Analysis of m6A methylome in ABRO1 Knockout heart
Ontology highlight
ABSTRACT:
ORGANISM(S): Mus musculus
PROVIDER: GSE188518 | GEO | 2023/12/01
REPOSITORIES: GEO
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Project description:Dynamic mRNA modification in the form of N6-methyladenosine (m6A) adds considerable richness and sophistication to gene regulation. The m6A mark is asymmetrically distributed along mature mRNAs, with a strong preference around the stop codon and 3’UTR. Nevertheless, approximately 35% of m6A residues are located within the coding region (CDS). It has been suggested that methylation in CDS slows down translation elongation by interfering the decoding process. However, neither the decoding feature of endogenous mRNAs nor the physiological significance of CDS m6A has been clearly defined. By integrating Ribo-seq and m6A-seq data sets, we found that CDS m6A methylation leads to ribosome pausing in a codon-specific manner. Unexpectedly, removing CDS m6A modification from these transcripts results in a further decrease of translation. A systemic analysis of RNA structural datasets revealed that CDS m6A methylation positively regulates translation by resolving mRNA secondary structures. We further demonstrate that the elongation-promoting effect of CDS methylation requires the RNA helicase-containing m6A reader YTHDC2. Our findings established the physiological significance of CDS methylation and uncovered non-overlapping function of m6A reader proteins.
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Project description:To elucidate the molecular mechanism by which cardiac-hypertrophy-associated piRNA (CHAPIR) regulates m6A modification, we performed m6A methylated RNA immunoprecipitation sequencing (MeRIP-seq) in control or CHAPIR-overexpressing mice heart. The sequential analysis of m6A peaks showed that RGACH motif was highly enriched within m6A sites in heart and that is aligning with the classical consensus sequence of mammals ‘RGACH’, where ‘R’ indicates purine (A/G) and ‘H’ indicates non-guanine base (A/C/U). In CHAPIR treated heart, m6A mostly occurred in mRNAs (89.5%) and only about 10.5% were identified in non-coding RNAs. The majority of mRNAs contain one or two m6A peaks (89.2%) and 10.8% mRNA contain >2 m6A peaks . M6A peaks were predominantly distributed in coding sequences (CDSs), 3’ untranslated regions (3’UTRs) and near stop codon.
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Project description:Here, the m6A modification patterns in chicken liver at the acute stage of LPS-stimulated inflammation and at the normal state were explored via m6A and RNA sequencing and bioinformatics analysis. A total of 7815 m6A peaks distributed in 5066 genes were identified in the normal chicken liver, and were mostly located in the CDS, 3’UTR region and around the stop codon. At 2 h after the LPS intraperitoneal injection, the m6A modification pattern changed, and showed 1200 different m6A peaks. The hyper- and hypo-m6A peaks were differentially located, with the former mostly located in the CDS region and the later in the 3’UTR and in the region near the stop codon. The hyper- or hypo methylated genes were enriched in different GO ontrology and pathways. Co-analysis revealed a significantly positive relationship between the fold change of m6A methylation level and the relative fold change of mRNA expression. Moreover, protein and protein interaction analysis showed that genes with altered m6A methylation and mRNA expression levels were clustered in processes involved in lipid metabolism, immune response, DNA replication and protein ubiquitination. CD18 and SREBP-1 were the two hub genes clustered in the immune process and lipid metabolism, respectively. Hub gene AGPAT2 was suggested to link the immune response and lipid metabolism clusters in the PPI network. This study presented the first m6A map of broiler chicken liver at the acute stage of LPS induced inflammation. The findings may shed lights on the possible mechanisms of m6A-mediated lipid metabolism disorder in inflammation.
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Project description:N6-methyladenosine (m6A), the most prevalent internal messenger RNA modification, plays critical roles in diverse biological processes. To characterize the potential involvement of METTL3 in macrophage function, we mapped m6A methylomes of METTL3-deficent and WT macrophages by m6A sequencing (m6A-seq) and RNA-seq, with independent biological replicates. Notably, among the m6A peaks with remarkable changes upon METTL3-depletion, the vast majority exhibited a significant (p < 0.05) decrease in m6A abundance.The most common m6A motif GGAC is significantly enriched in the m6A peaks in both WT and METTL3-deficent cells. A similar pattern of total and common m6A distribution in control and METTL3-deficient cells was observed, when the m6A peaks were especially abundant in the vicinity of CDS and 3’UTR regions.
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Project description:Background: Hepatic ischemia reperfusion injury (IRI) is a complex clinical complication during surgery and often leads to cell damage and dysfunction. N6-Methyladenosine (m6A) is an emerging epigenetic modification that plays key roles in the regulation of biological functions and cellular mechanisms in IR injury in different organs. However, the understanding of m6A-modified mRNAs in hepatic IRI is limited. Methods: Methylated RNA immunoprecipitation with high-throughput sequencing (MeRIP-seq) and RNA sequencing (RNA-seq) were used to profile the transcriptome-wide distribution of m6A methylation for hepatic IRI in mice. Results: In this study, there were 2061 nonoverlapping m6A peaks within 22471 coding gene transcripts (mRNAs) in the sham group and 2669 nonoverlapping m6A peaks within 22766 coding gene transcripts in the hepatic IR group. The distribution of m6A peaks was especially enriched in the coding sequence (CDS) and 3'UTR. Moreover, functional enrichment analysis demonstrated that the significantly enriched terms of genes with upmethylated m6A sites were the mRNA surveillance pathway, purine metabolism and metabolic pathways, and the significantly enriched terms of genes with downmethylated m6A sites were the Rap1 signaling pathway, sphingolipid signaling pathway, platelet activation, Wnt signaling pathway, chemokine signaling pathway and focal adhesion. Furthermore, we identified a relationship between differentially methylated genes and differentially expressed genes to obtain the three overlapping predicted target genes (Fnip2, Phldb2, and Pcf11). Conclusions: Our study first identified a transcriptome-wide map of m6A mRNAs in hepatic IRI. An in-depth analysis according to methylation modifications will provide effective treatment strategies and a theoretical basis for future research in terms of molecular mechanisms.
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Project description:The yak estrus is a seasonal phenomenon, probably involving the epigenetic regulation of the synthesis and secretion of sex hormones as well as the growth and development of follicles. In this study, we collected the yak ovarian tissues at the three different states of anestrus, estrus, and pregnancy, and obtained the full transcriptome m6A map in yak by MeRIP-seq. The RT-qPCR showed that the expression of METTL3, METTL14, FTO, YTHDC1 were significantly different across different periods in the ovaries. Next, we identified 20174, 19747 and 13523 m6A peaks in the three ovarian samples of YO-A, YO-F and YO-P using the methylated RNA immunoprecipitation sequencing (MeRIP-seq). The m6A peaks are highly enriched in the coding sequence (CDS) region and 3′untranslated region (3′UTR) as well as the conserved sequence of “RRACH.” Functional analysis revealed the involvement of m6A in many physiological activities of the yak’s ovary during estrus and pregnancy. The association analysis found that some genes such as BNC1, HOMER1, BMP15, BMP6, GPX3, and WNT11 were related to ovarian functions. The comparison of the distribution patterns of methylation peaks in the ovarian tissues across different periods further explored the m6A markers related to the regulation of ovarian ovulation and follicular development in the yak ovary. This comprehensive map provides a solid foundation for revealing the potential function of the mRNA m6A modification in the yak ovary.
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Project description:In this study, we aimed to systematically profile global RNA N6-methyladenosine (m6A) modification patterns in a mouse model of diabetic cardiomyopathy (DCM). Patterns of m6A in DCM and normal hearts were analyzed via m6A-specific methylated RNA immunoprecipitation followed by high-throughput sequencing (MeRIP-seq) and RNA sequencing (RNA-seq). A total of 973 m6A peaks were detected in DCM samples and 296 differentially methylated sites were selected for further study, including 106 hypermethylated and 190 hypomethylated m6A sites (fold change (FC) > 2, p < 0.05). Gene ontology and KEGG Pathway analyses indicated that unique m6A-modified transcripts in DCM were closely linked to cardiac fibrosis, myocardial hypertrophy, and myocardial energy metabolism. Overall, m6A modification patterns were altered in DCM, and modification of epitranscriptomic processes, such as m6A, is a potentially interesting therapeutic approach.
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Project description:A growing number of studies have demonstrated that N6 methyladenine (m6A) acts as an important role in the pathogenesis of reproductive diseases, which makes it essential to profile the genome-wide m6A modifications in embryo damage. In this study, due to the microscopicity of early villous tissue, we performed high-throughput sequencing for villous tissues from three patients with embryo damage and three patients with painless abortion. Based on meRIP-seq data, we identified 18,568 m6A peaks from these two samples. These m6A peaks were mainly located in the coding region near the stop codon and were mainly characterized by AUGGAC and UGGACG motif. Compared with the normal group, the embryo damage group had 2,159 significantly upregulated m6A peaks and 281 downregulated m6A peaks. Genes with altered m6A peaks were mainly involved in Hippo and Wnt signaling pathways. Based on RNA-seq data, we found that differentially expressed genes were mainly involved in Th17 cell differentiation, TNF signaling pathway, and ECM-receptor interaction. Based on the conjoint analysis of meRIP-seq and RNA-seq data, we identified 36 genes with differentially methylated m6A peaks and synchronously differential expression. These genes were mainly involved in the Wnt signaling pathway, phosphatase activity regulation, protein phosphatase inhibitor activity, and transcription inhibitor activity. In general, our study revealed the transcriptome-wide m6A methylome in early embryonic development, which may provide novel insights into the pathogenesis and treatment of embryo damage.
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