The inhibition of m6A modification on reporter mRNA by STM2457
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PROVIDER: PRJNA1141493 | ENA |
REPOSITORIES: ENA
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Project description:We present a spatiotemporal m6A imaging system (SMIS) that can monitor the m6A modification and the translation of mRNAs with high specificity and sensitivity in a single live cell. The SMIS system contains a m6A-modified reporter mRNA and fluorescence resonance energy transfer (FRET) biosensors. To quantify the methylation viariation achieved at m6A sites in the reporter mRNA after STM2457 treatment, a classical METTL3 inhibitor, we performed m6ACE-seq to measure the relative m6A level with single-base-resolusion.
2024-10-11 | GSE273366 | GEO
Project description:In this study we performed MeRIP-Seq to study N6-methyl adenosine (m6A) and and N6,2′ -O-dimethyladenosine (m6Am) modification of mRNA. We investigated the effect of the microbiota on the transcriptome and epitranscriptomic modifications in murine liver and cecum. We compared m6A/m modification profiles in cecum of conventionally raised (CONV) and germ-free (GF) mice. We additionally included GF mice colonised with the flora of CONV mice for four weeks (ex-GF), for which show that they exhibit similar patterns of the most abundant genera of gut bacteria as CONV mice. We added mice treated with several antibiotics to deplete the gut flora (abx)and vancomycin treated mice in which the genera Akkermansia, Escherichia/Shigella and Lactobacillus were enriched. Furthermore, we included GF mice colonised with the commensal bacterium Akkermansia muciniphila (Am), Lactobacillus plantarum (Lp) and Escherichia coli Nissle (Ec) and analysed their m6A/m modification profiles. In addition, we analysed changes in m6A/m- modified liver RNA for CONV, GF, and Am, Lp and Ec mice.
2020-02-12 | E-MTAB-6560 | biostudies-arrayexpress
Project description:N6-methyladenosine (m6A) is one of the most abundant modifications in eukaryotic RNA. Recent mapping of m6A methylomes in mammals, yeast, and plants as well as characterization of m6A methyltransferases, demethylases, and binding proteins have revealed regulatory functions of this dynamic RNA modification. In bacteria, although m6A is present in ribosomal RNA (rRNA), its occurrence in messenger RNA (mRNA) still remains elusive. Here, we used liquid chromatography-mass spectrometry (LC-MS) to calculate the m6A/A ratio in mRNA from a wide range of bacterial species, which demonstrates that m6A is an abundant mRNA modification in tested bacteria. Subsequent transcriptome-wide m6A profiling in Escherichia coli and Pseudomonas aeruginosa revealed a conserved distinct m6A pattern that is significantly different from that in eukaryotes. Most m6A peaks are located inside open reading frames (ORF), and carry a unique consensus motif (GCCAU). Functional enrichment analysis of bacterial m6A peaks indicates that the majority of m6A-modified transcripts are associated with respiration, amino acids metabolism, stress response, and small RNAs genes, suggesting potential regulatory roles of m6A in these pathways. m6A profiling in E.coli and P.aeruginosa mRNA
2015-07-08 | E-GEOD-65347 | biostudies-arrayexpress
Project description:RNA modifications are integral to regulation of RNA metabolism. One such abundant mRNA modification is m6A, which impacts various aspects of RNA metabolism including splicing, transport and degradation. Current knowledge about proteins recruited to m6A to carry out these molecular processes is still limited. Here we describe a comprehensive and systematic mass spectrometry-based screening of m6A interactors in various cell types and species. Amongst the main findings, we identified G3BP1 as a protein, which is repelled by m6A and which positively regulates mRNA stability in an m6A regulated manner. Furthermore, we identified FMR1 as a novel, RNA sequence context dependent m6A reader, thus revealing a connection between an mRNA modification and an autism spectrum disorder. Collectively, our data represents a rich resource for the community and sheds further light on the complex interplay between m6A, m6A interactors and mRNA homeostasis.
2017-08-22 | PXD006498 | Pride
Project description:Posttranscriptional and posttranslational modifications play crucial roles in plant immunity. However, how plant fine-tune these two modifications to activate antiviral immunity remains unknown. Here, we report that the m6A methyltransferase TaHAKAI is utilized by wheat yellow mosaic virus (WYMV) to increase viral genomic m6A modification and promotes viral replication. However, TaHAKAI also functions as an E3 ligase that targets the viral RNA silencing suppressor P2 for degradation and inhibits viral infection. A major allele of TaHAKAI in susceptible cultivar reduced the E3 ligase activity but not m6A methyltransferase activity, promoting viral infection. Interestingly, TaHAKAIR attenuates the mRNA stability of TaWPS1, the negative regulator of spike development, to increase panicle length and spikelet number by modulating its m6A modification. Our study reveals a new mechanisms of balancing disease resistance and yield by fine-tuning m6A modification and ubiquitination.
2024-10-09 | PXD056650 | Pride
Project description:In summary, we characterized the role of m6A modification in pulmonary fibrosis. We reveal that m6A modification is increased in bleomycin induced pulmonary fibrosis mice model, FMT-derived myofibroblasts and idiopathic pulmonary fibrosis patient lung samples. Lowering m6A level through silencing METTL3 suppress FMT process in vitro and vivo. Fundamentally, m6A modification regulates FMT by modulating the translation of KCNH6 mRNA in a YTHDF1 dependent manner. This study provides novel insights into the mechanism of FMT process and suggests m6A modification intervention may be a promising therapeutic strategy for pulmonary fibrosis.
2021-06-02 | GSE164151 | GEO
Project description:N6-methyl-adenosine (m6A) is the most abundant modification on messenger RNAs and is linked to human diseases, but its functions in mammalian development are poorly understood. Here we reveal the evolutionary conservation and function of m6A by mapping the m6A methylome in mouse and human embryonic stem cells. Thousands of messenger and long noncoding RNAs show conserved m6A modification, including transcripts encoding core pluripotency transcription factors. m6A is enriched over 3M-bM-^@M-^Y untranslated regions at defined sequence motifs, and marks unstable transcripts, including transcripts turned over upon differentiation. Genetic inactivation or depletion of mouse and human Mettl3, one of the m6A methylases, led to m6A erasure on select target genes, prolonged Nanog expression upon differentiation, and impaired ESCM-bM-^@M-^Ys exit from self-renewal towards differentiation into several lineages in vitro and in vivo. Thus, m6A is a mark of transcriptome flexibility required for stem cells to differentiate to specific lineages. Examing m6A modification differences in two different cell types
2014-10-20 | E-GEOD-52600 | biostudies-arrayexpress
Project description:Background: Maternal and zygotic mRNAs play critical roles in maternal-to-zygotic transition (MZT) stage and N6-methyladenosine (m6A) has been proven as an important RNA metabolism regulation system. However, the dynamic profiles of m6A modification during mammalian MZT and its potential functions remain largely unknown. Results: Here we utilized m6A-seq, low-input RNA-seq, LiRibo-seq and low-input proteomic analysis to examine the mRNA regulation dynamics during mouse MZT. We found that m6A could be inherited from maternal origin or de novo added after fertilization. Interestingly, we observed the de novo m6A modification on mRNA during zygotic genome activation (ZGA), especially at major ZGA. Further analysis showed that m6A modification on maternal mRNAs not only correlates with mRNA degradation after fertilization, but also maintains the stability of a small group of mRNAs thereby promoting their translation after fertilization. Using CRISPR-Cas13d mediated RNA editing, we systemically evaluated the functions of ten m6A regulators and identified Ythdc1 and Ythdf2 as key m6A readers for mouse preimplantation development. By combining low-input RNA-seq, RNA immunoprecipitation (RIP) and qRT-PCR, we uncovered and verified that Ythdc1 can associate with a small group of m6A-tagged mRNAs and participate in their mRNA stability regulation. Conclusions: Our integrated multi-omic analysis links m6A modification to the diverse fates of maternal and zygotic mRNAs and establishes a key role of m6A mediated RNA metabolism in mammalian MZT.
2023-03-28 | GSE228201 | GEO
Project description:Our study demonstrated that the expression of Igf2bp1 in activated microglia was significantly up-regulated, implying a role of Igf2bp1 in LPS-induced m6A modifications in microglia. To understand the roles of Igf2bp1 on LPS-induced m6A modification in microglia, we performed Igf2bp1 loss-of-function (LOF) approach. Microglia stimulated by LPS were transfected with either scrambled siRNA control or Igf2bp1 siRNA for 48 hours. To m6A modification profiles in control and Igf2bp1 LOF microglia were determined by MeRIP-seq analysis.
2022-12-31 | E-MTAB-11411 | biostudies-arrayexpress
Project description:A recently layer of gene expression regulation is N6-methyladenosine (m6A) mRNA modification. The role of gut microbiota in modulating host m6A epitranscriptomic and gene expression has not been studied. To decipher the role of gut microbiome, we profiled m6A mRNA modification epitranscriptomic mark in conventional mice compared to germ free mice. Transcriptome-wide mapping of host m6A mRNA modifications in four mice tissues allowed us to discover that gut microbiota can greatly impact host m6A mRNA modifications. The expression levels of m6A writers in mice tissues are regulated by gut microbiota. In conclusion, we report transcriptome-wide mapping of host m6A mRNA modifications regulated by gut microbiota. The present study can help better understand the role of the microbiome in host gene expression and host-microbiome interactions.
2018-12-28 | GSE120262 | GEO