Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

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

ABSTRACT: 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.

ORGANISM(S): Mus musculus

PROVIDER: GSE217883 | GEO | 2022/11/28

REPOSITORIES: GEO

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
		Other

Items per page:

1 - 1 of 1

Similar Datasets

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

Differential expression of microRNAs in adipose tissue with aging and caloric restriction

Project description:To further analyze the effect of aging and caloric restriction in the microRNA expression, we have employed microarray expression profiling as a discovery platform to identify differentially expressed microRNAs in middle-aged animals and the impact of caloric restriction in the microRNA expression profile. Subcutaneous and visceral adipose tissue were extracted from 3 groups of mice: 3 month-old, 12 month-old fed ad libitum and 12 month-old fed with a caloric restricted diet. Comparisons between young and middle-aged animals in subcutaneous and visceral adipose tissue, and between the 12 month old ad libitum and 12 month old caloric restricted diet in both adipose depots were made.

2022-11-30 | GSE217353 | GEO

Absolute Proteome Analysis of Hippocampus, Cortex and Cerebellum in Aged and Young Mice Reveals Changes in Energy Metabolism

Project description:Aging is associated with a general decline of cognitive functions, and it is widely accepted that this decline results from changes in expression of proteins involved in regulation of synaptic plasticity. However, several lines of evidence has accumulated that impaired function of aged brain may be related to significant alterations in the energy metabolism. In the current study, we employed the label-free „Total protein approach” (TPA) method to focus on similarities and differences in energy metabolism proteomes of young (1 month-old) and aged (22 month-old) murine brains. We quantified over 7,000 proteins in each of three analyzed brain structures: hippocampus, cerebral cortex and cerebellum. To the best of our knowledge, this is the most extensive quantitative proteomic description of energy metabolism pathways during physiological aging of mice. The analysis demonstrates that aging does not affect significantly the abundance of total proteins in the studied brain structures, however, the levels of proteins constituting energy metabolism pathways differ significantly between young and aged mice.

2022-02-17 | PXD025978 | Pride

Transcriptomic analysis of the follicle associated epithelium of Peyer's Patches, intestinal villous epithelium and ileum from young and aged mice

Project description:We have previously shown that aging affects the functional maturation of M cells in the follcile associated epithelium (FAE) of Peyer's patches in the small intestine. To further characterise how aging affects the FAE, mRNA-seq was performed on micro-dissected FAE and villous epithelial sheets as well as whole ileum from young (4 month old) and aged (26-28 month old) mice

2021-11-19 | GSE182252 | GEO

Proteomic characterizationof the circle of Willis during aging

Project description:The Circle of Willis (CoW), the ring of arteries at the base of the brain, links the intracerebral arteries to one another to maintain adequate cerebral perfusion. The CoW proteome is affected in cerebrovascular and neurodegenerative diseases, but changes related to aging have not been described. Here, we report on a quantitative proteomics analysis comparing the CoW from five young (two-three-month-old) and five aged (18–20-month-old) mice.

2024-06-26 | PXD043001 | Pride

Luminal cerebrovascular proteomic changes during aging

Project description:The blood-brain barrier (BBB) is highly specialized to protect the brain from harmful circulating factors in the blood and maintain brain homeostasis. However, during aging and neurodegenerative disease, the BBB undergoes numerous molecular changes that can promote inflammation and disease pathogenesis. In this work, we profile the luminal (blood-facing) surface of the cerebral vasculature using sulfo-NHS-biotin to tag and enrich proteins from acutely isolate microvessedls from young (3-month-old) and aged (21-month-old) mice.

2024-12-17 | PXD043964 | Pride

MicroRNA data in the hearts from young (8 week-old) and middle-aged (15 month-old) male mice

Project description:MicroRNAs have been reported to be involved in the regulation of cellular and organismal aging. However, little is known about the role of microRNAs in cardiac aging. We used microarrays to examine microRNA profiles in the hearts from young (8 week-old) and middle-aged (15 month-old) male mice.

2019-06-14 | GSE83329 | GEO

Aging Mouse Brain Mitochondria LC-MS/MS

Project description:This study investigates the proteomic alterations in brain mitochondria isolated from 5- (mature), 12- (old), and 24-month-old (aged) mice to examine normal "healthy" aging. Using quantitative mass-spectrometry based super-SILAC, our findings revealed global proteomic changes in brain mitochondria identifying several metabolic pathways including glycolysis, the tricarboxylic acid cycle, and oxidative phosphorylation. Overall, we found that the bioenergetic function of these mitochondria was preserved suggesting the proteomic alterations potentially allow for compensatory mechanisms to combat aging.

2015-01-27 | PXD001370 | Pride

MeRIPseq of Toxoplasma gondii

Project description:Toxoplasma gondii is an obligate intracellular parasite that can cause serious opportunistic disease in the immunocompromised or through congenital infection. To progress through its life cycle, Toxoplasma relies on multiple layers of gene regulation that includes an array of transcription and epigenetic factors. Over the last decade, the modification of mRNA has emerged as another important layer of gene regulation called epitranscriptomics. Here, we report that epitranscriptomics machinery exists in Toxoplasma, namely the methylation of adenosines (m6A) in mRNA transcripts. We identified novel components of the m6A methyltransferase complex and determined the distribution of m6A marks within the parasite transcriptome. m6A mapping revealed the modification to be preferentially located near transcription termination sites within the consensus sequence, YGCAUGCR. Knockdown of the m6A writer enzyme METTL3 resulted in diminished m6A marks, loss of a target transcript, and a complete arrest of parasite replication. Furthermore, we examined the two proteins in Toxoplasma that possess YTH domains, which bind m6A marks, finding them to be integral members of the cleavage and polyadenylation machinery that catalyzes the 3’-end processing of pre-mRNAs. Together, these findings establish that the m6A epitranscriptome is essential for parasite viability by contributing to the processing of mRNA 3’-ends.

2021-07-19 | GSE165067 | GEO

Restoring bone marrow niche function rejuvenates aged hematopoietic stem cells by reactivating the DNA Damage Response [4]

Project description:The bone marrow (BM) niche comprised of BM endothelial cells (BMECs) and LepR+ mesenchymal stromal cells (MSCs), plays a critical role in preserving the fitness of hematopoietic stem cells (HSCs). Aging is associated with defects in the BM niche that impair their ability to support HSC activity. However, mechanisms underlying age-related defects in the BM niche remain poorly understood. In this study, we identify BM niche derived Netrin-1 (NTN1) as a critical regulator of BM niche cell fitness during aging. Conditional deletion of NTN-1 specifically within BM MSCs or BMECs of young mice resulted in premature aging phenotypes within the BM niche including increased vascular leakiness, hypoxia, DNA damage and adiposity. On the other hand, supplementation of aged mice with NTN1 resulted in restoration of these hallmark niche defects and a rejuvenation of HSC activity. Mechanistically, we identify NTN1 as a critical regulator of DNA Damage Response (DDR) within BM niche cells and HSCs. In this experiment, RNA Seq analysis was performed on HSCs derived from young mice (3 month old), PBS treated aged mice (18 month old), and NTN1 treated aged mice (18 month old), to characterize transcriptional alterations within HSCs during aging, and following NTN1 treatment of aged mice.

2023-04-14 | GSE227146 | GEO

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data