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M6A full transcriptome map of human adenocarcinoma of esophagogastric junction

ABSTRACT: m6A full transcriptome map of human adenocarcinoma of esophagogastric junction

PROVIDER: PRJNA784934 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR17074165_1.fastq.gz	Fastqsanger.gz
	SRR17074165_2.fastq.gz	Fastqsanger.gz
	SRR17074166_1.fastq.gz	Fastqsanger.gz
	SRR17074166_2.fastq.gz	Fastqsanger.gz
	SRR17074167_1.fastq.gz	Fastqsanger.gz

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m6A full transcriptome map of human adenocarcinoma of esophagogastric junction

Project description:Here we systematically analyze the modification pattern of m6A mRNA in adenocarcinoma at the esophagogastric junction.In adenocarcinoma of esophagogastric junction samples, a total of 4775 new m6A peaks appeared, and 3054 peaks disappeared. The unique m6A-related genes in adenocarcinoma of esophagogastric junction are related to cancer-related pathways. There are hypermethylated or hypomethylated m6A peaks in AEG in differentially expressed mRNA transcripts. This study preliminarily constructed the first m6A full transcriptome map of human adenocarcinoma of esophagogastric junction. This has a guiding role in revealing the mechanism of m6A-mediated gene expression regulation.

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Exclusion of m6A from splice-site-proximal regions by the exon-junction complex dictates m6A topologies and mRNA stability

Project description:N6-methyladenosine (m6A), a widespread destabilizing mark on mRNA, is non-uniformly distributed across the transcriptome, yet the basis for its selective deposition is unknown. Here, we uncover that m6A deposition is not selective. Instead, m6A distribution is exclusion-based: m6A-consensus harboring sites are methylated by default, unless they are within a window of up to ~200 nt from an exon-intron junction. A simple model which we extensively validate, relying exclusively on presence of m6A motifs and exon-intron architecture allows high accuracy recapitulation of experimentally-measured m6A profiles and of the vast majority of m6A hallmarks. Finally, we provide strong evidence that this exclusion is mediated by the exon-junction complex. Our findings establish a mechanism by which the memory of nuclear RNA splicing is covalently etched on an mRNA in the form of m6A, and determines its cytoplasmic stability, with broad implications on the regulation, function, and evolution of the exon-junction complex and m6A.

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Project description:We present here a photo-crosslinking-assisted m6A sequencing strategy to more accurately define sites with m6A modifications. Using this strategy, we obtained a high-resolution map of m6A in a human transcriptome. The map resembles the general distribution pattern observed previously, and reveals new m6A sites at base resolution. Our results provide insights into the relationship between the methylation regions and the binding sites of RNA-binding proteins.

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Project description:N6-methyladenosine (m6A) is the most abundant post-transcriptional methylation of mature mRNA and plays a crucial regulatory role in various biological functions, involving development and cancer progression. m6A is deposited by methyltransferase complex composed of METTL3 and METTL14 cotranscriptionally, and removed by demethylase FTO or ALKBH5. m6A is highly enriched within the 3’ UTRs and in the vicinity of the stop codon of mature mRNA. However, the mechanism that causes this distribution pattern is still enigmatic. Here, we show that EJC packages mRNAs to shape mRNA m6A landscape. We first tested the possibility that demethylase removes m6A during spicing and found that ALKBH5 depletion had a minor effect on m6A levels. Thus, we ruled out the demethylation model. We then hypothesized that splicing factors inhibit the methylation process of internal exons, but not the 3’ UTR. Knockdown of EIF4A3, a core component of the exon junction complex, significantly increased m6A levels in mature mRNAs. The hypermethylated sites are enriched in short internal exons. Furthermore, EIF4A3 depletion upregulates METTL3 binding affinity to mRNA to deposit m6As. In conclusion, Our results demonstrate that EIF4A3 blocks METTL3 binding and methylating internal short exons of mRNA. These findings shed light on the fact that RNA packaging formed during splicing acts as a regulator that shapes mRNA modifications.

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