch acts as cofactors for DEAH-box RNA helicases, guiding them to specific sub-cellular sites and activating them in diverse RNA metabolic pathways. Despite its established importance in the betaretrovirus replication cycle, the function of the G-patch still needs to be discovered. Using MS analysis, we identified DHX15, a cellular DEAH-box RNA helicase, as host cell protein macked into mature virions. Further research illuminates the complex interplay between retroviruses and host cellular machinery, highlighting the pivotal role of helicases in viral replication processes.

2024-09-13 | PXD046672 | Pride

A transcriptional repressor and co-repressor induced by the STAT3-regulated anti-inflammatory signaling pathway.

Project description:IL-10 regulates anti-inflammatory signaling via the activation of STAT3, which in turn controls the induction of a gene expression program whose products execute inhibitory effects on pro-inflammatory mediator production. Here we show that IL-10 induces the expression of an ETS family transcriptional repressor, ETV3 and a helicase family co-repressor, SBNO2 (Strawberry notch homolog 2) in mouse and human macrophages. IL-10-mediated induction of ETV3 and SBNO2 expression was dependent upon both STAT3, and co-stimulus through the TLR pathway. We also observed that ETV3 expression was strongly induced by the STAT3 pathway induced by IL-10 but not STAT3 signaling activated by IL-6, which cannot activate the anti-inflammatory signaling pathway. ETV3 and SBNO2 specifically repressed NF-kB-mediated transcription and can physically interact. Collectively our data suggest that ETV3 and SBNO2 are components of the pathways that contribute to the downstream anti-inflammatory effects of IL-10. We compared expression profiles of macrophages isolated from IL-10 -/- mice. Macrophages were treated with either LPS or LPS plus IL-10. Treatment times were 10, 20 and 30 minutes. Keywords: time-course, treatment response, gene expression analysis

2007-12-01 | GSE9509 | GEO

Transcription profiling of mouse IL-10 -/- macrophages treated with LPS/LPS plus IL10 reveals a transcriptional repressor and co-repressor induced by the STAT3-regulated anti-inflammatory signaling pathway.

Project description:IL-10 regulates anti-inflammatory signaling via the activation of STAT3, which in turn controls the induction of a gene expression program whose products execute inhibitory effects on pro-inflammatory mediator production. Here we show that IL-10 induces the expression of an ETS family transcriptional repressor, ETV3 and a helicase family co-repressor, SBNO2 (Strawberry notch homolog 2) in mouse and human macrophages. IL-10-mediated induction of ETV3 and SBNO2 expression was dependent upon both STAT3, and co-stimulus through the TLR pathway. We also observed that ETV3 expression was strongly induced by the STAT3 pathway induced by IL-10 but not STAT3 signaling activated by IL-6, which cannot activate the anti-inflammatory signaling pathway. ETV3 and SBNO2 specifically repressed NF-kB-mediated transcription and can physically interact. Collectively our data suggest that ETV3 and SBNO2 are components of the pathways that contribute to the downstream anti-inflammatory effects of IL-10. We compared expression profiles of macrophages isolated from IL-10 -/- mice. Macrophages were treated with either LPS or LPS plus IL-10. Treatment times were 10, 20 and 30 minutes. Experiment Overall Design: Mouse IL-10 -/- macrophages were isolated and purified and set up in culture medium containing LPS or LPS plus IL-10. A total of 18 samples were analyzed. This set contains three replicates of each treatment condition where treatment (LPS versus LPS plus IL-10) and time (10min, 20min and 30min) were varied.

2008-06-16 | E-GEOD-9509 | biostudies-arrayexpress

Structural basis of RNA-induced autoregulation of the DExH-type RNA helicase maleless

Project description:RNA unwinding by DExH-type helicases underlies most RNA metabolism and function. It remains unresolved if and how the basic unwinding reaction of helicases is regulated by auxiliary domains. We explored the interplay between the RecA and auxiliary domains of the RNA helicase maleless (MLE) from Drosophila, using a suite of structural and functional studies. We discovered that MLE exists in a dsRNA bound open conformation and the auxiliary dsRBD2 domain aligns the substrate RNA with the accessible helicase tunnel. In an ATP-dependent manner, dsRBD2 associates with the helicase module, leading to tunnel closure around ssRNA. Furthermore, our structures provide a rationale for blunt ended dsRNA unwinding and 3’-5’ translocation by MLE. Structure-based MLE mutations confirm the functional relevance of our model for RNA unwinding. Our findings contribute to our understanding of fundamental mechanics of auxiliary domains in DExH helicase MLE which serves as model for its human ortholog and potentially therapeutic target, DHX9/RHA.

2023-11-27 | PXD045725 | Pride

DEAD-box ATPase Dbp2 mediates mRNA release after 3’-end formation

Project description:DEAD-box ATPases belong to an abundant class of proteins that are involved in virtually all aspects of RNA metabolism and are found in all kingdoms of life. When bound to a DEAD-box ATPase, the RNA substrate is forced into a kinked conformation that is incompatible with helical structures. Distortion of the RNA can result in unwinding of short RNA duplexes (helicase activity) or destabilize RNA-protein interactions, allowing DEAD-box ATPases to remodel mRNPs (RNPase activity). The RNPase activity makes DEAD-box ATPases suitable molecular building blocks for the implementation of checkpoints that confer directionality to the process of RNA biogenesis. Here, we provide data that characterizes the DEAD-box ATPase Dbp2 (SPBP8B7.16c) of the fission yeast Schizosaccharomyces pombe. Using ChIP-seq, we determined the sites where HTP-tagged Dbp2 associates with chromatin. ChIP-seq of Srp2-HTP is included as a reference protein that is known to associate with transcribing RNA polymerase II (RNAPII).

2024-06-30 | E-MTAB-13712 | biostudies-arrayexpress

Transcriptional profile analysis of uninfected or VSV-infected scrambled siRNA (siControl) and DDX23 knockdown (siDDX23) A549 cells

Project description:DExD/H-box helicases play essential roles in RNA metabolism, and emerging data suggest that they have additional functions in antiviral immunity across species. However, little is known about this evolutionarily conserved family in antiviral responses in lower species. Here, by isolation of poly(I:C)-binding proteins in amphioxus, an extant basal chordate, we found that DExD/H-box helicases DHX9, DHX15 and DDX23 to be responsible for cytoplasmic dsRNA detection in amphioxus. Since the antiviral roles of DDX23 have not been characterized in mammals, we performed further poly(I:C) pull down assays and found human DDX23 bind to LMW poly(I:C) through its N-terminal region, suggesting that DDX23 is an evolutionarily conserved dsRNA sensor. Knockdown of human DDX23 enhanced replication of VSV and reduced activation of the NF-κB and IRF3. Moreover, when stimulated with poly(I:C) or VSV, human DDX23 translocated from nucleus to cytoplasm and formed complexes with TRIF or MAVS to initiate downstream signaling. Collectively, this comparative immunological study not only defined DDX23 as an emerging nuclear pattern recognition receptor (PRR) for innate sensing of RNA virus, but also extended the essential role of the DExD/H helicase family in viral RNA sensing from mammals to basal chordate.

2019-06-18 | GSE132847 | GEO

DEAD-box ATPase Dbp2 mediates mRNA release after 3’-end formation - III

Project description:DEAD-box ATPases belong to an abundant class of proteins that are involved in virtually all aspects of RNA metabolism and are found in all kingdoms of life. When bound to a DEAD-box ATPase, the RNA substrate is forced into a kinked conformation that is incompatible with helical structures. Distortion of the RNA can result in unwinding of short RNA duplexes (helicase activity) or destabilize RNA-protein interactions, allowing DEAD-box ATPases to remodel mRNPs (RNPase activity). The RNPase activity makes DEAD-box ATPases suitable molecular building blocks for the implementation of checkpoints that confer directionality to the process of RNA biogenesis. Here, we provide data that characterizes the DEAD-box ATPase Dbp2 (SPBP8B7.16c) of the fission yeast Schizosaccharomyces pombe. Using RNA-seq, we determined RNA expression profiles of a conditional depletion strain of Dbp2 and the corresponding wild type. For this, we placed the endogenous dbp2 gene under the control of the P.nmt1 promoter, which is repressed in the presence of thiamine. Cells were harvested at the beginning (t0) or the end (t5 or t9) of shift to thiamine-containing YES medium. S. cerevisiae spike-in cells were added in a 1:5 OD600 ratio immediately before harvesting.

2024-06-30 | E-MTAB-13717 | biostudies-arrayexpress

DEAD-box ATPase Dbp2 mediates mRNA release after 3’-end formation - II

Project description:DEAD-box ATPases belong to an abundant class of proteins that are involved in virtually all aspects of RNA metabolism and are found in all kingdoms of life. When bound to a DEAD-box ATPase, the RNA substrate is forced into a kinked conformation that is incompatible with helical structures. Distortion of the RNA can result in unwinding of short RNA duplexes (helicase activity) or destabilize RNA-protein interactions, allowing DEAD-box ATPases to remodel mRNPs (RNPase activity). The RNPase activity makes DEAD-box ATPases suitable molecular building blocks for the implementation of checkpoints that confer directionality to the process of RNA biogenesis. Here, we provide data that characterizes the DEAD-box ATPase Dbp2 (SPBP8B7.16c) of the fission yeast Schizosaccharomyces pombe. Using calibrated RNAPII-ChIP-seq, we determined the transcription profiles of a conditional depletion strain of Dbp2 and the corresponding wild type. For this, we placed the endogenous dbp2 gene under the control of the P.nmt1 promoter, which is repressed in the presence of thiamine. Cells were crosslinked at the beginning (t0) or the end (t9) of a 9h shift to thiamine-containing YES medium. S. cerevisiae spike-in cells were added in a 1:5 OD600 ratio immediately before crosslinking.

2024-06-30 | E-MTAB-13714 | biostudies-arrayexpress

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data