The m6A Methylated mRNA Pattern and the Activation of the Wnt Signaling Pathway under Hyper-m6A modifying condition in the keloid [RIP-seq]
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ABSTRACT:
PROVIDER: PRJNA837549 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR19178185_1.fastq.gz | Fastqsanger.gz | |||
| SRR19178185_2.fastq.gz | Fastqsanger.gz | |||
| SRR19178186_1.fastq.gz | Fastqsanger.gz | |||
| SRR19178186_2.fastq.gz | Fastqsanger.gz | |||
| SRR19178187_1.fastq.gz | Fastqsanger.gz |
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Project description:Purpose: The present study was carried out to investigate the global m6A modified RNA pattern and possible mechanisms underlying the pathogenesis of keloid. Method: 14 normal skin and 14 keloid tissue were firstly collected on clinic. Then 3 samples from each group were randomly selected to be verified with the Western Blot to determine the level of methyltransferase and demethylase. The total RNA of all samples in each group was isolated and subjected to the analysis of MeRIP-sequencing and RNA-sequencing. With the software of MeTDiff and htseq-count, the m6A peaks and differentially expressed genes (DEGs) were determined within the fold change > 2 and p -value < 0.05. The top 10 pathways of m6A modified genes in each group and the differentially-expressed genes were enriched by the Kyoto Encyclopedia of Genes and Genomes signaling pathways. Finally, the closely associated pathway was determined with the Western Blot and immunofluorescence staining. Results: There was a higher protein level of WTAP and Mettl3 in the keloid than in the normal tissue. 21,020 unique m6A peaks with 6573 unique m6A-associated genetic transcripts appeared in the keloid samples. In the normal tissue, 4028 unique m6A peaks with 779-associated modified genes appeared in the keloid. In the RNA-sequencing, there were 847 genes significantly changed between these groups, transcriptionally. The genes with m6A methylated modification and the upregulated differentially expressed genes between two tissues were both mainly related to the Wnt signaling pathway. Moreover, the hyper-m6A modified Wnt / β-catenin pathway in keloid was verified with western blotting. From immunofluorescence staining results, we found that the accumulated fibroblasts were under a hyper-m6A condition in the keloid and the Wnt/β-catenin signaling pathway was mainly activated in the fibroblasts. Conclusion: The fibroblasts in the keloid were under a cellular hyper-m6A methylated condition, and the hyper-m6A modified highly-expressed Wnt / β-catenin pathway in the dermal fibroblasts might promote the pathogenesis of keloid.
2022-05-17 | GSE202855 | GEO
Project description:Purpose: The present study was carried out to investigate the global m6A modified RNA pattern and possible mechanisms underlying the pathogenesis of keloid. Method: 14 normal skin and 14 keloid tissue were firstly collected on clinic. Then 3 samples from each group were randomly selected to be verified with the Western Blot to determine the level of methyltransferase and demethylase. The total RNA of all samples in each group was isolated and subjected to the analysis of MeRIP-sequencing and RNA-sequencing. With the software of MeTDiff and htseq-count, the m6A peaks and differentially expressed genes (DEGs) were determined within the fold change > 2 and p -value < 0.05. The top 10 pathways of m6A modified genes in each group and the differentially-expressed genes were enriched by the Kyoto Encyclopedia of Genes and Genomes signaling pathways. Finally, the closely associated pathway was determined with the Western Blot and immunofluorescence staining. Results: There was a higher protein level of WTAP and Mettl3 in the keloid than in the normal tissue. 21,020 unique m6A peaks with 6573 unique m6A-associated genetic transcripts appeared in the keloid samples. In the normal tissue, 4028 unique m6A peaks with 779-associated modified genes appeared in the keloid. In the RNA-sequencing, there were 847 genes significantly changed between these groups, transcriptionally. The genes with m6A methylated modification and the upregulated differentially expressed genes between two tissues were both mainly related to the Wnt signaling pathway. Moreover, the hyper-m6A modified Wnt / β-catenin pathway in keloid was verified with western blotting. From immunofluorescence staining results, we found that the accumulated fibroblasts were under a hyper-m6A condition in the keloid and the Wnt/β-catenin signaling pathway was mainly activated in the fibroblasts. Conclusion: The fibroblasts in the keloid were under a cellular hyper-m6A methylated condition, and the hyper-m6A modified highly-expressed Wnt / β-catenin pathway in the dermal fibroblasts might promote the pathogenesis of keloid.
2022-05-17 | GSE202851 | GEO
Project description:The m6A Methylated mRNA Pattern and the Activation of the Wnt Signaling Pathway under Hyper-m6A modifying condition in the keloid
| PRJNA837555 | ENA
Project description:The m6A Methylated mRNA Pattern and the Activation of the Wnt Signaling Pathway under Hyper-m6A modifying condition in the keloid [RNA-seq]
| PRJNA837537 | ENA
Project description:This SuperSeries is composed of the SubSeries listed below.
2022-05-17 | GSE202861 | GEO
Project description:m6A RNA immunoprecipitation experiments were conducted to identify RNAs that are directly m6A-methylated by the METTL3 methylatransferase specifically in response to UV.
2017-03-21 | GSE92867 | GEO
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
Project description:Interest in mRNA methylation has exploded in recent years. The sudden interest in a 40 year old discovery was due in part to the recent finding of FTO?s (Fat Mass Obesity) N6-methyl-adenosine (m6A) deaminase activity, thus suggested a link between obesity-associated diseases and the presence of m6A in mRNA. Another catalyst of the sudden rise in mRNA methylation research was the release of mRNA methylomes for human, mouse and Saccharomyces cerevisiae. However, the molecular function, or functions of this mRNA ?epimark? remain to be discovered. There is supportive evidence that m6A could be a mark for mRNA degradation due to its binding to YTH domain proteins, and consequently being chaperoned to P bodies. Nonetheless, only a subpopulation of the methylome was found binding to YTHDF2 in HeLa cells. The model organism Saccharomyces cerevisiae, has only one YTH domain protein (Pho92, Mrb1), which targets PHO4 transcripts for degradation under phosphate starvation. However, mRNA methylation is only found under meiosis inducing conditions, and PHO4 transcripts are apparently non-methylated. In this paper we set out to investigate if m6A could function alternatively to being a degradation mark in S. cerevisiae, we also sought to test whether it can be induced under non-standard sporulation conditions. We find associations between the presence of m6A and message translatability. We also find m6A induction following prolonged rapamycin treatment. GeneChip analyses were performed to investigate the distribution of early meiotic transcripts (3hours) on different polysome and monosome fractions
2015-08-12 | E-GEOD-68435 | biostudies-arrayexpress
Project description:Purpose: To systematically analyze the overall m6A modification pattern in hyperplastic scars (HS). Methods: The m6A modification patterns in HS and normal skin (NS) tissues were described by m6A sequencing and RNA sequencing, and subsequently bioinformatics analysis was performed. The m6A-related RNA was immunoprecipitated and verified by real-time quantitative PCR. Results: The appearance of 14,791 new m6A peaks in the HS sample was accompanied by the disappearance of 7,835 peaks. The unique m6A-related genes in HS were thus associated with fibrosis-related pathways. We identified the differentially expressed mRNA transcripts in HS samples with hyper-methylated or hypo-methylated m6A peaks. Conclusion: This study is the first to map the m6A transcriptome of human HS, which may help clarify the possible mechanism of m6A-mediated gene expression regulation.
2022-01-24 | GSE194121 | GEO
Project description:This research aims at assessing the m6A methylome in the RA peripheral blood mononuclear cells (PBMCs) and perform potential drug targets prediction analysis. Five RA samples and ten control samples were obtained from China-Japan Friendship Hospital. The various expression of m6A methylation and genes in RA and control group were compared with methylated RNA immunoprecipitation sequencing (MeRIP-seq) and RNA sequencing (RNA-seq). Bioinformatics explorations were also made to explore the enriched biological roles and paths of the differentially expressed m6A methylation and genes. Potential drug targets prediction and validation were also constructed to provide potential therapeutic targets for RA. In total, 583 dysregulated m6A peaks, of which 295 were greatly upregulated and 288 were greatly downregulated, were identified. Similarly, 1570 differentially genes were acquired by RNA-seq, including 539 upregulated and 1031 downregulated. According to deeper joint exploration, the m6A methylation and mRNA expression degrees of 35 genes varied greatly, of which including 13 hyper-methylated as well as upregulated genes (hyper-up), 12 hyper-methylated and downregulated genes (hyper-down), 5 hypo-methylated as well as upregulated genes (hypo-up), and 5 hypo-methylated and downregulated genes (hypo-down) GO and KEGG explorations showed the enrichment of these distinct genes in “protein transport” “protein binding” and “lysosome”. In addition, the mRNA levels of TUBB2A, IGF2BP3, DYNC1I1 and FOSL1 were increased and consistent with the trend of our sequencing results. While after the treatment of TP and MTX, their mRNA levels were decreased. This research set up the transcriptional map of m6A in RA PBMCs and displayed the hidden association between RNA methylation alternation and associated genes in RA. The outcomes highlight the importance of m6A modification as a gene regulatory system in RA. Furthermore, TUBB2A, IGF2BP3, DYNC1I1 and FOSL1 might be potential therapeutic targets of TP and MTX during RA treatment.
2022-03-23 | GSE193193 | GEO