RNA m5C Methylation in breast cancer using MeRIP-Seq
Ontology highlight
ABSTRACT:
ORGANISM(S): Homo sapiens
PROVIDER: GSE53370 | GEO | 2014/02/20
SECONDARY ACCESSION(S): PRJNA231850
REPOSITORIES: GEO
Similar Datasets
Project description:RNA m5C methylation profile of MCF10A and MDA486 by using MeRIP-Seq protocol Immunoprecipitation of Methylated mRNA at Cytosine (m5C) residues: Affinity purified of anti-methyl cytosine (m5C) polyclonal antibody 7ug (Zymo Research, Catalog#A3001-50) was conjugated with protein-A magnetic beads for 2 h at 4°C in end to end rotator. After that, conjugated beads were extensively washed with RNA immunoprecipitation (RIP) wash buffer to remove unbound antibody. Fragmented 25 ug polyA RNA (mRNA) was incubated with m5C conjugated beads for overnight at 4°C in in the rotating platform in RIP buffer. RIP was done using Megna RNA Immunoprecipitation kit (Millipore, Catalog#17-700). m5C mRNA-immune bead complex was treated with proteinase K buffer to release m5C mRNA from the conjugated antibody. To isolate m5C, mRNA was treated with phenol:chloroform:isoamyl and mixed with 400 ul of chloroform, which was centrifuged at 14000 rpm for 10 minutes to separate aqueous phase. The aqueous phase was ethanol precipitated at -80°C for overnight, to get m5C mRNA. This precipitated m5C mRNA pellet was washed twice with 70% ethanol and air dried. Finally, m5C mRNA pellet was dissolved in nuclease free Water. The m5C mRNA integrity and conentration was quantified by bioanalyzer (Agilent) and Qubit 2.0 flurometer (Invitrogen). The fragmented mRNA was used by following TruSeq RNA Sample Preparation Guide to develop RNA-Seq library for sequencing.
2014-02-20 | E-GEOD-53370 | biostudies-arrayexpress
Project description:RNA m5C methylation profile of MCF10A and MDA486 by using MeRIP-Seq protocol Immunoprecipitation of Methylated mRNA at Cytosine (m5C) residues: Affinity purified of anti-methyl cytosine (m5C) polyclonal antibody 7ug (Zymo Research, Catalog#A3001-50) was conjugated with protein-A magnetic beads for 2 h at 4°C in end to end rotator. After that, conjugated beads were extensively washed with RNA immunoprecipitation (RIP) wash buffer to remove unbound antibody. Fragmented 25 ug polyA RNA (mRNA) was incubated with m5C conjugated beads for overnight at 4°C in in the rotating platform in RIP buffer. RIP was done using Megna RNA Immunoprecipitation kit (Millipore, Catalog#17-700). m5C mRNA-immune bead complex was treated with proteinase K buffer to release m5C mRNA from the conjugated antibody. To isolate m5C, mRNA was treated with phenol:chloroform:isoamyl and mixed with 400 ul of chloroform, which was centrifuged at 14000 rpm for 10 minutes to separate aqueous phase. The aqueous phase was ethanol precipitated at -80°C for overnight, to get m5C mRNA. This precipitated m5C mRNA pellet was washed twice with 70% ethanol and air dried. Finally, m5C mRNA pellet was dissolved in nuclease free Water. The m5C mRNA integrity and conentration was quantified by bioanalyzer (Agilent) and Qubit 2.0 flurometer (Invitrogen). The fragmented mRNA was used by following TruSeq RNA Sample Preparation Guide to develop RNA-Seq library for sequencing.
| S-ECPF-GEOD-53370 | biostudies-other
Project description:We discovered the YBX1 in the lipid-induced particles assembled by DDX49, YBX1 is an m5C reader and constitutively associates with Timp2 mRNA in hepatocytes, we examined whether their association was dependent on the m5C modification of Timp2 mRNA, then we performed m5C-MeRIP-seq.
2025-06-20 | GSE299800 | GEO
Project description:TET2 regulates histone H2AK119ub and leukemogenesis through LTR RNA m5C oxidation [seq_RNA-caRNA-m5C-MeRIP]
| PRJNA1007666 | ENA
Project description:Protocol for detecting m5C RNA modification at single-base resolution using m5C-TAC-seq
| PRJNA1166655 | ENA
Project description:The epigenetic modifications play important regulatory roles in tissue development, maintenance of physiological functions and pathological process. RNA methylations, including newly identified m1A, m5C, m6A and m7G, are important epigenetic modifications. However, how these modifications are distributed in the transcriptome of vertebrate brains and whether their abundance is altered under pathological conditions are still poorly understood. In this study, we chose the model animal of zebrafish to conduct a systematic study to investigate the mRNA methylation atlas in the brain. By performing unbiased analyses of the m1A, m5C, m6A and m7G methylation of mRNA, we found that within the whole brain transcriptome, with the increase of the gene expression levels, the overall level of each of these four modifications on the related genes was also progressively increased. Further bioinformatics analysis indicated that the zebrafish brain has an abundance of m1A modifications. In the hypoxia-treated zebrafish brains, the proportion of m1A is decreased, affecting the RNA splicing and zebrafish endogenous retroviruses. Our study presents the first comprehensive atlas of m1A, m5C, m6A and m7G in the epitranscriptome of the zebrafish brain and reveals the distribution of these modifications in mRNA under hypoxic conditions. These data provide an invaluable resource for further research on the involvement of m1A, m5C, m6A and m7G in the regulation of miRNA and repeat elements in vertebrates, and provide new thoughts to study the brain hypoxic injury on the aspect of epitranscriptome.
2022-01-26 | GSE194284 | GEO
Project description:A microarray assay of circRNA m5C methylation modification in human lung cancer tissues compared the altered RNA m5C methylation modification in cancerous and paraneoplastic tissues of lung cancer patients.
2025-07-23 | GSE232282 | GEO
Project description:Chromatin-associated LTR RNA m5C oxidation by TET2 regulates chromatin state and leukemogenesis [seq_RNA-caRNA-m5C-MeRIP]
| PRJNA1131476 | ENA
Project description:Toxoplasma gondii is a globally prevalent zoonotic parasite that chronically infects nearly one-third of the human population. Among emerging layers of gene regulation, 5-methylcytosine (m5C) has been recognized as a key post-transcriptional modification that modulates mRNA stability and translation in eukaryotes. However, the epitranscriptomic landscape of m5C in the tachyzoite stage of T. gondii remains uncharacterized. This study presents the first comprehensive profiling of m5C methylation across three major T. gondii genotypes—RH (type I), ME49 (type II), and VEG (type III)—using methylated RNA immunoprecipitation sequencing (MeRIP-seq) combined with RNA-Seq. Differentially m5C-methylated genes (DMMGs) were functionally annotated via Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analyses. Integration of methylation and transcriptomic data revealed strain-specific correlations between m5C modification and gene expression. Candidate m5C regulatory factors were identified through BLASTP searches in the ToxoDB database and further examined for expression and methylation patterns. We identified 5,129, 4,968, and 4,577 m5C-methylated genes in RH, ME49, and VEG tachyzoites, respectively, with methylation predominantly enriched within coding sequences (CDS). Comparative analysis revealed 1,710, 1,131, and 784 DMMGs across RH vs. ME49, RH vs. VEG, and ME49 vs. VEG comparisons. Functional enrichment highlighted DMMGs involved in catalytic activity, transport, phospholipid metabolism and transcription regulation. KEGG pathway analysis identified nucleocytoplasmic transport, DNA replication, and ATP-dependent chromatin remodeling as key m5C-regulated processes. Additionally, several putative m5C regulators were identified, displaying genotype-specific or conserved expression and methylation patterns, suggesting their potential roles in strain-specific phenotypic variation and as targets for therapeutic intervention. This study presents the first m5C epitranscriptomic atlas of T. gondii tachyzoites, revealing both conserved and genotype-specific mRNA modification networks. These findings offer critical insights into the regulatory role of m5C in T. gondii pathogenesis and open new avenues for the development of vaccines and therapeutics against zoonotic toxoplasmosis.
2025-08-27 | GSE294543 | GEO