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FTSJ1 patients RiboMethSeq

ABSTRACT: RiboMethSeq FTSJ1 tRNA Nm-MTase: new human targets and role in the regulation of brain-specific genes

PROVIDER: PRJEB46400 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	ERR6324081.fastq.gz	Fastqsanger.gz
	ERR6324082.fastq.gz	Fastqsanger.gz
	ERR6324083.fastq.gz	Fastqsanger.gz
	ERR6324084.fastq.gz	Fastqsanger.gz
	ERR6324085.fastq.gz	Fastqsanger.gz

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FTSJ1 patients RNASeq

Project description:RNASeq: FTSJ1 tRNA Nm-MTase: new human targets and role in the regulation of brain-specific genes

| PRJEB46399 | ENA

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

tRNA 2’-O-methylation by a duo of TRM7/FTSJ1 proteins modulates small RNA silencing in Drosophila.

Project description:2’-O-methylation (Nm) represents one of the most common RNA modifications. Nm affects RNA structure and function with crucial roles in various RNA-mediated processes ranging from RNA silencing, translation, self versus non-self recognition to viral defense mechanisms. Here, we identify two novel Nm methyltransferases (Nm-MTases) in Drosophila melanogaster (CG7009 and CG5220) as functional orthologs of yeast TRM7 and human FTSJ1. Genetic knockout studies together with MALDI-TOF mass spectrometry and RiboMethSeq mapping revealed that CG7009 is responsible for methylating the wobble position in tRNAPhe, tRNATrp and tRNALeu, while subsequently, CG5220 methylates position C32 in the same tRNAs and targets also additional tRNAs. CG7009 or CG5220 mutant animals were viable and fertile but exhibited various phenotypes such as life span reduction, small RNA pathways dysfunction and increased sensitivity to RNA virus infections. Our results provide the first detailed characterization of two TRM7 family members in Drosophila and uncover a molecular link between enzymes catalysing Nm at specific tRNAs and small RNA-induced gene silencing pathways.

2020-01-03 | GSE134354 | GEO

Human RiboMethSeq

Project description:Human RiboMetHSeq optimization

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P0.5 WT or Ftsj1 KO mouse brain or liver total mRNA or ribosome-contained mRNA

Project description:P0.5 WT or Ftsj1 KO mouse brain or liver ribosome-contained mRNAs or total mRNAs, and were sequenced using MiSeq and HiSeq.

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8-week WT or Ftsj1 KO mouse brain tRNA and tRF MiSeq

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RiboMethSeq of HCT116 cells treated with siCoilin

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Next Generation Sequencing identifies differential genes regulated by FTSJ1 overexpression

Project description:We report the application of RNA-sequencing for high-throughput profiling of transcriptomes in PC9 cells transfected with stably expressed FTSJ1.

2020-05-19 | GSE146604 | GEO

RiboMethSeq of HCT116 cells treated with siTFIP11 or siDHX15

Project description:RiboMethSeq of HCT116 cells treated with siTFIP11 or siDHX15 to investigate the effect of TFIP11 or DHX15 knockdown on RNA methylation as part of a larger study on the function of TFIP11.

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