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M6A-seq data analysis of control and PCIF1 knockdown transcriptome

ABSTRACT: m6A-seq data analysis of control and PCIF1 knockdown transcriptome

PROVIDER: PRJNA492247 | ENA |

REPOSITORIES: ENA

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Dataset's files

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			Action	DRS
	SRR7881530_1.fastq.gz	Fastqsanger.gz
	SRR7881530_2.fastq.gz	Fastqsanger.gz
	SRR7881531_1.fastq.gz	Fastqsanger.gz
	SRR7881531_2.fastq.gz	Fastqsanger.gz
	SRR7881532_1.fastq.gz	Fastqsanger.gz

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m6A-seq data analysis of control and PCIF1 knockdown transcriptome

Project description:Purpose: To identify the in vivo RNA targets of PCIF1, we performed meRIP experiments for PCIF1 KD and control cells using an anti-m6A antibody. We envisioned that the cap-specific PCIF1 should selectively alter the m6Am modification at the 5-terminal region of transcripts. Indeed, we observed a reduction of modification peaks at the 5’-end but not the 3’-UTR regions of mRNA upon PCIF1 KD.

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Project description:mRNAs are regulated by nucleotide modifications that influence their cellular fate. Two of the most abundant modified nucleotides are N6-methyladenosine (m6A), found within mRNAs, and N6,2′-O-dimethyladenosine (m6Am), which is found at the first transcribed nucleotide. Distinguishing these modifications in mapping studies has been difficult. Here, we identify and biochemically characterize PCIF1, the methyltransferase that generates m6Am. We find that PCIF1 binds and is dependent on the m7G cap. By depleting PCIF1, we generated transcriptome-wide maps that distinguish m6Am and m6A. We find that m6A and m6Am misannotations arise from mRNA isoforms with alternative transcription start sites (TSSs). These isoforms contain m6Am that maps to “internal” sites, increasing the likelihood of misannotation. We find that depleting PCIF1 does not substantially affect mRNA translation but is associated with reduced stability of a subset of m6Am-annotated mRNAs. The discovery of PCIF1 and our accurate mapping technique will facilitate future studies to characterize m6Am’s function.

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