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Genomic N6-methyladenosine promotes expression of genes important for chromosome maintenance in bacteria [pacbio_DnmA2]

ABSTRACT: We used Pacific Biosciences Single Molecule Real-Time sequencing platform to identify m6A modifications and putative methyltransferases in Bacillus subtilis

ORGANISM(S): Bacillus subtilis

PROVIDER: GSE130694 | GEO | 2019/05/04

REPOSITORIES: GEO

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Genomic N6-methyladenosine promotes expression of genes important for chromosome maintenance in bacteria [pacbio_DnmA]

Project description:We used Pacific Biosciences Single Molecule Real-Time sequencing platform to identify m6A modifications and putative methyltransferases in Bacillus subtilis

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Genomic N6-methyladenosine promotes expression of genes important for chromosome maintenance in bacteria

Project description:This SuperSeries is composed of the SubSeries listed below.

2019-05-04 | GSE130695 | GEO

A systematic reassessment of N6-methyladenine in metazoan genomes

Project description:We report the application of SMRT seqeuncing from Pacific Biosciences to study the DNA base modifications in dam-/dcm- and wild type E.coli.

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N6-methyladenosine mRNA methylation is important for the light response in soybean

Project description:N6-methyladenosine (m6A) modification of messenger RNA (mRNA) is the most prevalent and abundant modification in eukaryotic mRNA and posttranscriptionally modulates the transcriptome at almost all stages of mRNA metabolism. In plants, m6A is crucial for embryonic-phase growth, flowering time control, microspore generation and fruit maturation. However, the role of m6A in plant responses to light, the most important environmental stimulus, remains unexplored. Here, we profile the m6A transcriptome of Williams 82, a soybean cultivar, and reveal that m6A is highly conserved and plays an important role in the response to light stimuli in soybean. Similar to the case in Arabidopsis, m6A in soybean is enriched not only around the stop codon and within the 3’UTR but also around the start codon. Moreover, genes with methylation occurring in the 3’UTR have higher expression levels and are more prone to alternative splicing. The core genes in the light signaling pathway, GmSPA1a, GmPRR5e and GmBIC2b, undergo changes in methylation modification and transcription levels in response to light. KEGG pathway analysis revealed that differentially expressed genes with differential m6A peaks were involved in the “photosynthesis” and “circadian rhythm” pathways. Our results highlight the important role played by epitranscriptomic mRNA methylation in the light response in soybean and provide a solid basis for determining the functional role of light on RNA m6A modification in this plant.

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Effects of the Structural Maintenance of Chromosomes (SMC) protein on gene expression in Bacillus subtilis

Project description:We monitored changes in Bacillus subtilis global gene expression in response to deletion or disruption of smc or ftsY. Keywords: genetic modification

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Widespread N6-methyladenosine-dependent RNA Structural Switches Regulate RNA-Protein Interactions

Project description:We show that N6-methyladenosine (m6A), the most abundant internal modification in mRNA/lncRNA with still poorly characterized function, alters RNA structure to facilitate the access of RBM for heterogeneous nuclear ribonucleoprotein C (hnRNP C). We term this mechanism m6A-switch. Through combining PAR-CLIP with Me-RIP, we identify 39,060 m6A-switches among hnRNP C binding sites transcriptome-wide. We show that m6A-methyltransferases METTL3 or METTL14 knockdown decreases hnRNP C binding at 16,582 m6A-switches. Taken together, 2,798 m6A-switches of high confidence are identified to mediate RNA-hnRNP C interactions and affect diverse biological processes including cell cycle regulation. These findings reveal the biological importance of m6A and provide insights into the sophisticated regulation of RNA-RBP interactions through m6A-induced RNA structural remodeling. Measure the m6A methylated hnRNP C binding sites transcriptome-wide by PARCLIP-MeRIP; measure the differential hnRNP C occupancies upon METTL3/METTL14 knockdown by PAR-CLIP; measure RNA abundance and splicing level changes upon HNRNPC, METTL3 and METTL14 knockdown

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Genomic N6-methyladenosine promotes expression of genes important for chromosome maintenance in bacteria

Project description:Genomic N6-methyladenosine promotes expression of genes important for chromosome maintenance in bacteria

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The correlation between chemotherapy combined with immunotherapy and the evolution of intestinal flora in small cell lung cancer

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Genomic N6-methyladenosine promotes expression of genes important for chromosome maintenance in bacteria [pacbio_DnmA]

Project description:Genomic N6-methyladenosine promotes expression of genes important for chromosome maintenance in bacteria [pacbio_DnmA]

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