M6A-CLIP identified major presence of m6A in last exons
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA290463 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR2120850.fastq.gz | Fastqsanger.gz | |||
| SRR2120860.fastq.gz | Fastqsanger.gz | |||
| SRR2120870.fastq.gz | Fastqsanger.gz | |||
| SRR2120880.fastq.gz | Fastqsanger.gz | |||
| SRR2120890.fastq.gz | Fastqsanger.gz |
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Project description:By adapting UV cross-linking immune precipitation for m6A (m6A-CLIP), we developed several novel genomic approaches with single-nucleotide resolution to accurately locate tens of thousands of m6A residues in human cells and mouse brain mRNAs. We found over 70% of these residues in the last exon with a very sharp rise (six-fold) within 150-400 nucleotides of the last exon, which overlaps the beginning of many 3′ untranslated region (UTRs). The 3′ UTRs contain ~two-thirds of the last exon m6A and 40 to 45% of the total of this base modification in mRNA. Contrary to earlier studies, we found no preference for location of m6A sites in the coding sequences around STOP codons. Many mRNA 3′ UTRs contain multiple polyA sites at least some of which are subject to regulated choices when cells change growth rate or differentiation state. The m6A density is at a peak early in the 3′ UTR and gradually diminishes in the more distal region of the last exon suggesting a possible inhibitory role of the proximal m6A residues to allow polyA choice of more distal polyA sites. This possibility was supported by finding that a main switch from distal to proximal polyA site choice is associated with m6A loss after triple knockdown of the m6A methylase complex. There is a significant overlap of m6A with identified binding sites for Ago complexes that carry microRNAs known to regulate mRNA stability which might possibly represent cooperation in function. With higher accuracy of m6A identification it is now more realistic to engage in highly localized mutagenesis to more definitively identify m6A function.
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Project description:m6A and YTHDF1, YTHDF2, YTHDF3 mapping of IAV RNA with PAR-CLIP and pA-m6A-seq
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Project description:The N6-methyladenosine (m6A) is the most abundant internal modification in almost all eukaryotic messenger RNAs, and is dynamically regulated. Therefore, identification of m6A readers is especially important in determining the cellular function of m6A. YTHDF2 has recently been characterized as the first m6A reader that regulates the cytoplasmic stability of methylated RNA. Here we show that YTHDC1 is a nuclear m6A reader and report the crystal structure of the YTH domain of YTHDC1 bound to m6A-containing RNA. We further determined the structure of another YTH domain, YTHDF1, and found that the YTH domain utilizes a conserved aromatic cage to specifically recognize the methyl group of m6A. Our structural characterizations of the YTHDC1-m6A RNA complex also shed light on the molecular basis for the preferential binding of the GG(m6A)C sequence by YTHDC1 and confirm the YTH domain as a specific m6A RNA reader. PAR-CLIP (Photoactivatable-Ribonucleoside-Enhanced Crosslinking and Immunoprecipitation) was applied to human YTHDC1 protein to identify its binding sites.
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Project description:N6-methyladenosine (m6A) is the most prevalent internal modification present in the mRNA of all higher eukaryotes. Here we present that m6A is selectively recognized by human YTH domain family (YTHDF2) protein to regulate mRNA degradation. By using crosslinking and immunoprecipitation, we have identified over 4000 substrate RNA of YTHDF2 with conserved core motif of G(m6A)C. We further estabilshed the role of YTHDF2 in RNA metabolism by a combination of ribosome profiling, RNA sequencing, m6A level quantification and cell-based imaging: the C-terminal domain of YTHDF2 selectively binds to m6A of mRNA and the N-terminal domain is responsive for localizing mRNA from translatable pool to processing body where mRNA decay occurs. PAR-CLIP and RIP was used to identify YTHDF2 binding sites followed by ribosome profling and RNA seq to assess the consequences of YTHDF2 siRNA knock-down
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Project description:Since m6A demethylases (FTO and ALKBH5) have been reported to be involved in pre-mRNA splicing regulation, we hypothesized that dynamic m6A distribution during mRNA maturation might involve removal of m6A in internal exons by FTO or ALKBH5 accompanied by splicing factors. To explore this we performed pull-down assays coupled with protein mass spectrometry.
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Project description:Alternative 3’-terminal exons, which use intronic polyadenylation sites, are generally unconserved and lowly expressed, while the main gene products end in the last exon of genes. In this study, we discover a class of human genes, where the last exon appeared recently during evolution, and the major gene product uses an alternative 3’-terminal exon corresponding to the ancestral last exon of the gene. This novel class of alternative 3’-terminal exons are down-regulated on a large scale by doxorubicin, a cytostatic drug targeting topoisomerase II, and play a role in cell cycle regulation, including centromere-kinetochore assembly. The RNA-binding protein, HuR/ELAVL1 is a major regulator of this specific set of alternative 3’-terminal exons. HuR binding to the alternative 3’-terminal exon in the pre-messenger RNA promotes its splicing, and is reduced by topoisomerase inhibitors. These findings provide new insights into the evolution, function and molecular regulation of alternative 3’-terminal exons.
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