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Quantitative and whole-transcriptome N6-Methyladenosine profiling at single-nucleotide resolution [shRNA RNA-seq]

ABSTRACT: Quantitative and whole-transcriptome N6-Methyladenosine profiling at single-nucleotide resolution [shRNA RNA-seq]

PROVIDER: PRJNA800444 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR17746984_1.fastq.gz	Fastqsanger.gz
	SRR17746984_2.fastq.gz	Fastqsanger.gz
	SRR17746985_1.fastq.gz	Fastqsanger.gz
	SRR17746985_2.fastq.gz	Fastqsanger.gz
	SRR17746986_1.fastq.gz	Fastqsanger.gz

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Quantitative and whole-transcriptome N6-Methyladenosine profiling at single-nucleotide resolution

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Quantitative and whole-transcriptome N6-Methyladenosine profiling at single-nucleotide resolution [polyA_RNA]

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Quantitative and whole-transcriptome N6-Methyladenosine profiling at single-nucleotide resolution [Ribo-minus_RNA]

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Single-nucleotide resolution mapping of m6A and m6Am throughout the transcriptome

Project description:N6-methyladenosine (m6A) is the most abundant modified base in eukaryotic mRNA and has been linked to diverse effects on mRNA fate and function. Current m6A mapping approaches rely on immunoprecipitation of m6A-containing RNA fragments to identify regions of transcripts that contain m6A. This approach localizes m6A residues to 100-200 nt-long regions of transcripts. The precise position of m6A in mRNAs cannot be identified on a transcriptome-wide level because there are no chemical methods to distinguish between m6A and adenosine. Here we show that anti-m6A antibodies can induce specific mutational signatures at m6A residues after ultraviolet light-induced antibody-RNA crosslinking and reverse transcription. Similarly, we find these antibodies induce mutational signatures at N6, 2’-O-dimethyladenosine (m6Am), a nucleotide found at the first encoded position of certain mRNAs. Using these mutational signatures, we map m6A and m6Am at single-nucleotide resolution in human and mouse mRNA and identify snoRNAs as a novel class of m6A-containing ncRNAs. UV-crosslinking and immunoprecipitation with m6A-specific antibodies was used to map m6A and m6Am in cellular RNA with single nucleotide resolution.

2015-06-29 | E-GEOD-63753 | biostudies-arrayexpress

Quantitative and whole-transcriptome N6-Methyladenosine profiling at single-nucleotide resolution [shRNA RNA-seq]

Project description:We introduce m6A Selective Allyl Chemical labeling and Sequencing (m6A-SAC-Seq), a novel method for transcriptome-wide quantitative mapping of m6A at single-nucleotide resolution. The m6A-SAC-Seq employs a dimethyltransferase to selectively label m6A followed by introducing mutations with reverse transcriptase during sequencing. We identified the widespread distributions of m6A and quantitated their fractions in the transcriptome of HeLa, HEK293, HepG2, and human CD34+ hematopoietic stem/progenitor cells (HSPCs).

2022-01-27 | GSE194410 | GEO

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Project description:Hypoxia as a crucial pathogenesis factor usually results in huge harmful effects on cardiac injury and dysfunction. In our previous study (PMID: 33294289), We observe a series of differential expressed genes between transcription and translation, which may be attributed to the hypoxia-specific binding affinity of Nuclear cap-binding subunit 3 (NCBP3) at 5’ un-translation region of target genes. But the underlying molecular mechanism of NCBP3 for gene translation modulation remains unclear. Here, we conducted RIP-seq of N6-Methyladenosine methylation in H9C2 cells with the conditions of normoxic, hypoxic and with additional NCBP3 knockdown.

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N6-methyladenosine Modulates Messenger RNA Translation Efficiency

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

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