N6-Methyladenosine mediates alternative intron/exon inclusion in the nascent transcriptome
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ABSTRACT:
PROVIDER: PRJNA647274 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR12266500_1.fastq.gz | Fastqsanger.gz | |||
| SRR12266500_2.fastq.gz | Fastqsanger.gz | |||
| SRR12266501_1.fastq.gz | Fastqsanger.gz | |||
| SRR12266501_2.fastq.gz | Fastqsanger.gz | |||
| SRR12266502_1.fastq.gz | Fastqsanger.gz |
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Similar Datasets
Project description:N6-Methyladenosine mediates alternative intron/exon inclusion in the nascent transcriptome [4sU-seq]
| PRJNA647276 | ENA
Project description:N6-methyladenosines (m6A) are stoichiometrically deposited on exons of nearly one third of RNA Pol II transcriptome, mainly catalysed by METTL3/14 complex. However, neither the intronic methylation pattern and its functional relevance nor the immediate response upon m6A loss have been fully understood. Here we applied MeRIP-seq on mESC nascent transcriptome and thus revealed that approximately 6-10% of m6A peaks occurred at intronic regions, preferentially the conserved and alternative exon/intron part of longer introns, proximately to 5’-splice sites. These intronic m6A deposition correlates with both Rbm15 binding and H3K36me3. Moreover, coupled 4sU-seq with METTL3 dTAG system in mESC, we found that m6A mediates alternative exon/intron inclusive in nascent transcriptome. Intriguingly, m6A self-regulation including writers and readers are early response and partially contributed by alternative splicing changes. Collectively, our study presents a unified model that m6A mediates alternative splicing, and dTAG METTL3 opens an avenue to interrogate the direct response of functional m6A disruption.
2020-09-15 | GSE154705 | GEO
Project description:This SuperSeries is composed of the SubSeries listed below.
2020-09-15 | GSE154709 | GEO
Project description:RNA N 6-methyladenosine (m6A) modification plays important roles in multiple aspects of RNA regulation. m6A is installed cotranscriptionally by the METTL3/14 complex, but its direct roles in RNA processing remain unclear. Here, we investigate the presence of m6A in nascent RNA of mouse embryonic stem cells. We find that around 10% of m6A peaks are located in alternative introns/exons, often close to 5' splice sites. m6A peaks significantly overlap with RBM15 RNA binding sites and the histone modification H3K36me3. Acute depletion of METTL3 disrupts inclusion of alternative introns/exons in the nascent transcriptome, particularly at 5' splice sites that are proximal to m6A peaks. For terminal or variable-length exons, m6A peaks are generally located on or immediately downstream from a 5' splice site that is suppressed in the presence of m6A and upstream of a 5' splice site that is promoted in the presence of m6A. Genes with the most immediate effects on splicing include several components of the m6A pathway, suggesting an autoregulatory function. Collectively, our findings demonstrate crosstalk between the m6A machinery and the regulation of RNA splicing.
| S-EPMC8327914 | biostudies-literature
Project description:METTL14 is a chromatin regulator independent of RNA N6-methyladenosine (nascent tRNA)
| PRJNA760512 | ENA
Project description:Spliceosome recognition of pre-mRNA junctions requires binding of splicing factors to the 3' splice site. Most splicing occurs co-transcriptionally, but how splicing factors bind expressed gene is not understood. We show that the SF3B1, U2AF1, and U2AF2 splicing factors bind active promoters of both intron-containing and intronless genes. RNase A treatment reduces binding at promoters, implicating general interactions with nascent transcripts in promoter localization. Strikingly, U2AF2 also accumulates on the bodies of some genes and is not eliminated by RNase treatment. Neither RNA polymerase II nor the active gene body chromatin mark H3K36me3 is required to maintain U2AF2 on chromatin. We found that most exons in U2AF2-bound have phased nucleosomes at their exon-intron boundaries. However, some exons are poorly phased, and these require U2AF2 for inclusion in mature mRNA. We propose that nucleosome phasing and U2AF2 binding ensure exon inclusion.
2025-04-10 | GSE270327 | GEO
Project description:N6-methyladenosine (m6A) is the most abundant internal messenger (mRNA) modification in mammalian mRNA. This modification is reversible and non-stoichiometric, which potentially adds an additional layer of variety and dynamic control of mRNA metabolism. The m6A-modified mRNA can be selectively recognized by the YTH family “reader” proteins. The preferential binding of m6A-containing mRNA by YTHDF2 is known to reduce the stability of the target transcripts; however, the exact effects of m6A on translation has yet to be elucidated. Here we show that another m6A reader protein, YTHDF1, promotes ribosome loading of its target transcripts. YTHDF1 forms a complex with translation initiation factors to elevate the translation efficiency of its bound mRNA. In a unified mechanism of translation control through m6A, the YTHDF2-mediated decay controls the lifetime of target transcripts; whereas, the YTHDF1-based translation promotion increases the translation efficiency to ensure effective protein production from relatively short-lived transcripts that are marked by m6A. PAR-CLIP and RIP was used to identify YTHDF1 binding sites followed by ribosome profling and RNA seq to assess the consequences of YTHDF1 siRNA knock-down
2015-06-09 | E-GEOD-63591 | biostudies-arrayexpress
Project description:N6-methyladenosine (m6A) residues occur at internal positions in most cellular and viral RNAs; both heterogeneous nuclear RNA and mRNA are involved. This modification arises by enzymatic transfer of a methyl group from S-adenosylmethionine to the central adenosine residue in the canonical sequence G/AAC. Thus far, m6A has been mapped to specific locations in eucaryotic mRNA and viral genomic RNA. We have now examined an intron-specific sequence of a modified bovine prolactin precursor RNA for the presence of this methylated nucleotide by using both transfected-cell systems and a cell-free system capable of methylating mRNA transcripts in vitro. The results indicate the final intron-specific sequence (intron D) of a prolactin RNA molecule does indeed possess m6A residues. When mapped to specific T1 oligonucleotides, the predominant site of methylation was found to be within the consensus sequence AGm6ACU. The level of m6A at this site is nonstoichiometric; approximately 24% of the molecules are modified in vivo. Methylation was detected at markedly reduced levels at other consensus sites within the intron but not in T1 oligonucleotides which do not contain either AAC or GAC consensus sequences. In an attempt to correlate mRNA methylation with processing, stably transfected CHO cells expressing augmented levels of bovine prolactin were treated with neplanocin A, an inhibitor of methylation. Under these conditions, the relative steady-state levels of the intron-containing nuclear precursor increased four to six times that found in control cells.
| S-EPMC361031 | biostudies-other
Project description:Targeted paired-end sequencing of cDNA from unfragmented nascent RNA from exponentially growing S. cerevisiae cells was employed to obtain Pol II transcription elongation and splicing information from single transcripts. Nascent RNA was prepared from the yeast chromatin fraction (Carrillo Oesterreich, Preibisch, Neugebauer, Mol Cell 2010) or enriched from total RNA with polyadenylated RNA depletion. The nascent 3â end was labeled with a 3â DNA adaptor through ligation. A PCR with a forward primer in the first exon of select intron-containing genes amplifies nascent transcripts of specific genes and ensures sequencing adaptor attachment for paired-end sequencing. With this approach co-transcriptional splicing progression with distance from the intron end could be analyzed for 87 genes. Note that the unmapped and mapped data also include genes that did not pass the read coverage requirements in SMIT analysis. Nascent RNA profiles for mainly intron-containing genes were generated with paired-end sequencing with Illumina HiSeq technology.
2016-03-24 | E-GEOD-70907 | biostudies-arrayexpress
Project description:The Exon Junction Complex (EJC) has roles in mRNA export and cytoplasmic quality control. Yet EJC is recruited to pre-mRNA by the spliceosome, prior to the second catalytic step of splicing. Because splicing often occurs co-transcriptionally, EJC can be deposited on nascent RNA almost immediately after introns are synthesized and excised, raising the question of whether EJC regulates downstream RNA processing decisions. Here, we show that degron-mediated depletion of EJC component EIF4A3 leads to substantial skipping of neighboring pairs of two or more exons. These exon skipping events occurred on the same molecule of mRNA, detected by long read sequencing, suggesting that “exon blocks” require EJC for inclusion. Introns flanking EJC-dependent exon blocks were longer and spliced after internal introns. Thus, block exons form a larger EJC-marked exon prior to surrounding splicing events. These findings identify a previously unknown nuclear function of EJC that coordinates co-transcriptional inclusion of exon blocks.
2025-10-14 | GSE291593 | GEO