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Transcriptome-wide mapping of m6A sites with or without YTHDF2 (DF2) knock-down in U2OS cells.

ABSTRACT: Transcriptome-wide mapping of m6A sites with or without YTHDF2 (DF2) knock-down in U2OS cells.

PROVIDER: PRJNA902824 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR22325753_1.fastq.gz	Fastqsanger.gz
	SRR22325753_2.fastq.gz	Fastqsanger.gz
	SRR22325754_1.fastq.gz	Fastqsanger.gz
	SRR22325754_2.fastq.gz	Fastqsanger.gz
	SRR22325755_1.fastq.gz	Fastqsanger.gz

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Transcriptome-wide mapping of m6A sites with or without YTHDF2 (DF2) knock-down in U2OS cells.

Project description:Transcriptome-wide mapping of m6A sites with or without YTHDF2 (DF2) knock-down in U2OS cells.

| PRJNA750647 | ENA

Transcriptomic Analysis of the m6A Reader YTHDF2 in the Maintenance and Differentiation of Human Embryonic Stem Cells

Project description:As the most abundant internal modification on mRNAs, N6-methyladenosine (m6A) has been discovered to be involved in different biological processes. Mostly determined by m6A methyl-transferases (m6A writers) and demethylases (m6A erasers), different cell types possess differential m6A profiles of transcriptomes. However, the interpretation of the m6A-encoded epitranscriptomic information needs m6A readers to bind and recruit different machinery for regulating the target mRNAs, which in turn, may regulate cell fates. The functions of the m6A readers in the regulation of the maintenance and differentiation of human embryonic stem cells (hESCs) remain largely unknown. In this study, we deleted the whole genomic region of the m6A reader YTHDF2, and discovered that YTHDF2 is dispensible for the maintenance, but probably important for the differention of hESCs, especially for the differentiation towares ectoderm. Furthermore, we identified ROBO1 as a potential target gene by DF2 in regulating hESC to neuroectoderm differentiation. This study reveals the potential roles of the m6A reader DF2 in regulating the specification of neuroectodermal cell fate.

2025-03-11 | GSE268806 | GEO

Transcriptome-wide mapping of m6A sites with or without YTHDF2 (DF2) knock-down in U2OS cells.

Project description:The goal was to see whether and how mRNA stability is linked to m6A peak position in mRNA. The RNA-seq data set in this submission represents a technical RNA-seq repeat of samples 1, 3, 5, 6, 7, and 8 described in a previous GEO submission (GSE181079).

2025-02-01 | GSE218264 | GEO

Transcriptome-wide mapping of m6A sites with or without YTHDF2 (DF2) knock-down in U2OS cells.

Project description:The goal was to see whether and how mRNA stability is linked to m6A peak position in mRNA.

2025-02-01 | GSE181079 | GEO

YTHDF2 mediates the mRNA degradation in prostate cancer in m6A-dependent way

Project description:As the crucial m6A reader, YTHDF2 usually degrades the target mRNAs by recognizing the m6A modified sites, consequently altering m6A levels of each mRNA. In this study, we used m6A MeRIP sequencing to detect the m6A modification alterations in prostate cancer (PCa) cell line after knocking down YTHDF2 and identify how YTHDF2 promote the PCa progression by mediating the mRNA degradation in m6A-dependent way.

2020-11-09 | GSE129408 | GEO

Expression data from YTHDF1 or YTHDF2 down-regulated PC9

Project description:Expression data from YTHDF1 or YTHDF2 down-regulated PC9

| PRJNA720377 | ENA

m6A-dependent regulation of messenger RNA stability

Project description:N6-methyladenosine (m6A) is the most prevalent internal modification present in the mRNA of all higher eukaryotes. Here we present that m6A is selectively recognized by human YTH domain family (YTHDF2) protein to regulate mRNA degradation. By using crosslinking and immunoprecipitation, we have identified over 4000 substrate RNA of YTHDF2 with conserved core motif of G(m6A)C. We further estabilshed the role of YTHDF2 in RNA metabolism by a combination of ribosome profiling, RNA sequencing, m6A level quantification and cell-based imaging: the C-terminal domain of YTHDF2 selectively binds to m6A of mRNA and the N-terminal domain is responsive for localizing mRNA from translatable pool to processing body where mRNA decay occurs. PAR-CLIP and RIP was used to identify YTHDF2 binding sites followed by ribosome profling and RNA seq to assess the consequences of YTHDF2 siRNA knock-down

2013-11-29 | E-GEOD-49339 | biostudies-arrayexpress

Ythdf2-mediated m6A mRNA clearance modulates neural development in mice

Project description:We found that the proliferation and differentiation capabilities of NSPCs decrease significantly in Ythdf2 null mutants.To explore the underlying molecular mechanism, we performed transcriptomics and well-established m6A-methylome analyses of NSPCs dervied from wild type and Ythdf2-/- embryo brains. RNA-seq data revealed that expressions of genes enriched in neural development pathways were significantly disturbed. The inhibitory genes, like Flrt2, Ptprd, et al. in regulation of JAK-STAT cascade, which contributes to the neuroprotection and neurite outgrowth, showed increased gene expressions and m6A enrichment by m6A-seq. We identified that without the recognizing and binding of Ythdf2, the degradation of neuron differentiation related m6A-modified mRNAs were delayed in Ythdf2-/-, thereby disturbing the proliferation and differentiation of NSPCs. In summary, our findings uncovered that Ythdf2 modulates neural developmental via regulating the clearance of mRNA targets.

2018-01-01 | GSE104867 | GEO

Gene regulation by m6A demethylase ALKBH5 in U2OS osteosarcoma

Project description:To identify target genes regulated by ALKBH5 in osteosarcoma, we silenced the expression of ALKBH5 in osteosarcoma cell line-U2OS and tested its effect on U2OS transcriptome.

2023-12-31 | GSE171671 | GEO

Expression data from YTHDF1 or YTHDF2 down-regulated PC9

Project description:The human YTH domain family protein (YTHDF) family is RNA binding protein which specifically recognizes N6-methyladenosine (m6A), and exerts distinct roles in eukaryocytes; YTHDF1 promotes the translation of m6A modified mRNAs collaborating with initiation factors, and YTHDF2 reduces the stability of the m6A-modified transcripts. We used the Nanostring nCounter to detail the differential gene expression by YTHDF1 and YTHDF2.

2021-08-24 | GSE171634 | GEO

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