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

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

PROVIDER: PRJNA432352 | 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 [eCLIP]

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

| PRJNA432353 | 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

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

Ribose utilization by the human commensal Bifidobacterium breve UCC2003

2009-12-01 | GSE17325 | GEO

The ribose methylation enzyme FTSJ1 has a conserved role in neuron morphology and learning performance

Project description:FTSJ1 is a conserved human 2’-O-methyltransferase (Nm-MTase) that modifies several transfer RNAs (tRNAs) at position 32 and the wobble position 34 in the AntiCodon Loop (ACL). Its loss of function has been linked to Non-Syndromic X-Linked Intellectual Disability (NSXLID), and more recently to cancers. However, the molecular mechanisms underlying these pathologies are currently unclear. Here we report a novel FTSJ1 pathogenic variant from a NSXLID patient. Using blood cells derived from this patient and other affected individuals carrying FTSJ1 mutations, we performed an unbiased and comprehensive RiboMethSeq analysis to map the ribose methylation (Nm) on all tRNAs and identify novel targets. In addition, we performed a transcriptome analysis in these cells and found that several genes previously associated with intellectual disability and cancers were deregulated. We also found changes in the miRNA population that suggest potential cross-regulation of some miRNAs with these key mRNA targets. Finally, we show that differentiation of FTSJ1-depleted human neuronal progenitor cells (NPC) into neurons displays long and thin spine neurites compared to control cells. These defects are also observed in Drosophila and are associated with long term memory deficit in this organism. Altogether, our study adds insight into FTSJ1 pathologies in human by the identification of novel FTSJ1 targets and the defect in neuron morphology.

2023-01-06 | GSE179384 | GEO

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