Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Investigate the effect of depletion of Mettl14 or Ythdf2 on RNA stability in primary cultured cortical neurons

ABSTRACT: Across the transcriptome, m6A-modified transcripts showed increased relative stability in the Mettl14 cKO condition , and the number of m6A sites affected the stability. The stability of transcripts with m6A only in the CDS changed slightly less, while the stability of transcripts with m6A only in the 3' UTR or with m6A in both regions increased more significantly, suggesting that m6A in the 3' UTR has a more pronounced effect on mRNA stability. Unexpectedly, m6A-modified transcripts showed only a slight stability change in the DF2 cKO condition.

ORGANISM(S): Mus musculus

PROVIDER: GSE277231 | GEO | 2026/01/01

REPOSITORIES: GEO

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
		Other

Items per page:

1 - 1 of 1

Similar Datasets

m6A sites in the coding region trigger translation-dependent mRNA decay (YTHDF2 iCLIP2)

Project description:N6-Methyladenosine (m6A) is the predominant internal RNA modification in eukaryotic messenger RNAs (mRNAs) and plays a crucial role in mRNA stability. In this study, we reveal that m6A sites in the coding sequence (CDS) trigger CDS–m6A decay (CMD), a novel mRNA decay pathway that is distinct from previously reported m6A-dependent degradation mechanisms. Importantly, CDS m6A sites act considerably faster and more efficiently than those in the 3' untranslated region, which to date have been considered the main effectors of m6A-mediated RNA decay. Mechanistically, CMD depends on translation whereby m6A deposition in the CDS induces ribosome pausing and transcript destabilization. We found that the target transcripts of CMD are recognized by the m6A reader protein YTHDF2, selectively enriched in processing bodies (P-bodies) and degraded via the decapping factor DCP2. Our findings highlight CMD as a previously unknown pathway for m6A-mediated decay, which is particularly important for controlling the expression of developmental regulators and retrogenes.

2024-11-20 | GSE248574 | 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

m6A in mRNA coding regions promotes translation via the RNA helicase-containing YTHDC2

Project description:Dynamic mRNA modification in the form of N6-methyladenosine (m6A) adds considerable richness and sophistication to gene regulation. The m6A mark is asymmetrically distributed along mature mRNAs, with a strong preference around the stop codon and 3’UTR. Nevertheless, approximately 35% of m6A residues are located within the coding region (CDS). It has been suggested that methylation in CDS slows down translation elongation by interfering the decoding process. However, neither the decoding feature of endogenous mRNAs nor the physiological significance of CDS m6A has been clearly defined. By integrating Ribo-seq and m6A-seq data sets, we found that CDS m6A methylation leads to ribosome pausing in a codon-specific manner. Unexpectedly, removing CDS m6A modification from these transcripts results in a further decrease of translation. A systemic analysis of RNA structural datasets revealed that CDS m6A methylation positively regulates translation by resolving mRNA secondary structures. We further demonstrate that the elongation-promoting effect of CDS methylation requires the RNA helicase-containing m6A reader YTHDC2. Our findings established the physiological significance of CDS methylation and uncovered non-overlapping function of m6A reader proteins.

2019-07-01 | GSE129194 | GEO

m6A-seq map of wild type P6497 and methyltransferase knockout mutant of Phytophthora sojae

Project description:N6-methyladenosine (m6A) modification, as an important post-transcriptional regulator, is the most prevalent RNA modification in eukaryotes. However, the biological role of m6A in oomycetes remains unclear. Here, we characterized three m6A methyltransferases PsMETTL3A, PsMETTL3B, and PsMETTL16 that mainly affected the m6A levels in the CDS and 3’UTR in Phytophthora sojae. They play an important role in production of sporangia and oospores, mycelial growth, and virulence. PsMETTL3A/3B/16-mediated m6A positively regulated mRNA stability and translation efficiency of genes involved in chromatin remodeling and epigenetic regulation. Interestingly, PsMETTL3A, PsMETTL3B, or PsMETTL16 function in “independent” and “overlap” synergetic pattern. PsMETTL16 could interact with PsMETTL3A and PsMETTL3B to mediate m6A on some of the transcripts. Moreover, PsMETTL3A and PsMETTL3B positively regulated the expression of PsMETTL16 in an m6A-dependent manner. More importantly, m6A-modified PsBdf1 regulate chromatin accessibility to maintain DNA damage repair and tolerate host ROS stress in a PsMETTL3A/3B/16-dependent manner. Overall, these results indicate that m6A-mediated RNA metabolism are associated with development and pathogenicity of P. sojae, highlighting epigenetic variation as a mechanism of plant pathogenic oomycetes adaptive plasticity.

2023-12-23 | GSE221689 | GEO

Roles of Mettl14 in mouse limb bud development

Project description:m6A regulates virtually every step in RNA metabolism. However, its toles in limb development remains largely unknown. To understand the roles, we created a limb bud-specific conditional knockout (cKO) mice and control heterozygous (cHet) mice of the Mettl14 gene, which encodes an essential subunit in the m6A methyltransferase complex METTL3/METTL14. We harvested limb buds from the mice on E12.5 and applied the proteins to quantitative mass spectrometry to understand how the depletion of Mettl14 affected the proteomes.

2025-04-03 | PXD049092 | Pride

Genome-wide maps of m6a state in RA FLSs with or without ALKBH5 knockdown.

Project description:To investigate how ALKBH5 modulates RA FLSs functions, we conducted m6A sequencing (MeRIP-seq) of RA FLSs. Consistent with previous studies, in both scramble controls and ALKBH5 knockdown cells, m6A modifications were highly enriched within the GGAC motif. m6A peaks are located mainly in the protein-coding region (CDS) and 3’ untranslated region (3’ UTR) of mRNA transcripts

2023-12-31 | GSE203269 | GEO

m6A epitranscriptomic changes in response to hypoxic condition or ALKBH5 knock-down in U87

Project description:Compared with the normoxia control, 174 m6A peaks from 58 m6A-modified transcripts are significantly increased while 2032 m6A peaks from 556 m6A-modified transcripts are significantly decreased in hypoxia. Among the downregulated m6A peaks in hypoxia compared with normoxia condition, ALKBH5 depletion leads to 847 increased m6A peaks in 276 transcripts (fold change≥1.5).

2024-03-31 | GSE171497 | GEO

RBM15B Regulates progression of MLL-rearranged leukemia

Project description:We identified RBM15B that promotes progression of MLL-r leukemia. In this study, we preformed the m6A RIP-seq, RNA-seq and RBM15B CUT& Tag sequensing to found that RBM15B selectively regulated m6A modified region in the 5′ UTR and in part of the CDS around the start codon (two wings around start codon (TWINS)) of mRNA transcribed from target genes of MLL-fusion proteins, which is guided by histone modification H3K79me2.

2025-12-05 | GSE237261 | GEO

m6A sites in the coding region trigger translation-dependent mRNA decay (ribosome profiling)

2024-11-20 | GSE248572 | GEO

m6A sites in the coding region trigger translation-dependent mRNA decay (RNA-seq)

2024-11-20 | GSE248571 | GEO