Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

MRNA m6A regulates porcine intramuscular fat deposition via YTHDF1-dependent enhancement of MTCH2 translation

ABSTRACT: We performed m6A sequencing to compare N6 transcriptome methylation profiles of the longissimus dorsi muscles (LDMs) between Landrace pigs (a Danish pig breed) and Jinhua (a Chinese pig breed with higher levels of intramuscular fat). The results show m6A is widely spread and highly conserved in pig mRNA. m6A occurs in the conserved sequence motif of GGACU and exhibits a unique topology in pig.Transcriptome-wide m6A profiling revealed that about 20% of transcribed genes were modified by m6A, with the consensus sequence GGACU appearing highly in m6A-modified genes. Functional enrichment analysis showed that genes differentially methylated in LDMs of the two porcine breeds were related to gene regulation and muscle development and differentiation,suggesting that the m6A modification is tissue-specific and influences mRNA stability or translation.

ORGANISM(S): Sus scrofa

PROVIDER: GSE113237 | GEO | 2019/05/26

REPOSITORIES: GEO

ACCESS DATA

Json Xml

Similar Datasets

Comprehensive profiling of mRNA m6A methylome revealed by m6A-seq in porcine adipose and muscle tissues

Project description:Using Jinhua and Landrace pigs as fat and lean models, we present a comprehensive transcriptome-wide m6A profiling in adipose and muscle tissues from these two pig breeds.The results show m6A is widely spread and highly conserved in pig mRNA. m6A occurs in the conserved sequence motif of GGACU and exhibits a unique topology in pig. m6A peak enrichment correlates positively with gene expression, and transcripts with m6A at 5’UTR or CDS are correlated with gene activation than those at 3’UTR. Common m6A peaks in both layer of backfat from Landrace (L-LB) and Jinhua (J-LB) pigs are involved in lipid metabolism, while common m6A peaks in both longissimus dorsi muscle from Landrace (L-LDM) and Jinhua (J-LDM) mapped to muscle development, suggesting m6A-containing genes are involved in many biological processes especially related to tissue-specific functions.

2018-10-05 | GSE87625 | 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

Comparative analyses of sperm DNA methylomes among three commercial pig breeds reveal vital hypomethylated regions associated with spermatogenesis and embryonic development

Project description:This study is the first to report a genome-wide comparative DNA methylation map of adult pig sperm in three commercial pig breeds using WGBS technology. Our results showed that DNA methylation was more conserved in the three commercial pig breeds. Moreover, our results indicated that breed-specific HMRs are related to phenotypic changes and economically complex traits for each breed. The conserved HMRs between pig sperm and testis close to or located in the promoter regions of important genes are mainly involved in DNA repair and spermatogenesis.

2023-07-01 | GSE180099 | GEO

mRNA m6A regulates porcine intramuscular fat deposition via YTHDF1-dependent enhancement of MTCH2 translation

Project description:mRNA m6A regulates porcine intramuscular fat deposition via YTHDF1-dependent enhancement of MTCH2 translation

| PRJNA450530 | ENA

YTHDF1-regulated oncogenic translation program offers a therapeutic target for acute myeloid leukemia

Project description:N6-methyladenosine (m6A), the most abundant modification in mRNAs, has been defined as a crucial modulator in the progression of acute myeloid leukemia (AML), while the detailed mechanism remains elusive. Here we report that YTHDF1, an m6A reader protein, is overexpressed in human AML samples with enrichment in leukemia stem cells (LSCs). Whereas YTHDF1 is dispensable for normal hematopoiesis in mice, depletion of YTHDF1 attenuates self-renewal and proliferation of patient-derived LSCs, and impedes leukemia establishment in immunodeficient mice. Mechanistically, YTHDF1 promotes the translation of diverse m6A-modified oncogene mRNAs particularly cyclin E2. We applied a structure-based virtual screening of FDA-approved drugs and identified tegaserod as a potential YTHDF1 inhibitor. Tegaserod blocks the direct binding of YTHDF1 with m6A-modified mRNAs and inhibits YTHDF1-regulated mRNA translation. Moreover, tegaserod inhibits leukemogenesis in vitro and in mice, phenocopying the loss of YTHDF1. Together, our study defines YTHDF1 as an integral regulator of AML progression at the translational level and identifies tegaserod as a potential therapeutic agent for AML by targeting YTHDF1.

2021-09-28 | GSE184842 | GEO

Gene expression and m6A profiling for AGS cells with sh-NC or sh-YTHDF1 [RNA-seq and MeRIP-seq]

Project description:N6-methyladenosine (m6A) RNA methylation is implicated in the progression of multiple cancers via influencing mRNA modification. Intersection of RNA-seq, Methylated RNA immune-precipitation (MeRIP)-seq, co-immunoprecipitation, RNA pull-down and MeRIP-PCR were used to identify YTHDF1- modified USP14 and its m6A levels in GC cells. Intersection assays revealed that YTHDF1 promoted USP14 protein translation in an m6A-dependent manner. Our data suggested that m6A reader YTHDF1 facilitated tumorigenesis and metastasis of GC by promoting USP14 protein translation and might act as a clinical therapy for GC.

2021-04-07 | GSE166972 | GEO

N6-methyladenosine reader YTHDF1 promotes stemness and therapeutic resistance in hepatocellular carcinoma by enhancing NOTCH1 expression

Project description:N6-methyladenosine (m6A) RNA modification is the most common and conserved epigenetic modification in mRNA and has been shown to play important roles in cancer biology. As the m6A reader YTHDF1 has been reported to promote progression of hepatocellular carcinoma (HCC), it represents a potential therapeutic target. In this study, we evaluated the clinical significance of YTHDF1 using human HCC samples and found that YTHDF1 was significantly upregulated in HCCs with high stemness scores and was positively associated with recurrence and poor prognosis. Analysis of hepatoma spheroids revealed that YTHDF1 was highly expressed in liver cancer stem cells (CSCs). Stem cell-specific conditional Ythdf1 knock-in (CKI) mice treated with diethylnitrosamine showed elevated tumor burden compared with wild type mice. YTHDF1 promoted CSC renewal and resistance to the multiple tyrosine kinase inhibitors lenvatinib and sorafenib in patient-derived organoids and HCC cell lines, which could be abolished by catalytically inactive mutant YTHDF1. RNA immunoprecipitation sequencing, m6A methylated RNA immunoprecipitation sequencing, ribosome profiling, and RNA sequencing identified NOTCH1 as a direct downstream of YTHDF1. YTHDF1 bound to m6A modified NOTCH1 mRNA to enhance its stability and translation, which led to increased NOTCH1 target genes expression. NOTCH1 overexpression rescued HCC stemness in YTHDF1 deficient cells in vitro and in vivo. Lipid nanoparticles targeting YTHDF1 significantly enhanced the efficacy of lenvatinib and sorafenib in HCC in vivo. Taken together, YTHDF1 drives HCC stemness and drug resistance through a YTHDF1-m6A-NOTCH1 epitranscriptomic axis, and YTHDF1 is a potential therapeutic target for treating HCC.

2024-01-11 | GSE252752 | GEO

Widespread Occurrence of m6A in bacterial mRNA

Project description:N6-methyladenosine (m6A) is one of the most abundant modifications in eukaryotic RNA. Recent mapping of m6A methylomes in mammals, yeast, and plants as well as characterization of m6A methyltransferases, demethylases, and binding proteins have revealed regulatory functions of this dynamic RNA modification. In bacteria, although m6A is present in ribosomal RNA (rRNA), its occurrence in messenger RNA (mRNA) still remains elusive. Here, we used liquid chromatography-mass spectrometry (LC-MS) to calculate the m6A/A ratio in mRNA from a wide range of bacterial species, which demonstrates that m6A is an abundant mRNA modification in tested bacteria. Subsequent transcriptome-wide m6A profiling in Escherichia coli and Pseudomonas aeruginosa revealed a conserved distinct m6A pattern that is significantly different from that in eukaryotes. Most m6A peaks are located inside open reading frames (ORF), and carry a unique consensus motif (GCCAU). Functional enrichment analysis of bacterial m6A peaks indicates that the majority of m6A-modified transcripts are associated with respiration, amino acids metabolism, stress response, and small RNAs genes, suggesting potential regulatory roles of m6A in these pathways. m6A profiling in E.coli and P.aeruginosa mRNA

2015-07-08 | E-GEOD-65347 | biostudies-arrayexpress

Identification of YTHDF1 targeted m6A modified transcripts in lung cancer cells

Project description:Identification of YTHDF1 targeted m6A modified transcripts in lung cancer cells

| PRJNA562532 | ENA

mRNA-seq of neuronal compartments in shRNA-mediated knockdown of Ythdf1, -2 and -3 in mouse primary cortical neurons (mPCN)

Project description:To study the effect of m6A modifications on subcellular mRNA localization we depleted m6A readers Ythdf1, -2 and -3 with shRNAs from mouse primary cortical neurons (mPCN) and sequenced neuritic and somatic compartments in parallel with scrambled shRNA control.

2023-07-12 | E-MTAB-11569 | biostudies-arrayexpress

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data