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High-throughput microarray reveals the epitranscriptome-wide landscape of m6A-circRNA in oral squamous cell carcinoma

ABSTRACT: We report an epitranscriptome-wide mapping of m6A-modified circRNAs (m6A-circRNA) in oral squamous cell carcinoma (OSCC). Utilizing the data of m6A-circRNAs epitranscriptomic microarray analysis, we found that m6A-circRNAs exhibited their particular modification style in OSCC. anti-m6A antibody Synaptic Systems, cat. No. 202003)

ORGANISM(S): Homo sapiens

PROVIDER: GSE198105 | GEO | 2022/07/19

REPOSITORIES: GEO

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High-throughput microarray reveals the epitranscriptome-wide landscape of m6A-circRNA in large for gestational age placental tissues.

Project description:We report an epitranscriptome-wide mapping of m6A-modified circRNAs (m6A-circRNA) in large for gestational age(LGA) placental tissues versus normal gestational age (NGA). Utilizing the data of m6A-circRNAs epitranscriptomic microarray analysis, we found that m6A-circRNAs exhibited their particular modification style in LGA.

2024-08-01 | GSE212958 | GEO

Expression of m6A methylation-modified circRNA in malignant transformation of oral leukoplakia tissue

Project description:Objective This study aimed to investigate the expression and clinical significance of N6-methyladenosine (m6A) modification of circular RNA (circRNA) in oral leukoplakia (OLK) and oral squamous carcinoma cell (OSCC) tissues. Methods Using methylation RNA immunoprecipitation high-throughput sequencing technology (MeRIP-seq) and RNA high-throughput sequencing technology (RNA-seq), the first circRNA transcriptome analysis for detecting m6A methylationome profiles in OLK and OSCC tissues was obtained, followed by bioinformatics analysis. The qRT-PCR technique and protein immunoblotting technique were used to detect the expression of m6A methylesterase in OLK versus OSCC tissues. Results In this study, 275 differential m6A methylation peaks were identified in OLK and OSCC, among which 193 peaks were up-regulated and 82 were down-regulated. Additionally, 198 differential m6A methylation modified circRNAs were observed, with 127 up-regulated and 71 down-regulated (FC ≥ 2, P < 0.05). Most of the identified circRNAs that underwent m6A methylation alterations were derived from overlapping regions. It was found that the differential expression of circRNAs was not correlated with the joint analysis of significantly different m6A-circRNAs between the two groups. Furthermore, downregulation of mETTL14 and FTO protein levels was observed in OSCC tissues, although there were no discernible alterations in RNA levels. Conclusion Our study suggests that m6A methylation modification of circRNA may play a role in the development of oral leukoplakia, and that METTL14 and FTO may be important methylation enzymes that influence the development of oral leukoplakia. These findings may open up new research directions for in-depth investigations to clarify the molecular mechanisms of OLK carcinogenesis.

2023-09-20 | GSE243097 | GEO

Mouse retina m6A epitranscriptome

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

2022-12-03 | GSE180814 | 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

Alteration of the N6-methyladenosine Epitranscriptome Profile in Synthetic Phthalate-treated Human Induced Pluripotent Stem Cell-Derived Endothelial Cells [array]

Project description:Background: This study aims to characterize the N6-methyladensosine epitranscriptomic profile induced by mono(2-ethylhexyl) phthalate (MEHP) exposure using a human-induced pluripotent stem cell-derived endothelial cell model. Methods: A multi-omic approach was employed by performing RNA sequencing in parallel with an m6A-specific microarray to identify mRNAs, lncRNAs, and miRNAs affected by MEHP exposure. Results: An integrative multi-omic analysis identified relevant biological features affected by MEHP, while functional assays provided a phenotypic characterization of these effects. Transcripts regulated by the epitranscriptome were validated with qPCR and Me-RIP. Conclusion: Our findings offer important information regarding the alterations occurring within the m6A epitranscriptome and the gene expression changes which occur in response to treatment with a synthetic phthalate in hiPSC-ECs and may be an important resource for future research.

2022-10-11 | GSE214419 | GEO

Alteration of the N6-methyladenosine Epitranscriptome Profile in Synthetic Phthalate-treated Human Induced Pluripotent Stem Cell-Derived Endothelial Cells [RNA-seq]

2022-10-11 | GSE212641 | 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

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

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

Signatures and Molecular Mechanisms of N6-Methyladenosine circRNAs in Human Rheumatoid Arthritis from Microarray Data

Project description:We used the m6A-circRNA epitranscriptomic microarray to measure the m6A methylated quantities and levels of circRNAs in the synovial tissues of human rheumatoid arthritis and osteoarthritis.

2023-02-28 | GSE226044 | GEO

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