Interplay between m6A modification and transcripts quantity: Impacts on mRNA composition in plant stress granules
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA1136863 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR29860541_1.fastq.gz | Fastqsanger.gz | |||
| SRR29860541_2.fastq.gz | Fastqsanger.gz | |||
| SRR29860542_1.fastq.gz | Fastqsanger.gz | |||
| SRR29860542_2.fastq.gz | Fastqsanger.gz | |||
| SRR29860543_1.fastq.gz | Fastqsanger.gz |
Items per page: 5 1 - 5 of 18 |
Similar Datasets
Project description:Stress granules (SGs) are cytoplasmic structures that emerge in response to unfavorable environmental conditions. The mechanisms governing the accumulation of transcripts in SGs are only partially understood. Despite the recognized role of m6A in plant transcriptome regulation, its impact on SGs' composition and assembly remains elusive. In L. angustifolius, SGs display a distinctive bi-zonal structure comprising of a ring and a central area with differences in ultrastructure and composition. Subsequent to the transcriptome analysis, specific mRNA were chosen for investigating their localization within SGs and assessing m6A levels. Transcripts of hypoxia-responsive genes (ADH1 and HUP7) showed significantly lower levels of m6A compared to housekeeping genes, but only ADH1 was absent in SGs. HUP7 mRNA, characterized by a low quantity of m6A, is present both in the SGs and cytoplasm, probably due to extremely high expression level. The high amount of m6A was observed only during the assembly of SGs. In mutants of A. thaliana with reduced levels of m6A, ECT2 was not observed in SGs, and poly(A) RNA levels and the number of SGs were slightly reduced. In summary, our findings demonstrate a limited impact of m6A modification on SGs assembly. However, the interplay between m6A modification and the overall transcript quantity in the cytoplasm appears to play a regulatory role in mRNA partitioning and assembly of SGs
2025-04-08 | GSE272430 | GEO
Project description:Stress granules are small RNA-protein granules that modify the translational landscape during cellular stress to promote survival. The RhoGTPase RhoA is implicated in the formation of RNA stress granules. Our data demonstrate that the cytokinetic proteins ECT2 and AurkB are localized to stress granules in human astrocytoma cells. AurkB and its downstream target histone-3 are phosphorylated during arsenite-induced stress. Chemical (AZD1152-HQPA) and siRNA inhibition of AurkB results in fewer and smaller stress granules when analyzed utilizing high throughput fluorescent based cellomics assays. RNA immunoprecipitation with the known stress granule aggregates TIAR and G3BP1 was performed on astrocytoma cells and subsequent analysis revealed that astrocytoma stress granules harbour unique mRNAs for various cellular pathways including cellular migration, metabolism, translation and transcriptional regulation. Human astrocytoma cell stress granules contain mRNA that are known to be involved in glioma signaling and the mTOR pathway. These data provide evidence that RNA stress granules are a novel form of epigenetic regulation in astrocytoma cells, which may be targetable by chemical inhibitors and enhance astrocytoma susceptiblity to conventional therapy such as radiation and chemotherapy. Astrocytoma cells were either untreated or treated with arsenite to induce stress granule formation and RNA immunoprecipitates were analyzed by exon array analysis. RNA species that were enriched in TIAR RIPs and G3BP1 RIPS, respectively were compared to compared to TIAR and G3BP1 RIPs from untreated cells and input controls. Ingenuity pathway analysis was performed on the stress granule enriched mRNAs from the TIAR and G3BP1 RIPs to identify significant functional biology networks.
2016-02-29 | E-GEOD-76814 | biostudies-arrayexpress
Project description:We investigated the contentious role of mitochondrial reactive oxygen species (ROS) on mitochondrial DNA (mtDNA) quality and quantity in female reproductive aging. By conditionally knocking out the Sod2 gene in female mouse germline, we observed increased mitochondrial ROS and decreased oocyte quality, primarily due to impacts on OXPHOS complex II and mtDNA encoded mRNA levels. Interestingly, we found no increased mtDNA mutations, but alterations in mtDNA quantity, indicating the susceptibility of mtDNA to the mitochondrial ROS during reproductive aging. Notably, when we further decreased the basal level of mtDNA quantity by deactivating the mtSSB protein in Sod2 conditional knockout females, we observed an exacerbation of reproductive aging effects. This highlights the crucial role of mtDNA quantity in mitigating the impact of oxidative stress on fertility.
2024-09-09 | GSE251734 | GEO
Project description:Light quantity impacts early response to cold and cold acclimation in young leaves of Arabidopsis
| PRJNA1169808 | ENA
Project description:Stress granules are small RNA-protein granules that modify the translational landscape during cellular stress to promote survival. The RhoGTPase RhoA is implicated in the formation of RNA stress granules. Our data demonstrate that the cytokinetic proteins ECT2 and AurkB are localized to stress granules in human astrocytoma cells. AurkB and its downstream target histone-3 are phosphorylated during arsenite-induced stress. Chemical (AZD1152-HQPA) and siRNA inhibition of AurkB results in fewer and smaller stress granules when analyzed utilizing high throughput fluorescent based cellomics assays. RNA immunoprecipitation with the known stress granule aggregates TIAR and G3BP1 was performed on astrocytoma cells and subsequent analysis revealed that astrocytoma stress granules harbour unique mRNAs for various cellular pathways including cellular migration, metabolism, translation and transcriptional regulation. Human astrocytoma cell stress granules contain mRNA that are known to be involved in glioma signaling and the mTOR pathway. These data provide evidence that RNA stress granules are a novel form of epigenetic regulation in astrocytoma cells, which may be targetable by chemical inhibitors and enhance astrocytoma susceptiblity to conventional therapy such as radiation and chemotherapy.
2016-02-29 | GSE76814 | GEO
Project description:Analysis of stress granules in HeLa cells, after exposure to different stimuli. Granules were collected by a newly devised enrichment method, described in manuscript. Proteomics sample preparation of granules was carried out using the Single-pot, solid phase-enhanced sample preparation, SP3 method (Hughes CS et al. Nat Protoc 14, 68 85 (2019)). Desalting, clean-up and loading to the MS was done using an Evosep one EV1000 instrument, following manufacturers protocol, but loading of sample to Evotips was done a pre-existing volume of A Buffer. Samples were measured on a Thermo Exploris 480 mass spectrometer, using data-independent acquisition (DIA) (30 SPD, 44 LC min gradient (Evosep), MS1: 120000 res, 350-1400 m/z, inj. time 50 ms, MS2: 14 m/z isolation windows, 1 /mz overlap, precursor mass range. 350-1020 m/z, stepped collision energy 25,27.5,30, 22 ms inj. time.
RAW files were analyzed using Spectronaut v16, using directDIA mode with default settings, using as database the Homo Sapiens EBI Reference proteome, downloaded on 03/2021 and including an in-house curated contaminants list based on the MaxQuant's contaminants list. Protein summarisation was done with MSstats, using default settings.
2022-11-02 | MSV000090634 | MassIVE
Project description:Cell division ensures that both genetic information and non-genetic contents are inherited by daughter cells. Whereas considerable detail has been learned about the processing of intact or damaged DNA during the cell cycle (Branzei & Foiani, 2008; Klaasen et al., 2022),(Bakhoum & Cantley, 2018),(Hustedt & Durocher, 2016), how daughter cells deal with other forms of inherited damage is unknown. Here we identified a special kind of cytoplasmic granules responsible for the compartmentalisation of parental RNA damage. We found that ultraviolet (UV)-induced RNA, but not DNA, damage triggered assembly of this unique type of granules characterized by the presence of RNA helicase DHX9. By developing a novel methodology, FANCI, we discovered that DHX9 granules are enriched in damaged intron RNA and pre-mRNA-binding proteins, which is in contrast to other classical stress granules (SGs) that are composed of mature mRNA. Intron damage impeded proper splicing and intron decay, and induced generation of circRNA and dsRNA in the granules. Moreover, we showed that intron damage induced DHX9 granules assembled specifically in postmitotic daughter cells and triggered a cellular dsRNA immune response. Condensation with dsRNA is crucial for DHX9 localization to the granules and the modulation of dsRNA in these granules by DHX9 was crucial for daughter cell survival. Our observations revealed that DHX9 granules constitute a dedicated non-membrane-bound cytoplasmic compartment that protects daughter cells from parental damaged RNA.
2023-11-11 | GSE218180 | GEO
Project description:P granules in C. elegans are required for fertility and function to maintain germ cell identity and pluripotency. Sterility in the absence of P granules is often accompanied by the mis-expression of soma-specific proteins and the initiation of somatic differentiation in germ cells. To investigate whether this is caused by the accumulation of somatic transcripts, we performed mRNA-seq on dissected germlines with and without P granules. Strikingly, we found that somatic transcripts do not increase in the young adult germline when P granules are impaired. Instead, we found that impairing P granules causes sperm-specific mRNAs to become highly overexpressed. This includes the accumulation of major sperm protein (MSP) transcripts in germ cells, a phenotype that is suppressed by feminization of the germline. A core component of P granules, the endo-siRNA-binding Argonaute protein CSR-1, has recently been ascribed with the ability to license transcripts for germline expression. However, impairing CSR-1 has very little effect on the accumulation of its mRNA targets. Instead, we found that CSR-1 functions with P granules to prevent MSP and sperm-specific mRNAs from being transcribed in the hermaphrodite germline. These findings suggest that P granules protect germline integrity through two different mechanisms, by 1) preventing the inappropriate expression of somatic proteins at the level of translational regulation, and by 2) functioning with CSR-1 to limit the domain of sperm-specific expression at the level of transcription. Four biological replicates of each condition (empty vector control, P granule RNAi, and CSR-1 RNAi germlines) were collected for total RNA.
2015-05-20 | E-GEOD-67954 | biostudies-arrayexpress
Project description:T bruce were heat shocked for 1 h at 41C then granules were prepared as per Fritz et al. 2015. After spinning down cytoskeletons with trapped contents and lysing them we sequenced the supernatant (trapped RNA) and pellet (granule) fractions. Input total RNA is included for comparison.
2016-06-13 | E-MTAB-4557 | biostudies-arrayexpress