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Conserved Methyltransferase Spb1 Targets mRNAs for Regulated Modification with 2′-O-Methyl Ribose [eCLIP]

ABSTRACT: Conserved Methyltransferase Spb1 Targets mRNAs for Regulated Modification with 2′-O-Methyl Ribose [eCLIP]

PROVIDER: PRJNA432353 | ENA |

REPOSITORIES: ENA

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Conserved Methyltransferase Spb1 Targets mRNAs for Regulated Modification with 2′-O-Methyl Ribose [eCLIP]

Project description:Non-coding RNAs contain dozens of chemically distinct modifications, of which only a few have been identified in mRNAs. The recent discovery that certain tRNA modifying enzymes also target mRNAs suggests the potential for many additional mRNA modifications. Here, we show that conserved tRNA 2′-O-methyltransferases Trm3, 7,13 and 44, and rRNA 2′-O-methyltransferase Spb1, interact with specific mRNA sites in yeast by crosslinking immunoprecipitation and sequencing (CLIP-seq). We developed sequencing of methylation at two prime hydroxyls (MeTH-seq) for transcriptome-wide mapping of 2′-O-methyl ribose (Nm) with single-nucleotide resolution, and discover thousands of potential Nm sites in mRNAs. Genetic analysis identified hundreds of mRNA targets for the Spb1 methyltransferase, which can target both mRNA and non-coding RNA for environmentally regulated modification. Our work identifies Nm as a prevalent mRNA modification that is likely to be conserved and provides methods to investigate its distribution and regulation.

2019-01-16 | GSE109926 | GEO

Conserved Methyltransferase Spb1 Targets mRNAs for Regulated Modification with 2′-O-Methyl Ribose [meTH-Seq]

2019-01-16 | GSE109925 | GEO

Conserved Methyltransferase Spb1 Targets mRNAs for Regulated Modification with 2′-O-Methyl Ribose

Project description:Conserved Methyltransferase Spb1 Targets mRNAs for Regulated Modification with 2′-O-Methyl Ribose

| PRJNA432351 | ENA

Conserved Methyltransferase Spb1 Targets mRNAs for Regulated Modification with 2′-O-Methyl Ribose [meTH-Seq]

Project description:Conserved Methyltransferase Spb1 Targets mRNAs for Regulated Modification with 2′-O-Methyl Ribose [meTH-Seq]

| PRJNA432352 | ENA

Conserved Methyltransferase Spb1 Targets mRNAs for Regulated Modification with 2′-O-Methyl Ribose

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

2019-01-16 | GSE109927 | GEO

RBM33 eCLIP

Project description:RBM33 eCLIP

| PRJNA791310 | ENA

METTL5, an 18S rRNA-specific m6A methyltransferase, regulates the Integrated Stress Response [eCLIP]

Project description:METTL5, an 18S rRNA-specific m6A methyltransferase, regulates the Integrated Stress Response [eCLIP]

| PRJNA574656 | ENA

SETMAR methyl-lysine (3xMBT) pull-down

Project description:SILAC labeled HT-1080 cell lysate (K0R0 and K8R10) were treated with active or catalytic inactive SETMAR methyltransferase enzyme. Samples were combined and proteins modified by methyl-lysine enriched by 3xMBT. Quantitative comparison identified candidate proteins with increase methylation following incubation with SETMAR.

2016-06-24 | PXD001635 | Pride

Transcription profiling by array of Lactobacillus sakei strains grown on ribose or glucose to study ribose catabolism

Project description:We used a whole-genome microarray based on the sequenced strain Lactobacillus sakei 23K to study ribose catabolism in three Lactobacillus sakei strains by screening for differentially expressed genes when grown on ribose compared to glucose

2010-12-01 | E-MEXP-2892 | biostudies-arrayexpress

Ribose utilization by the human commensal Bifidobacterium breve UCC2003

Project description:Growth of B. breve UCC2003 on ribose leads to the transcriptional induction of the rbsACBDK gene cluster. Generation and phenotypic analysis of an rbsA insertion mutant established that the rbs gene cluster is essential for ribose utilization, and that its transcription is likely regulated by a LacI-type regulator encoded by rbsR, located immediately upstream of rbsA. Gel mobility shift assays using purified RbsRHis indicate that the promoter upstream of rbsABCDK is negatively controlled by RbsRHis binding to an 18-bp inverted repeat and that RbsRHis binding activity is modulated by D-ribose. The rbsK gene of the rbs operon of B. breve UCC2003 was shown to specify a ribokinase (EC 2.7.1.15), which specifically directs its phosphorylating activity towards D-ribose, converting this pentose sugar to ribose-5-phosphate. In order to investigate differences in global gene expression upon growth of B. breve UCC2003 on ribose, or a combination of ribose and glucose, as compared to glucose, DNA microarray experiments were performed. Total RNA was isolated from B. breve UCC2003 cultures grown on ribose, a combination of ribose and glucose, or glucose. All experiments were performed in duplicate. A dye swap was performed in one of the two biological replicates.

2010-05-19 | E-GEOD-17325 | biostudies-arrayexpress

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