Genome-wide mapping of m6A modified chromatin associated RNA
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ABSTRACT:
ORGANISM(S): Mus musculus
PROVIDER: GSE173517 | GEO | 2021/06/01
REPOSITORIES: GEO
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Project description:Genome-wide mapping of m6A modified chromatin associated RNA
| PRJNA725884 | ENA
Project description:We developed a novel approach, m6A-seq, for high-resolution mapping of the transcriptome-wide m6A landscape, based on antibody-mediated capture followed by massively parallel sequencing. Identification of m6A modified sequences in HepG2 cells. HepG2 cells were incubated with either IFNg (200ng/ml) or HGF/SF (10 ng/ml) over night. Stress effects were tested in HepG2 cells by either 30 minutes incubation at 43M-BM-:C (heat shock) or UV irradiation of 0.04 J/cm2 followed by 4 hours of recovery in normal growing conditions prior to harvesting using Trypsin.
2012-04-25 | E-GEOD-37002 | biostudies-arrayexpress
Project description:Using murine embryonic stem (mES) cells, here we show that two RNAi factors, Dgcr8 and the RNAseIII Drosha, physically associate with chromatin. We found that these known microRNA-processing factors associate with a subset of actively transcribed genes, as well as non-coding genes, including snoRNA, and lncRNA genes. Dgcr8 recruitment to chromatin was dependent on Methyltransferase-like 3 (Mettl3), which catalyzes N6-methyladenosine (m6A) of RNAs. Chemical inhibition of RNA polymerase II (RNAPII) disrupted the association of Dgcr8 and Mettl3 with chromatin, strongly suggesting RNA methylation and processing events occur co-transcriptionally. We also found that temperature stress causes a radical relocalization of Dgcr8 and Mettl3 to stress-induced genes including Hsp70. Genetic ablation of Dgcr8 or Mettl3 led to the accumulation of Hsp70 mRNA, elongation of its half-life, and increased protein levels only in cells subjected to acute heat stress. This indicates that acute heat-stress co-transcriptionally marks Hsp70 mRNAs by Mettl3 and Dgcr8 for subsequent RNA degradation to control the timing and magnitude of the heat shock response.
2017-05-18 | GSE92257 | GEO
Project description:Rainbow trout is a typical cold-water fish, with the intensification of global warming, high temperatures severely restrict the development of aquaculture in summer. Understanding the molecular regulation mechanisms of rainbow trout in response to heat stress will be salutary to alleviate heat stress-related damage. In the present study, we performed transcriptome analysis of liver tissues in rainbow trout under heat stress (24℃) and control (18℃) conditions to identify induced lncRNAs and pathways by heat stress. More than 658 million clean reads and 5,916 lncRNAs were identified from six liver libraries. A total of 927 novel lncRNAs were generated and 428 differentially expressed lncRNAs were screened through stringent thresholds. The RNA-seq results were verified by RT-qPCR. In addition, the regulatory network of important functional lncRNA-mRNA were constructed. GO and KEGG enrichment analysis of target gene of differentially expressed lncRNAs were performed. Many target genes involved in maintaining homeostasis or adapting to stress and stimuli were highly induced under heat stress. Several important regulatory pathways were involved in heat stress, including thyroid hormone signaling pathway, PI3K-Akt signaling pathway, estrogen signaling pathway, etc. This result broadens our understanding of lncRNA associated with heat stress and provides new insights into lncRNA-mediated regulation of rainbow trout heat stress.
2019-08-11 | GSE135668 | GEO
Project description:The aging brain is highly vulnerable to cellular stress, and neurons often employ numerous mechanisms to combat neurotoxic proteins and promote healthy brain aging. The RNA modification m6A has been shown to be a critical regulator of RNA stability and translation in cells during stress. m6A is highly enriched in the Drosophila brain and is critical for the acute heat stress response. Here we examine m6A response to chronic stresses of aging and degenerative disease. In the brain, m6A levels dynamically increased with age and disease, marking critical signaling pathway transcripts that become downregulated in age and disease. Unexpectedly, there is opposing regulation of m6A transcript translation in neural vs glial cells, which conferred different outcomes on animal healthspan with Mettl3 knockdown to reduce m6A. Moreover, these data reveal that knockdown of Mettl3 in glial tauopathy is beneficial, leading to increased animal survival. These findings provide mechanistic insight into regulation of m6A modified transcripts with age and disease that varies based on cell type.
2023-12-28 | GSE235989 | GEO
Project description:The post-translational protein modification known as SUMOylation has conserved roles in the heat stress responses of various species. The functional connection between the global regulation of gene expression and chromatin-associated SUMOylation in plant cells isunknown. Here, we uncovereda genome-wide relationship between chromatin-associated SUMOylation and transcriptional switches in Arabidopsis thaliana grown at room temperature, exposed to heat stress, and exposed to heat stress followed by recovery. The small ubiquitin-like modifier (SUMO)-associated chromatin sites, characterized by whole-genome ChIP-seq, were generally associated with active chromatin markers. In response to heat stress, chromatin-associated SUMO signals increased at promoter-transcriptional start site regions and decreased in gene bodies. RNAseqanalysissupportedthe role ofchromatin-associatedSUMOylationin transcriptionalactivation duringrapid responses to high temperature. Changes inSUMO signals on chromatinwere associated with the upregulation ofheat-responsivegenesandthedownregulationofgrowth-relatedgenes.DisruptionoftheSUMOligasegene SIZ1 abolished SUMO signals on chromatin and attenuated rapid transcriptional responses to heat stress. The SUMO signal peaks were enriched in DNA elements recognized by distinct groups of transcription factors under different temperature conditions. These observations provide evidence that chromatin-associated SUMOylation regulates the transcriptional switch between development and heat stress response in plant cells.
2020-08-04 | GSE140508 | GEO
Project description:Extensive tracts of the mammalian genome that lack protein-coding function are still transcribed into long noncoding RNA. While these lncRNA are generally short-lived, length-restricted and non-polyadenylated, how their expression is distinguished from protein-coding genes remains enigmatic. Surprisingly depletion of the ubiquitous Pol II associated transcription elongation factor SPT6, promotes a redistribution of H3K36me3 histone marks from active protein coding to lncRNA genes which correlates with increased lncRNA transcription. SPT6 knockdown also impairs the recruitment of Integrator complex to chromatin which results in a transcriptional termination defect for lncRNA genes. This leads to the formation of extended, polyadenylated lncRNA that are both chromatin restricted and form increased levels of RNA:DNA hybrid (R-loops) that are associated with DNA damage. Additionally, these deregulated lncRNA overlap with DNA replication origins leading to localized DNA replication stress and a cellular senescence phenotype. Overall our results underline the importance of restricting lncRNA expression.
2018-11-15 | GSE120371 | GEO
Project description:We used illumina-based next generation sequencing technology to to identify the regions bound by HSFA1b in the Arabidopsis genome. We sequenced HSFA1b chromatin immunoprecipitated genomic sequences under non-stress and heat stress conditions to understand the changes in the HSFA1b binding map when the growth conditions are switched from favorable to heat stress. We show that the binding map of HSFA1b in the Arabidopsis genome is subject to reconfiguration when the growth conditions are switched from non-stress to heat stress response. We also show that HSFA1b is targeting genes involved in developmental processes beside genes involved in stress response under both conditions indicating that HSFA1b possibly regulates the expression of both developmental and stress genes under non-stress and under heat stress, possibly for a limited duration prior heat acclimation.
2018-05-30 | GSE85651 | GEO
Project description:SUMOylation, a post-translational protein modification, is dramatically upregulated and critically involved in heat stress response conservatively among species. Previous studies in Arabidopsis indicated that numerous chromatin associated proteins are SUMOylation substrates and most of heat-enhancing SUMOylation reactions occur in nucleus. However, the global functional connection between gene expression regulation and SUMOylation on chromatin is completely unknown in plant cells. Here we show a genome-wide relationship of chromatin-associated SUMOylation and transcription switches under room temperature, heat stress, and recovering conditions in Arabidopsis. The SUMO-associated chromatin sites, characterized via whole-genome ChIP-seq assays, are generally correlated with active chromatin markers. In response to heat stress, we found chromatin-associated SUMO signals increased at promoter-transcriptional start site regions and decreased in the gene bodies. Further RNA-seq analysis supported the role of chromatin-associated SUMOylation in activation of transcription during rapid responses to high temperature. Changing of SUMO signals on chromatin is correlated with upregulation of heat-responsive genes and downregulation of growth-related genes. Disruption of the SUMO ligase gene SIZ1 abolishes SUMO signals on chromatin and attenuates the rapid transcriptional responses to heat stress. Interestingly, the SUMO signal peaks are enriched in DNA elements recognized by distinguished groups of transcription factors under different temperature conditions. Collectively, our data provide evidence that SUMOylation on chromatin regulates transcription switches during development and heat stress response, improving our understanding on the precise roles of SUMOylation in plant cells.
2020-08-04 | GSE140507 | GEO
Project description:SUMOylation, a post-translational protein modification, is dramatically upregulated and critically involved in heat stress response conservatively among species. Previous studies in Arabidopsis indicated that numerous chromatin associated proteins are SUMOylation substrates and most of heat-enhancing SUMOylation reactions occur in nucleus. However, the global functional connection between gene expression regulation and SUMOylation on chromatin is completely unknown in plant cells. Here we show a genome-wide relationship of chromatin-associated SUMOylation and transcription switches under room temperature, heat stress, and recovering conditions in Arabidopsis. The SUMO-associated chromatin sites, characterized via whole-genome ChIP-seq assays, are generally correlated with active chromatin markers. In response to heat stress, we found chromatin-associated SUMO signals increased at promoter-transcriptional start site regions and decreased in the gene bodies. Further RNA-seq analysis supported the role of chromatin-associated SUMOylation in activation of transcription during rapid responses to high temperature. Changing of SUMO signals on chromatin is correlated with upregulation of heat-responsive genes and downregulation of growth-related genes. Disruption of the SUMO ligase gene SIZ1 abolishes SUMO signals on chromatin and attenuates the rapid transcriptional responses to heat stress. Interestingly, the SUMO signal peaks are enriched in DNA elements recognized by distinguished groups of transcription factors under different temperature conditions. Collectively, our data provide evidence that SUMOylation on chromatin regulates transcription switches during development and heat stress response, improving our understanding on the precise roles of SUMOylation in plant cells.
2020-08-04 | GSE140506 | GEO