Structured and disordered regions of Ataxin-2 contribute differently to the specificity and efficiency of mRNP granule formation
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ABSTRACT:
PROVIDER: PRJNA807136 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR18033723_1.fastq.gz | Fastqsanger.gz | |||
| SRR18033723_2.fastq.gz | Fastqsanger.gz | |||
| SRR18033724_1.fastq.gz | Fastqsanger.gz | |||
| SRR18033724_2.fastq.gz | Fastqsanger.gz |
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Project description:Ataxin-2 (ATXN2) is a gene implicated in spinocerebellar ataxia type II (SCA2), amyotrophic lateral sclerosis (ALS) and Parkinsonism. The encoded protein is a therapeutic target for ALS and related conditions. ATXN2 (or Atx2 in insects) functions in translational regulation, mRNA stability, and in the assembly of mRNP-granules, a process mediated by intrinsically disordered regions (IDRs). Previous work has shown that the LSm (Like-Sm) domain of Atx2, which mediates translational activation of some target mRNAs, antagonizes mRNP-granule assembly. Here we advance these findings through a series of experiments on Drosophila and human Ataxin-2 proteins. Results of Targets of RNA-Binding Proteins Identified by Editing (TRIBE) experiments indicate that a polyA-binding protein (PABP) interacting, PAM2 motif of Ataxin-2 may be a major determinant of the mRNA content of Ataxin-2 mRNP granules. Co-localization and co-immunoprecipitation analyses show that structured interactions between Ataxin-2 and PABP additionally help determine protein components of Ataxin-2-associated mRNP granules and contribute to Ataxin-2’s association with stress granules. Finally, in vivo experiments in Drosophila indicate that while the Atx2-LSm domain protects against neurodegeneration, structured PAM2- and unstructured IDR- interactions both promote degeneration. Taken together the data: (a) lead to a proposal for how Ataxin-2 interactions are remodelled during different stages of translational control; (b) show how structured and non-structured interactions of Ataxin-2 contribute differently to the specificity and efficiency of RNP granule condensation; and (c) demonstrate that the Ataxin-2 protein contains multiple activities that may respectively prevent or promote neurodegeneration.
2024-04-22 | GSE196739 | GEO
Project description:Ataxin-2 is a conserved translational control protein as well as an important target for ALS therapeutics under development. Despite its clinical and biological significance, Ataxin-2’s activities, mechanisms and functions are not well understood. Using Drosophila Ataxin-2 (Atx2) we investigate how Ataxin-2 IDRs work with structured (Lsm, Lsm-AD and PAM2) domains to enable positive and negative regulation of target mRNAs. Using TRIBE (Targets of RNA-Binding Proteins Identified by Editing) technology, we identified and analysed Atx-2 target mRNAs in the Drosophila brain.
2021-03-03 | GSE153985 | GEO
Project description:Antagonistic roles for Ataxin-2 structured and disordered domains in RNP condensatation
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Project description:We recently identified the RNA targets of Ataxin-2 by using PAR-CLIP. To elucidate the functional role of Ataxin-2 on target-binding, we have knocked down or overexpressed Ataxin-2 in HEK293T cells and extracted RNAs 48 hrs after transfection. Then, these total RNAs were subjected to whole transcripts microarray analysis to examine how the perturbation of Ataxin-2 expression affects target gene expression. Ataxin-2 was either knocked down using siRNA or overexpressed using the expression construct of Halo-Ataxin-2.Control siRNA was transfected as a control of knockdown experiment. The expression construct of Halo-tag alone was used as a control of overexpression experiment. Forty-eight hrs after transfection, total RNAs were extracted and subjected to microarray analysis.
2014-06-20 | E-GEOD-53189 | biostudies-arrayexpress
Project description:We recently identified the RNA targets of Ataxin-2 by using PAR-CLIP. To elucidate the functional role of Ataxin-2 on target-binding, we have knocked down or overexpressed Ataxin-2 in HEK293T cells and extracted RNAs 48 hrs after transfection. Then, these total RNAs were subjected to whole transcripts microarray analysis to examine how the perturbation of Ataxin-2 expression affects target gene expression.
2014-06-20 | GSE53189 | GEO
Project description:Ataxin-2 (Atx2) is a translational control molecule mutated in spinocerebellar ataxia type II and amyotrophic lateral sclerosis. While intrinsically disordered domains (IDRs) of Atx2 facilitate mRNP condensation into granules, how IDRs work with structured domains to enable positive and negative regulation of target mRNAs remains unclear. Using the Targets of RNA-Binding Proteins Identified by Editing technology, we identified an extensive data set of Atx2-target mRNAs in the Drosophila brain and S2 cells. Atx2 interactions with AU-rich elements in 3'UTRs appear to modulate stability/turnover of a large fraction of these target mRNAs. Further genomic and cell biological analyses of Atx2 domain deletions demonstrate that Atx2 (1) interacts closely with target mRNAs within mRNP granules, (2) contains distinct protein domains that drive or oppose RNP-granule assembly, and (3) has additional essential roles outside of mRNP granules. These findings increase the understanding of neuronal translational control mechanisms and inform strategies for Atx2-based interventions under development for neurodegenerative disease.
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Project description:A protein aggregation model of human ataxin-1(Q82) was generated in human mesenchymal cells using the Sleeping Beauty transposon system. These cells inducibly express the pathogenic protein that causes SCA1 disease. Here, we describe the transcriptional changes occurring in cells which contain different types of ataxin-1(Q82) protein inclusions
2020-02-18 | E-MTAB-7713 | biostudies-arrayexpress
Project description:Gene-based therapeutic strategies to lower ataxin-2 levels are emerging for neurodegenerative diseases amyotrophic lateral sclerosis (ALS) and spinocerebellar ataxia type 2 (SCA2). To identify additional ways of reducing ataxin-2 levels, we performed a genome-wide screen in human cells for regulators of ataxin-2 and identified RTN4R, the gene encoding the RTN4/NoGo-Receptor, as a top hit. This dataset contains the RNA-sequencing data used to support the conclusions from this study.
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Project description:RNA-binding proteins (RBPs) control every RNA metabolic process by multiple protein-RNA and protein-protein interactions. Their roles have largely been analyzed by crude mutations, which abrogate several functions at once and likely impact the structural integrity of the large mRNP assemblies, these proteins often function in. Thus, the function of the RNA-binding activity of RBPs is often unknown. Using UV-induced RNA-protein crosslinking and subsequent mass spectrometric (MS) analysis, we first identified more than 100 in vivo RNA crosslinks in 16 nuclear mRNP components. For functional analysis, we chose Npl3, for which we identified crosslinks in its two RNA recognition motifs (RRMs) as well as in the flexible linker connecting the two. Both RRM domains and the linker uniquely contribute to RNA recognition. Interestingly, mutations in each of these three regions cause different phenotypes, indicating distinct functions of the different RNA-binding domains of Npl3. Notably, the npl3-Linker mutant strongly impairs recruitment of some mRNP components to chromatin and the incorporation of other mRNP components into nuclear mRNPs, establishing a function of Npl3 in mRNP assembly. Taken together, we determined the specific function of the RNA-binding activity of a nuclear mRNP component, an approach that can be applied to many RBPs in any RNA metabolic process.
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