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

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

PROVIDER: PRJNA901175 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR22270346_1.fastq.gz	Fastqsanger.gz
	SRR22270346_2.fastq.gz	Fastqsanger.gz
	SRR22270347_1.fastq.gz	Fastqsanger.gz
	SRR22270347_2.fastq.gz	Fastqsanger.gz
	SRR22270348_1.fastq.gz	Fastqsanger.gz

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The N6-methyladenosine RNA landscape in aged mouse hippocampus [meRIP-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 | GSE217882 | GEO

The N6-methyladenosine RNA landscape in aged mouse hippocampus

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

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

2022-11-28 | GSE217883 | GEO

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

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

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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

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

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N6-methyladenosine RNA methylome analyses in cyclophosphamide-treated neonatal rat cardiac myocytes.

Project description:To identify N6-methyladenosine RNA methylome in cyclophosphamide-treated neonatal rat cardiac myocytes (NRCMs), MeRIP-seq of NRCMs treated with cyclophosphamide (CYP) or solvent control (DMSO) were performed.

2021-09-23 | GSE184294 | GEO

Genome-wide identification of N6-methyladenosine by microarray

Project description:Although internal PolyA RNA modification N6-methyladenosine (m6A) plays essential roles in diverse biological processes, technology to detect precise m6A sites at transcriptome-wide scale is lacking. Here, we discovered that m6A interferes A (Adenine) – U (Uracil) or A-T (Thymidine) pairing. Based on differential hybridization between methylated vs. unmethylated RNAs to a DNA probe, we developed tiling microarray to pinpoint m6A sites in mouse transcriptome. We validated some of the identified sites and provided evidence to suggest that one functional mechanism of m6A is to block small RNA targeting to methylated mRNA. We designed a custom tiling array with to examine the precise location of m6A within meRIP-seq peaks from mouse embryonic stem cells determined in our previous publication (Wang et al., 2014). Each custom two-channel Agilent tiling array harbors 947,952 probes. Each probe is 25 nucleotides (nt), and any two adjacent probes in the genomic coordinate overlap each other by 19 nt. The Cy5 or red channel corresponds to Mettl14 knockout (M14) or DZA mutant mESC cell line, and Cy3 or green channel is associated with wild type cell line treated with scramble hairpin (SCR). Thus, in principle a higher Cy5/Cy3 signal for each probe reflects an increased hybridization to the oligonucleotide due to de-methylation of a particular RNA molecule in M14 or DZA condition relative to the SCR control. Moreover, we employed additional arrays with both channels dedicated for M14 as an external control for technical difference between the Cy5 and Cy3 dye (details below). For each comparison, we have three biological replicates, and therefore there are 9 tiling arrays in total (i.e., 3 arrays for M14 vs SCR, 3 arrays for DZA vs SCR, and 3 arrays for M14 vs M14).

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METTL14 is a chromatin regulator independent of RNA N6-methyladenosine (m6A MeRIP-Seq)

Project description:METTL14 is a chromatin regulator independent of RNA N6-methyladenosine (m6A MeRIP-Seq)

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N6-methyladenosine regulates RNA metabolism and neurodegeneration in C9ORF72-ALS/FTD [seq_total_RNA-MeRIP]

Project description:N6-methyladenosine regulates RNA metabolism and neurodegeneration in C9ORF72-ALS/FTD [seq_total_RNA-MeRIP]

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