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The N6-methyladenosine RNA landscape in aged mouse hippocampus [RNA-seq]

ABSTRACT: The N6-methyladenosine RNA landscape in aged mouse hippocampus [RNA-seq]

PROVIDER: PRJNA901176 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR22270340_1.fastq.gz	Fastqsanger.gz
	SRR22270340_2.fastq.gz	Fastqsanger.gz
	SRR22270341_1.fastq.gz	Fastqsanger.gz
	SRR22270341_2.fastq.gz	Fastqsanger.gz
	SRR22270342_1.fastq.gz	Fastqsanger.gz

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The N6-methyladenosine RNA landscape in aged mouse hippocampus

Project description:The N6-methyladenosine RNA landscape in aged mouse hippocampus

| PRJNA901173 | ENA

The N6-methyladenosine RNA landscape in aged mouse hippocampus [meRIP-seq]

Project description:The N6-methyladenosine RNA landscape in aged mouse hippocampus [meRIP-seq]

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The N6-methyladenosine RNA landscape in aged mouse hippocampus [RNA-seq]

Project description:Aged brain is associated with an inevitable decline in cognitive functions and increased vulnerability to neurodegenerative disorders. Multiple molecular hallmarks have been associated with the aging nervous system through transcriptomics and proteomic studies. Recently, the field of epitranscriptomics highlights the role of RNA chemical modification in various biological processes. In particular, N6-methyladenosine (m6A), the most abundant internal modification in eukaryotic mRNAs, has been functionally linked to multiple aspects of RNA processing. Importantly, the functional roles of m6A in neurophysiology, such as in the process of learning and memory, have led to our current investigation of how m6A-transcriptomic landscape is shaped during aging. Using the inbred C57Bl/6 line, we compared the m6A-transcriptomic profiles from the hippocampi of young (3-month-old) and aged (20-month-old) mice. The methylated RNA immunoprecipitation (MeRIP)-sequencing analysis revealed hyper- and hypo-methylation in 426 and 102 genes, respectively, in the aged hippocampus (fold-change >1.5, FDR<0.05). By correlating the methylation changes to their steady state transcript levels in the RNA-seq, we found a significant concordance between m6A and transcript levels in either direction.

2022-11-28 | GSE217883 | GEO

The N6-methyladenosine RNA landscape in aged mouse hippocampus [meRIP-seq]

2022-11-28 | GSE217882 | GEO

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

2015-06-09 | E-GEOD-63591 | biostudies-arrayexpress

Widespread N6-methyladenosine-dependent RNA Structural Switches Regulate RNA-Protein Interactions

Project description:We show that N6-methyladenosine (m6A), the most abundant internal modification in mRNA/lncRNA with still poorly characterized function, alters RNA structure to facilitate the access of RBM for heterogeneous nuclear ribonucleoprotein C (hnRNP C). We term this mechanism m6A-switch. Through combining PAR-CLIP with Me-RIP, we identify 39,060 m6A-switches among hnRNP C binding sites transcriptome-wide. We show that m6A-methyltransferases METTL3 or METTL14 knockdown decreases hnRNP C binding at 16,582 m6A-switches. Taken together, 2,798 m6A-switches of high confidence are identified to mediate RNA-hnRNP C interactions and affect diverse biological processes including cell cycle regulation. These findings reveal the biological importance of m6A and provide insights into the sophisticated regulation of RNA-RBP interactions through m6A-induced RNA structural remodeling. Measure the m6A methylated hnRNP C binding sites transcriptome-wide by PARCLIP-MeRIP; measure the differential hnRNP C occupancies upon METTL3/METTL14 knockdown by PAR-CLIP; measure RNA abundance and splicing level changes upon HNRNPC, METTL3 and METTL14 knockdown

2015-02-27 | E-GEOD-56010 | biostudies-arrayexpress

N6-Methyladenosine Modification Controls Circular RNA Immunity.

Project description:N6-Methyladenosine Modification Controls Circular RNA Immunity.

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Arabidopsis Messenger RNA N6-methyladenosine Demethylation Regulates Plant Development

Project description:N6-methyladenosine (m6A) is the most abundant internal modification in the messenger RNA (mRNA) of all higher eukaryotes. This modification has been shown to be reversible in mammals; it is installed by a methyltransferase heterodimer complex of METTL3 and METTL14 bound with WTAP, and reversed by iron(II)- and Î±-ketoglutarate-dependent demethylases FTO and ALKBH5. This modification exhibits significant functional roles in various biological processes. The m6A modification as a RNA mark is recognized by reader proteins, such as YTH domain family proteins and HNRNPA2B1; m6A can also act as a structure switch to affect RNA-protein interactions for biological regulation. In Arabidopsis thaliana, the methyltransferase subunit MTA (the plant orthologue of human METTL3, encoded by At4g10760) was well characterized and FIP37 (the plant orthologue of human WTAP) was first identified as the interacting partner of MTA. Here we report the discovery and characterization of reversible m6A methylation mediated by AtALKBH10B (encoded by At4g02940) in A. thaliana, and noticeable roles of this RNA demethylase in affecting plant development and floral transition. Our findings reveal potential broad functions of reversible mRNA methylation in plants. m6A peaks were identified from wild type Columbia-0 and atalkbh10b-1 mutant in two biological replicates

2016-03-24 | E-GEOD-79523 | biostudies-arrayexpress

N6-methyladenosine RNA methylome analyses in human prostate cell lines.

Project description:To identify N6-methyladenosine RNA methylome in human prostate cell lines, MeRIP-seq of RWPE-1 and LNCaP were performed.

2021-08-11 | GSE147885 | GEO

N6-methyladenosine-Mediated Nuclear Export of Messenger RNA

Project description:N6-methyladenosine-Mediated Nuclear Export of Messenger RNA

| PRJNA300279 | ENA