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Widespread Occurrence of m6A in bacterial mRNA

ABSTRACT: 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.

ORGANISM(S): Escherichia coli K-12 Pseudomonas aeruginosa PAO1

PROVIDER: GSE65347 | GEO | 2015/07/08

SECONDARY ACCESSION(S): PRJNA273742

REPOSITORIES: GEO

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Widespread Occurrence of m6A in bacterial mRNA

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

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Transcriptome-wide m6A Methylation Profiling of dHL-60 human neutrophils by m6A-seq

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Effect of depletion of CBX1 on gene expression of SUNE1 cells [RNA-seq]

Project description:Nasopharyngeal carcinoma (NPC), which arises from the nasopharyngeal pharynx, is a metastasis-prone malignancy highly prevalent in East and Southeast Asia, especially southern China. Despite progress in chemo-radiotherapeutic strategies, about 20% of NPC patients still suffer from distant metastasis, thus developing new therapeutic strategies for NPC is of vital importance. N6-methyladenosine (m6A) RNA modification, the most abundant epitranscriptomic modification in eukaryotic mRNA, has attracted great attention in cancer research because of its vital biological functions. However, little is known about the underlying molecular mechanisms between m6A modification and NPC progression. We aimed to identified differential m6A peaks by analyzing the m6A modification profile in NPC with paired tissues with or without metastasis using m6A-seq. For RNA-seq and ChIP-seq, we aimed to identified the downstream targets of CBX1 in NPC.

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m6A-seq and RNA-seq of 4 pairs NPC tissues with or without metastasis

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Transcriptome-wide N6-methyladenosine modification profiling of mRNAs during infection of Newcastle disease virus in Chicken Macrophages

Project description:N6-methyladenosine (m6A) modification is the most prevalent post-transcriptional modification of mRNA in eukaryotes and has been reported to play an important role in viral infection. However, the role of m6A modification during Newcastle disease virus infection (NDV) is not clear. In this study, we profiled the transcriptome-wide m6A modification of mRNA in NDV-infected chicken macrophages using MeRIP-seq. we identified a total of 9496 significantly changed peaks, of which 7015 peaks distributed across 3320 genes were significantly up-regulated and 2481 peaks distributed across 1264 genes were significantly down-regulated. Combined analysis of m6A peaks and mRNA expression revealed 1234 mRNAs with significantly altered methylation and expression levels after NDV infection, and m6A modification tended to have a negatively correlation with mRNA expression, suggesting that m6A modification may regulate the process of NDV infection by regulating gene expression, especially innate immunity-related genes. To our knowledge, This is the first comprehensive characterization of m6A patterns of the mRNA in chicken macrophages after NDV infection, and provides a valuable basis for further exploring the role of m6A modification in the process of NDV infection.

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The Alteration of M6A-tagged Transcript Profiles in The Retina of Rats After Traumatic Optic Neuropathy

Project description:Messager RNA (mRNA) can be modified in a variety of ways, among which the modification of N6-methyladenosine (m6A) is one of the most common ones. Recent studies have found that the m6A modification in mRNA could functionally regulate the splicing, localization, translation and stability of mRNA, which might be closely related to multiple diseases. However, the roles of m6A modification in traumatic optic neuropathy (TON) are unknown. Herein, we detected the expression of m6A-related genes via quantitative real-time PCR (qRT-PCR) and performed methylated RNA immunoprecipitation sequencing (MeRIP-seq) as well as RNA-sequencing to analyze the alteration profiles of m6A modification after TON. The results showed that the expression of m6A-related genes (METTL3, WTAP, FTO and ALKBH5) were all upregulated after TON. In all, 2810 m6A peaks were differentially upregulated and 689 m6A peaks were downregulated. In addition, the hypermethylated and hypomethylated profiles of mRNA transcripts were also identified. To sum up, our study revealed the differentially expressed m6A modification in the early stage of TON, which may provide novel insights into the mechanism and treatment of TON.

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