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Transcriptomic approach reveals splicing dysregulation in spinocerebellar ataxia type 1

ABSTRACT: Transcriptomic approach reveals splicing dysregulation in spinocerebellar ataxia type 1

PROVIDER: PRJNA971864 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR24519958_1.fastq.gz	Fastqsanger.gz
	SRR24519958_2.fastq.gz	Fastqsanger.gz
	SRR24519959_1.fastq.gz	Fastqsanger.gz
	SRR24519959_2.fastq.gz	Fastqsanger.gz
	SRR24519960_1.fastq.gz	Fastqsanger.gz

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Similar Datasets

Transcriptomic approach reveals splicing dysregulation in spinocerebellar ataxia type 1

Project description:Spinocerebellar ataxia type 1 (SCA1) is caused by a polyglutamine expansion in the ATXN1 gene leading to an expanded polyglutamine tract in the ATAXIN-1 protein. Ataxin-1 is broadly expressed throughout the brain and is known to be involved in regulating gene expression; however, it is not yet determined if mutant ataxin-1 regulates alternative splicing events. Utilizing SCA1 mouse models, we performed bulk RNA sequencing and looked for misregulated alternative splicing (mAS) events in SCA1 mouse cerebella. We found that mutant ataxin-1 causes mAS events to occur in the SCA1 mouse cerebella. Furthermore, we showed that abnormal splicing events predominantly occur in cell types that express mutant ataxin-1. Less than 25% of the mAS events were also differentially expressed genes (DEGs) and therefore their transcriptional dysregulation was previously unknown in the context of SCA1. We show through gene ontology analysis that mAS events reveal new biological pathways: mAS events showed changes in structural morphogenesis whereas DEGs showed changes in ion channel and transmembrane transport. We also report that mutant ataxin-1 causes dysregulation of expression of other ataxia-causing genes, providing evidence for molecular basis of clinical similarity among otherwise heterogeneous inherited cerebellar ataxias. We also identified the potential mechanism by which mutant ATXN1 causes mAS through its interaction with RBFOX1.

2023-10-20 | GSE232368 | GEO

Transcriptome analysis of Spinocerebellar Ataxia 17 Aug

Project description:Transcriptome analysis of extracted total RNA from the the cerebellum and muscle of Spinocerebellar Ataxia 17 knock-in mouse model

2015-08-19 | GSE72176 | GEO

MicroRNA dysregulation in Ataxia Telangiectasia

Project description:MicroRNA dysregulation in Ataxia Telangiectasia

| PRJNA1107187 | ENA

Epigenetic dysregulation impairs high-fidelity DNA repair to promote cerebellar degeneration in spinocerebellar ataxia type 7

Project description:Epigenetic dysregulation impairs high-fidelity DNA repair to promote cerebellar degeneration in spinocerebellar ataxia type 7

| PRJNA699293 | ENA

RNA-seq of Spinocerebellar Ataxia Type2 (SCA2) transgenic mouse lines and age-matched wild-type

Project description:Spinocerebellar ataxia type 2 (SCA2) is among the progressive neurodegenerative polyglutamine (polyQ) diseases. It is caused by a CAG repeat expansion in an encoded region of the ATXN2 gene giving rise to an expanded polyQ domain in the encoded ATXN2 protein. SCA2 is an autosomal dominant disorder characterized by symptoms resulting from neurodegeneration of cerebellar Purkinje cells. To molecularly characterize SCA2 disease progression, we analyzed RNA-sequencing data produced using the cerebella of ATXN2Q127 mice collected at three distinct time points. The ATXN2Q127 mouse model contains 127 CAG repeats in the full-length ATXN2 cDNA under the control of the PC targeted Pcp2 promoter.

2017-12-09 | E-MTAB-6293 | biostudies-arrayexpress

Transcription profiling of ataxin-null (Atxn-null) vs. wild type mice to investigate spinocerebellar ataxia type 1 (SCA1)

Project description:Ataxin 1 (Atxn1) is a protein of unknown function associated with cerebellar neurodegeneration in spinocerebellar ataxia type 1 (SCA1). SCA1 is caused by an expanded polyglutamine within Atxn1 by gain-of-function mechanisms. Lack of Atxn1 in mice triggers motor deficits in the absence of neurodegeneration or apparent neuropathological abnormalities.We extracted RNA from cerebellum of 5 Atxn1-null mice and 5 WT. Cerebellar gene expression profiles at 15 weeks of age were generated usSCA1 ing Affymetrix MOE430A arrays. Identifying the molecular pathways regulated by Atxn1 can provide insights into the early molecular mechanisms underlying neuronal dysfunction.

2006-12-01 | E-MEXP-886 | biostudies-arrayexpress

Transcription profiling of mouse spinocerebellar ataxia type 3 (SCA3) transgenic and wild type animals treated with CCI-779 or placebo

Project description:Spinocerebellar ataxia type 3 is a neurodegenerative disorder caused by the expansion of the polyglutamine repeat region within the ataxin-3 protein. The mutant protein forms intracellular aggregates in the brain. However, the cellular mechanisms causing toxicity are still poorly understood and there are currently no effective treatments. In this study we show that administration of a rapamycin ester, CCI-779, improves motor performance in a transgenic mouse model of SCA3. CCI-779 inhibits mammalian target of rapamycin (mTOR) and hence upregulates protein degradation by autophagy. CCI-779 reduces the number of aggregates seen in the brains of transgenic mice and decreases levels of cytosolic soluble mutant ataxin-3, while endogenous wild-type protein levels remain unaffected. CCI-779 is designed for long-term use in patients and therefore represents a possible therapeutic strategy for the treatment of SCA3. Using this disease model and treatment paradigm we employed a microarray approach to investigate transcriptional changes that might be important in the pathogenesis of SCA3. This approach identified Usp15, which showed expression changes at both the mRNA and protein level. Usp15 levels were also changed in mice expressing another mutant polyglutamine protein, huntingtin. In total we identified 16 transcripts that were decreased in transgenic ataxin-3 mice that were normalised following CCI-779 treatment, as the number of transcripts changed was low and the magnitude of these changes was small we suggest that transcriptional dysregulation may not be an important step in the primary pathogenesis of SCA3. Experiment Overall Design: We analyzed 19 brain samples in total. 4 samples from wt animals after placebo treatment. 5 samples from wt animals after CCI-779 treatment. 5 samples from SCA3 tg animals after placebo treatment. 5 samples from SCA3 tg animals after CCI-779 treatment.

2009-09-18 | E-GEOD-17994 | biostudies-arrayexpress

Spinocerebellar ataxia type 3 RNA-sequencing study

Project description:RNA-Sequencing from human post-mortem Spinocerebellar ataxia type 3 patients. This sequencing experiment was carried out to validate that the transcriptional changes of an Ataxin-3 knock-in mouse model (expressing an expansion of 304 CAG/CAAs either heterozygous or homozygous in the murine Ataxin-3 locus) represent that transcriptional changes seen in the human disease.

| EGAS00001004241 | EGA

Molecular pathway analysis towards understanding tissue vulnerability in spinocerebellar ataxia type 1

Project description:Molecular pathway analysis towards understanding tissue vulnerability in spinocerebellar ataxia type 1

| PRJNA503578 | ENA

Dysregulation of zebrin-II cell subtypes in the cerebellum is a shared feature across polyglutamine ataxia mouse models and patients

Project description:Spinocerebellar ataxia type 7 (SCA7) is a genetic neurodegenerative disorder caused by a CAG-polyglutamine repeat expansion. Purkinje cells (PCs) are central to the pathology of ataxias, but their low abundance in the cerebellum underrepresents their transcriptomes in sequencing assays. To address this issue, we developed a PC enrichment protocol and sequenced individual nuclei from mice and patients with SCA7. Single-nucleus RNA sequencing in SCA7-266Q mice revealed dysregulation of cell identity genes affecting glia and PCs. Specifically, genes marking zebrin-II PC subtypes accounted for the highest proportion of DEGs in symptomatic SCA7-266Q mice. These transcriptomic changes in SCA7-266Q mice were associated with increased numbers of inhibitory synapses as quantified by immunohistochemistry and reduced spiking of PCs in acute brain slices. Dysregulation of zebrin-II cell subtypes was the predominant signal in PCs of SCA7-266Q mice and was associated with the loss of zebrin-II striping in the cerebellum at motor symptom onset. We furthermore demonstrated zebrin-II stripe degradation in additional mouse models of polyglutamine ataxia and observed decreased zebrin-II expression in the cerebella of patients with SCA7. Our results suggest that a breakdown of zebrin subtype regulation is a shared pathological feature of polyglutamine ataxias.

2024-08-14 | GSE269430 | GEO

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