Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Epitranscriptome profiling of m6A in colon cancer cell lines

ABSTRACT: N6-methyl adenosine (m6A) is one of the most important RNA modifications involved in several biological and pathological processes, including cancer. Dysregulation of m6A has been linked with tumor initiation, progression, and metastasis of several cancer types, including colon cancer. A transcriptome of colon cancer describes the dysregulated coding and non-coding RNAs but does not reveal the mechanisms like m6A modifications that determine the post-transcriptional and pre-translational regulations. Epi-transcriptome profiling of m6A in colon cancer cell lines was performed using Methylated RNA Immunoprecipitation (MeRIP) sequencing. Overall, the study illustrates the distribution of m6A across the transcriptome of various colon cancer cell lines.

ORGANISM(S): Homo sapiens

PROVIDER: GSE240438 | GEO | 2023/12/30

REPOSITORIES: GEO

ACCESS DATA

Json Xml

Similar Datasets

Impact of gut microbiota on the m6A epitranscriptome in mouse cecum and liver tissues

Project description:The intestinal microbiota modulates host physiology and gene expression via mechanisms that are not fully understood. A recently discovered layer of gene expression regulation is N6-methyladenosine (m6A) and N6,2′ -O-dimethyladenosine (m6Am) modifications of mRNA. To unveil if these epitranscriptomic marks are affected by the gut microbiota, we performed methylated RNA-immunoprecipitation and sequencing (MeRIP-seq) to examine m6A-modifications in transcripts of mice displaying either a conventional, or a modified, or no gut microbiota and discovered that the microbiota has a strong influence on m6A- modifications in the cecum, and also, albeit to a lesser extent, in the liver, affecting pathways related to metabolism, inflammatory and antimicrobial responses . We furthermore analysed expression levels of several known writer and eraser enzymes and found the methyltransferase Mettl16 to be downregulated in absence of a microbiota. As a consequence, one of its targets, the S-adenosyl methionine synthase Mat2a was less expressed in mice without gut flora. We furthermore show that distinct commensal bacteria, Akkermansia muciniphila, Lactobacillus plantarum can affect specific m6A modifications. Together, we report here epitranscriptomic modifications as an additional level of interaction in the complex interplay between commensal bacteria and their host.

2020-02-17 | PXD016099 | Pride

Mouse retina m6A epitranscriptome

Project description:m6A epitranscriptome of postnatal day 6 mouse retina was sequenced using MeRIP-seq.

2022-12-03 | GSE180814 | GEO

Refined RIP-seq protocol for epitranscriptome analysis with low input materials

Project description:We optimized the key parameters of m6A MeRIP-seq, including the starting amount of RNA, RNA fragmentation, antibody selection, MeRIP washing/elution conditions, methods for RNA library construction and the bioinformatics analysis pipeline. With the optimized immunoprecipitation conditions and a post-amplification rRNA depletion strategy, we were able to profile the m6A epitranscriptome using 2 µg of total RNA. We identified ~12,000 m6A peaks with a high signal/noise ratio from two lung adenocarcinoma (ADC) patient tumors. Through integrative analysis of the transcriptome, m6A epitranscriptome and proteome data in the same patient tumors, we identified dynamics at the m6A level that accounts for the discordance between mRNA and protein levels in these tumors.

2018-09-06 | GSE116002 | GEO

m6A level and isoform characterization sequencing (m6A-LAIC-seq) reveal the census and complexity of the m6A epitranscriptome

Project description:N6-methyladenosine (m6A) is a widespread reversible chemical modification of RNAs, implicated in many aspects of RNA metabolism. Little quantitative information exists as to either how many transcript copies of particular genes are m6A modified (âm6A levelsâ), or the relationship of m6A modification(s) to alternative RNA isoforms. To deconvolute the m6A epitranscriptome, we developed m6A level and isoform-characterization sequencing (m6A-LAIC-seq). We found that cells exhibit a broad range of non-stoichiometric m6A levels with cell type specificity. At the level of isoform characterization, we discovered widespread differences in use of tandem alternative polyadenylation (APA) sites by methylated and nonmethylated transcript isoforms of individual genes. Strikingly, there is a strong bias for methylated transcripts to be coupled with proximal APA sites, resulting in shortened 3â untranslated regions (3â-UTRs), while nonmethylated transcript isoforms tend to use distal APA sites. m6A-LAIC-seq yields a new perspective on transcriptome complexity and links APA usage to m6A modifications. m6A-LAIC-seq of H1-ESC and GM12878 cell lines, each cell line has two replicates

2016-06-24 | E-GEOD-66086 | biostudies-arrayexpress

Transcriptome m6A sequencing (MeRIP-seq)of human colon cancer samples

Project description:We analyze Aberrant Global M6A Abundance in colon Cancer by MeRIP-seq

2021-06-29 | GSE179042 | GEO

neonatal and adult mouse retina m6A epitranscriptome [meRIP-seq]

Project description:m6A epitranscriptome of newborn and adult mouse retina was sequenced using MeRIP-seq

2022-12-02 | GSE188607 | GEO

GPX8 deficiency-induced oxidative stress reprogrammed m6A epitranscriptome of oral cancer cells

Project description:Glutathione peroxidase 8 (GPX8) is a key regulator of redox homeostasis. Whether its antioxidant activity participates in the regulation of m6A modification is a crucial issue, which has important application value in cancer treatment. MeRIP-seq was used to explore the characteristics of transcriptome-wide m6A modification in GPX8-deficient oral cancer cells in this study. Oxidative stress caused by lack of GPX8 resulted in 1,279 hyper- and 2,287 hypo-methylated m6A peaks and 2,036 differentially expressed genes in GPX8-KO cells. Twenty-eight differentially expressed genes were related to the cell response to oxidative stress, and half of them changed their m6A modification. In GPX8-KO cells, m6A regulators IGF2BP2 and IGF2BP3 were upregulated, while FTO, RBM15, VIRMA, ZC3H13 and YTHDC2 were downregulated. After H2O2 treatment, the expression changes of RBM15, IGF2BP2 and IGF2BP3 were further enhanced. These data indicated that GPX8-mediated redox homeostasis regulated m6A modification, thereby affecting the expression and function of downstream genes. This study highlights the possible significance of GPX8 and the corresponding m6A regulatory or regulated genes as novel targets for antioxidant intervention in cancer therapy

2023-08-10 | GSE224718 | GEO

Transcriptome-wide m6A methylome of endometrioid ovarian cancer and ovarian endometriosis

Project description:Emerging studies have revealed that N6-methyladenosine modification is involved in the development of various cancers. However, the m6A modification pattern of endometrioid ovarian cancer (EOC) has not been demonstrated. In the present study, high-throughput sequencing combined with methylated RNA immunoprecipitation (MeRIP-seq) and RNA sequencing were used to obtain the transcriptome-wide m6A modifications of endometrioid ovarian cancer for the first time.

2022-02-18 | GSE196748 | GEO

Transcriptome m6A sequencing (MeRIP-seq)of human colon cancer samples

Project description:Transcriptome m6A sequencing (MeRIP-seq)of human colon cancer samples

| PRJNA742008 | ENA

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

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