Senataxin Promotes RNA Polymerase II Elongation [PROseq]
Ontology highlight
ABSTRACT:
ORGANISM(S): Homo sapiens
PROVIDER: GSE280012 | GEO | 2025/11/13
REPOSITORIES: GEO
Similar Datasets
Project description:Senataxin (SETX) is recognized as a critical regulator of RNA Polymerase II (RNAPII) transcription and plays a pivotal role in maintaining genomic stability. Despite its importance, the direct in vivo functions of SETX remain inadequately characterized. Employing the degradation tag (dTAG) system for acute protein depletion, we demonstrate that SETX does not influence transcription termination but significantly enhances RNAPII elongation. Through in vitro reconstitution assays, we show that SETX actively drives RNAPII forward across complex transcriptional landscapes, akin to the way bacterial ribosomes mitigate transcriptional pauses. In vivo analyses further reveal an accumulation of pausing RNAPII at early transcription stages and a corresponding increase in R-loop formation at these sites following SETX depletion. These insights not only redefine our understanding of SETX's role in transcriptional regulation but also highlight its potential as a therapeutic target in disorders linked to transcriptional dysregulation.
2025-11-13 | GSE280010 | GEO
Project description:Senataxin (SETX) is recognized as a critical regulator of RNA Polymerase II (RNAPII) transcription and plays a pivotal role in maintaining genomic stability. Despite its importance, the direct in vivo functions of SETX remain inadequately characterized. Employing the degradation tag (dTAG) system for acute protein depletion, we demonstrate that SETX does not influence transcription termination but significantly enhances RNAPII elongation. Through in vitro reconstitution assays, we show that SETX actively drives RNAPII forward across complex transcriptional landscapes, akin to the way bacterial ribosomes mitigate transcriptional pauses. In vivo analyses further reveal an accumulation of pausing RNAPII at early transcription stages and a corresponding increase in R-loop formation at these sites following SETX depletion. These insights not only redefine our understanding of SETX's role in transcriptional regulation but also highlight its potential as a therapeutic target in disorders linked to transcriptional dysregulation.
2025-11-13 | GSE280011 | GEO
Project description:Senataxin (SETX) is recognized as a critical regulator of RNA Polymerase II (RNAPII) transcription and plays a pivotal role in maintaining genomic stability. Despite its importance, the direct in vivo functions of SETX remain inadequately characterized. Employing the degradation tag (dTAG) system for acute protein depletion, we demonstrate that SETX does not influence transcription termination but significantly enhances RNAPII elongation. Through in vitro reconstitution assays, we show that SETX actively drives RNAPII forward across complex transcriptional landscapes, akin to the way bacterial ribosomes mitigate transcriptional pauses. In vivo analyses further reveal an accumulation of pausing RNAPII at early transcription stages and a corresponding increase in R-loop formation at these sites following SETX depletion. These insights not only redefine our understanding of SETX's role in transcriptional regulation but also highlight its potential as a therapeutic target in disorders linked to transcriptional dysregulation.
2025-11-13 | GSE297203 | GEO
Project description:Senataxin (SETX) is recognized as a critical regulator of RNA Polymerase II (RNAPII) transcription and plays a pivotal role in maintaining genomic stability. Despite its importance, the direct in vivo functions of SETX remain inadequately characterized. Employing the degradation tag (dTAG) system for acute protein depletion, we demonstrate that SETX does not influence transcription termination but significantly enhances RNAPII elongation. Through in vitro reconstitution assays, we show that SETX actively drives RNAPII forward across complex transcriptional landscapes, akin to the way bacterial ribosomes mitigate transcriptional pauses. In vivo analyses further reveal an accumulation of pausing RNAPII at early transcription stages and a corresponding increase in R-loop formation at these sites following SETX depletion. These insights not only redefine our understanding of SETX's role in transcriptional regulation but also highlight its potential as a therapeutic target in disorders linked to transcriptional dysregulation.
2025-11-13 | GSE280013 | GEO
Project description:Senataxin (SETX) is recognized as a critical regulator of RNA Polymerase II (RNAPII) transcription and plays a pivotal role in maintaining genomic stability. Despite its importance, the direct in vivo functions of SETX remain inadequately characterized. Employing the degradation tag (dTAG) system for acute protein depletion, we demonstrate that SETX does not influence transcription termination but significantly enhances RNAPII elongation. Through in vitro reconstitution assays, we show that SETX actively drives RNAPII forward across complex transcriptional landscapes, akin to the way bacterial ribosomes mitigate transcriptional pauses. In vivo analyses further reveal an accumulation of pausing RNAPII at early transcription stages and a corresponding increase in R-loop formation at these sites following SETX depletion. These insights not only redefine our understanding of SETX's role in transcriptional regulation but also highlight its potential as a therapeutic target in disorders linked to transcriptional dysregulation.
2025-11-13 | GSE297204 | GEO
Project description:The human helicase senataxin (SETX) has been linked to the neurodegenerative diseases amyotrophic lateral sclerosis (ALS4) and ataxia with oculomotor apraxia (AOA2). Here we identified a role for SETX in controlling the antiviral response. Cells that had undergone depletion of SETX and SETX-deficient cells derived from patients with AOA2 had higher expression of antiviral mediators in response to infection than did wild-type cells. Mechanistically, we propose a model whereby SETX attenuates the activity of RNA polymerase II (RNAPII) at genes stimulated after a virus is sensed and thus controls the magnitude of the host response to pathogens and the biogenesis of various RNA viruses (e.g., influenza A virus and West Nile virus). Our data indicate a potentially causal link among inborn errors in SETX, susceptibility to infection and the development of neurologic disorders. This SuperSeries is composed of the SubSeries listed below.
2015-03-30 | GSE52937 | GEO
Project description:Senataxin, encoded by the SETX gene, contributes to multiple aspects of gene expression, including transcription and RNA processing. Mutations in SETX cause the recessive disorder ataxia with oculomotor apraxia type 2 (AOA2) and a dominant juvenile form of amyotrophic lateral sclerosis (ALS4). To assess the functional role of senataxin in disease, we examined differential gene expression in AOA2 patient fibroblasts, identifying a core set of genes showing altered expression by microarray and RNA-sequencing. To determine whether AOA2 and ALS4 mutations differentially affect gene expression, we overexpressed disease-specific SETX mutations in senataxin-haploinsufficient fibroblasts and observed changes in distinct sets of genes. This implicates mutation-specific alterations of senataxin function in disease pathogenesis and provides a novel example of allelic neurogenetic disorders with differing gene expression profiles. Weighted gene co-expression network analysis (WGCNA) demonstrated these senataxin-associated genes to be involved in both mutation-specific and shared functional gene networks. To assess this in vivo, we performed gene expression analysis on peripheral blood from members of 12 different AOA2 families and identified an AOA2-specific transcriptional signature. WGCNA identified two gene modules highly enriched for this transcriptional signature in the peripheral blood of all AOA2 patients studied. These modules were disease-specific and preserved in patient fibroblasts and in the cerebellum of Setx knockout mice demonstrating conservation across species and cell types, including neurons. These results identify novel genes and cellular pathways related to senataxin function in normal and disease states, and implicate alterations in gene expression as underlying the phenotypic differences between AOA2 and ALS4. Total RNA samples obtained from 1) an AOA2 patient and carrier fibroblast cell lines, 2) 2 biological replicates of haploinsufficient SETX fibroblast cell lines transfected with one of 4 different wild-type and mutant SETX constructs, 3) peripheral blood from 33 patients and carriers across 12 families, and 4) 2 tissues from 2 Setx knockout and 2 control mice were analyzed using expression microarray. This submission represents the microarray component of study.
2014-09-15 | E-GEOD-61320 | biostudies-arrayexpress
Project description:Senataxin, encoded by the SETX gene, contributes to multiple aspects of gene expression, including transcription and RNA processing. Mutations in SETX cause the recessive disorder ataxia with oculomotor apraxia type 2 (AOA2) and a dominant juvenile form of amyotrophic lateral sclerosis (ALS4). To assess the functional role of senataxin in disease, we examined differential gene expression in AOA2 patient fibroblasts, identifying a core set of genes showing altered expression by microarray and RNA-sequencing. To determine whether AOA2 and ALS4 mutations differentially affect gene expression, we overexpressed disease-specific SETX mutations in senataxin-haploinsufficient fibroblasts and observed changes in distinct sets of genes. This implicates mutation-specific alterations of senataxin function in disease pathogenesis and provides a novel example of allelic neurogenetic disorders with differing gene expression profiles. Weighted gene co-expression network analysis (WGCNA) demonstrated these senataxin-associated genes to be involved in both mutation-specific and shared functional gene networks. To assess this in vivo, we performed gene expression analysis on peripheral blood from members of 12 different AOA2 families and identified an AOA2-specific transcriptional signature. WGCNA identified two gene modules highly enriched for this transcriptional signature in the peripheral blood of all AOA2 patients studied. These modules were disease-specific and preserved in patient fibroblasts and in the cerebellum of Setx knockout mice demonstrating conservation across species and cell types, including neurons. These results identify novel genes and cellular pathways related to senataxin function in normal and disease states, and implicate alterations in gene expression as underlying the phenotypic differences between AOA2 and ALS4. Total RNA samples obtained from 1) an AOA2 patient and carrier fibroblast cell lines, 2) 2 biological replicates of haploinsufficient SETX fibroblast cell lines transfected with one of 4 different wild-type and mutant SETX constructs, 3) peripheral blood from 33 patients and carriers across 12 families, and 4) 2 tissues from 2 Setx knockout and 2 control mice were analyzed using expression microarray. This submission represents the microarray component of study.
2014-09-15 | E-GEOD-61324 | biostudies-arrayexpress
Project description:Senataxin, encoded by the SETX gene, contributes to multiple aspects of gene expression, including transcription and RNA processing. Mutations in SETX cause the recessive disorder ataxia with oculomotor apraxia type 2 (AOA2) and a dominant juvenile form of amyotrophic lateral sclerosis (ALS4). To assess the functional role of senataxin in disease, we examined differential gene expression in AOA2 patient fibroblasts, identifying a core set of genes showing altered expression by microarray and RNA-sequencing. To determine whether AOA2 and ALS4 mutations differentially affect gene expression, we overexpressed disease-specific SETX mutations in senataxin-haploinsufficient fibroblasts and observed changes in distinct sets of genes. This implicates mutation-specific alterations of senataxin function in disease pathogenesis and provides a novel example of allelic neurogenetic disorders with differing gene expression profiles. Weighted gene co-expression network analysis (WGCNA) demonstrated these senataxin-associated genes to be involved in both mutation-specific and shared functional gene networks. To assess this in vivo, we performed gene expression analysis on peripheral blood from members of 12 different AOA2 families and identified an AOA2-specific transcriptional signature. WGCNA identified two gene modules highly enriched for this transcriptional signature in the peripheral blood of all AOA2 patients studied. These modules were disease-specific and preserved in patient fibroblasts and in the cerebellum of Setx knockout mice demonstrating conservation across species and cell types, including neurons. These results identify novel genes and cellular pathways related to senataxin function in normal and disease states, and implicate alterations in gene expression as underlying the phenotypic differences between AOA2 and ALS4. Total RNA samples obtained from 1) an AOA2 patient and carrier fibroblast cell lines, 2) 2 biological replicates of haploinsufficient SETX fibroblast cell lines transfected with one of 4 different wild-type and mutant SETX constructs, 3) peripheral blood from 33 patients and carriers across 12 families, and 4) 2 tissues from 2 Setx knockout and 2 control mice were analyzed using expression microarray. This submission represents the microarray component of study.
2014-09-15 | E-GEOD-61321 | biostudies-arrayexpress
Project description:Senataxin, encoded by the SETX gene, contributes to multiple aspects of gene expression, including transcription and RNA processing. Mutations in SETX cause the recessive disorder ataxia with oculomotor apraxia type 2 (AOA2) and a dominant juvenile form of amyotrophic lateral sclerosis (ALS4). To assess the functional role of senataxin in disease, we examined differential gene expression in AOA2 patient fibroblasts, identifying a core set of genes showing altered expression by microarray and RNA-sequencing. To determine whether AOA2 and ALS4 mutations differentially affect gene expression, we overexpressed disease-specific SETX mutations in senataxin-haploinsufficient fibroblasts and observed changes in distinct sets of genes. This implicates mutation-specific alterations of senataxin function in disease pathogenesis and provides a novel example of allelic neurogenetic disorders with differing gene expression profiles. Weighted gene co-expression network analysis (WGCNA) demonstrated these senataxin-associated genes to be involved in both mutation-specific and shared functional gene networks. To assess this in vivo, we performed gene expression analysis on peripheral blood from members of 12 different AOA2 families and identified an AOA2-specific transcriptional signature. WGCNA identified two gene modules highly enriched for this transcriptional signature in the peripheral blood of all AOA2 patients studied. These modules were disease-specific and preserved in patient fibroblasts and in the cerebellum of Setx knockout mice demonstrating conservation across species and cell types, including neurons. These results identify novel genes and cellular pathways related to senataxin function in normal and disease states, and implicate alterations in gene expression as underlying the phenotypic differences between AOA2 and ALS4. Total RNA samples obtained from 1) an AOA2 patient and carrier fibroblast cell lines, 2) 2 biological replicates of haploinsufficient SETX fibroblast cell lines transfected with one of 4 different wild-type and mutant SETX constructs, 3) peripheral blood from 33 patients and carriers across 12 families, and 4) 2 tissues from 2 Setx knockout and 2 control mice were analyzed using expression microarray. This submission represents the microarray component of study.
2014-09-15 | E-GEOD-61322 | biostudies-arrayexpress