Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Activity-Dependent Regulation of Alternative Cleavage and Polyadenylation (APA) During Hippocampal Long-Term Potentiation (LTP) [RNA-Seq]

ABSTRACT: This study was aimed at elucidating the mechanisms underlying activity-dependent gene regulation during long-term potentiation (LTP) of mouse hippocampal CA3-CA1 synapses. Transcriptome analysis allowed to identify changes in gene expression and alternative splicing induced 1 hour and 3 hours after LTP induction.

ORGANISM(S): Mus musculus

PROVIDER: GSE84503 | GEO | 2018/02/22

REPOSITORIES: GEO

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
		Other

Items per page:

1 - 1 of 1

Similar Datasets

Activity-Dependent Regulation of Alternative Cleavage and Polyadenylation (APA) during hippocampal Long-Term Potentiation (LTP) [3'READS]

Project description:This study was aimed at elucidating the mechanisms underlying activity-dependent gene regulation during LTP of mouse hippocampal CA3-CA1 synapses. Deep sequencing of the 3’ end of transcripts allowed to identify changes in APA induced 1 hour and 3 hours after LTP induction. We detected APA changes that only affected the 3'UTR (3'UTR-APA events) and APA changes that also affected the coding sequence (CDS-APA events).

2018-02-22 | GSE84643 | GEO

Activity-Dependent Regulation of Alternative Cleavage and Polyadenylation (APA) During Hippocampal Long-Term Potentiation (LTP)

Project description:Activity-Dependent Regulation of Alternative Cleavage and Polyadenylation (APA) During Hippocampal Long-Term Potentiation (LTP)

| PRJNA330721 | ENA

Activity-Dependent Regulation of Alternative Cleavage and Polyadenylation (APA) During Hippocampal Long-Term Potentiation (LTP)

Project description:This SuperSeries is composed of the SubSeries listed below.

2018-02-22 | GSE84644 | GEO

Mapping Gene Expression in Excitatory Neurons During Hippocampal Late-Phase Long-term Potentiation

Project description:The long-lasting changes in synaptic connectivity that underlie long-term memory require new RNA and protein synthesis for their persistence. To elucidate the temporal pattern of gene expression that gives rise to long-lasting, learning-related neuronal plasticity, we profiled RNAs in mouse hippocampal CA3-CA1 slices following induction of late phase long-term potentiation (LTP), analyzing differential expression (DE) specifically within pyramidal excitatory neurons by Translating Ribosome Affinity Purification RNA sequencing (TRAP-seq). We detected time-dependent changes in up- and down-regulated ribosome-associated mRNAs over the two hours following LTP induction, with minimal overlap of DE transcripts between time points. TRAP-seq revealed greater numbers and amplitudes of LTP-induced changes than RNA-seq of all cell types in the hippocampus. Transcripts that were DE by TRAP-seq but not RNA-seq were enriched in mRNAs encoding cytoskeletal and cell adhesion proteins, while RNA-seq identified DE in many non-neuronal mRNAs. Together our results highlight the importance of considering both the time course and the cell-type specificity of activity-dependent gene expression during memory formation.

2017-02-23 | GSE79790 | GEO

A marker chromosome in psychosis identifies glycine decarboxylase (GLDC) as a novel negative regulator of excitatory synaptic activity in the hippocampus

Project description:The biological significance of a small supernumerary marker chromosome generating a 9p24.1 duplication/triplication including a triplication of the GLDC gene encoding glycine decarboxylase in two patients with psychosis is unclear. Performing functional genomic fine-mapping using a series of copy number variant mouse models, we identify that additional copies of Gldc reduce extracellular glycine levels as determined by optical FRET in dentate gyrus (DG) but not in CA1, suppressed long-term potentiation (LTP) in mPP-DG synapses but not in CA3-CA1 synapses, reduced the activity of biochemical pathways implicated in schizophrenia and mitochondrial bioenergetics, and displayed prepulse inhibition, startle habituation, latent inhibition, working memory, sociability and social preference deficits. Our results thus provide a link between a genomic copy number variation, biochemical, cellular and behavioral phenotypes, demonstrating that GLDC negatively regulates excitatory neurotransmission, supporting the view that extra copies of GLDC in the genome may contribute significantly to the development of neuropsychiatric disorders.

2024-10-21 | GSE230871 | GEO

DNA-methylation of LTP-associated genes.

Project description:Long-term potentiation (LTP) of synaptic transmission is recognized as a cellular mechanism for learning and memory storage. Although de novo gene transcription is known to be required in the formation of stable LTP, the molecular mechanisms underlying synaptic plasticity remain elusive.This study investigates the DNA-methylation levels of promoters and CpG-islands of LTP-associated genes identified from Maag et al. 2015 (DOI: 10.3389/fnins.2015.00351) (See E-MTAB-3375).

2017-03-16 | E-MTAB-4919 | biostudies-arrayexpress

Branch point evolution controls species-specific alternative splicing and regulates long term potentiation

Project description:Regulation and functionality of species-specific alternative splicing has remained enigmatic for many years. Calcium/calmodulin-dependent protein kinase IIβ (CaMKIIβ) is expressed in several splice variants and plays a key role in learning and memory. Here, we identify and characterize several primate-specific CAMK2B splice isoforms, which show altered kinetic properties and changes in substrate specificity. Furthermore, we demonstrate that primate-specific Camk2β alternative splicing is achieved through branch point weakening during evolution. We show that reducing branch point and splice site strength during evolution globally renders constitutive exons alternative, thus providing a paradigm for cis-directed species-specific alternative splicing regulation. Using CRISPR/Cas9 we introduced the weaker human branch point into the mouse genome, resulting in human-like CAMK2B splicing in the brain of mutant mice. We observe a strong impairment of long-term potentiation in CA3-CA1 synapses of mutant mice, thus connecting branch point-controlled, species-specific alternative splicing with a fundamental function in learning and memory.

2022-12-19 | PXD035346 | Pride

mRNA sequencing analysis of transcripts from CA1 regions 90 minutes after Long-Term Potentiation was induced

Project description:Purpose: Study the differentially expressed genes in hippocampal rat CA1 regions 90 minutes after Long-Term Potentiation (LTP) was induced using field recordings Methods: hippocampal rat CA1 region mRNA profiles of control (unstimulated) and 90 minutes after LTPwas induced (LTP 90) were generated by deep sequencing. A pool of approximately 10 CA1 regions collected from at least 3 different animals were used. The seq library was prepared using TruSeq RNA Sample Prep Kit v2 protocol (Illumina, CA, USA). For the RNA-Seq data analysis Tophat 2.0.13, bowtie 2.1.0 , samtool 0.1.7 and cufflinks 1.3.0 were used. The rn5-bowtie2 index was generated with the command 'bowtie2-build rn5.fa rn5'. The 'rn5.fa'-file was downloaded from the UCSC genome browser. The mm10-bowtie2 index was downloaded from http://bowtie-bio.sourceforge.net/bowtie2/manual.shtml. RefSeq geneTracks and GTF-files for the rn5 and mm10 genome assembly were downloaded from UCSC genome browser. Common gene ids in the GTF-files were matched to individual transcript_ids using the corresponding official symbols obtained from the geneTracks files. Conclusions: Our study illustrates the nature of the different transcripts in acute rat hippocampal slices after LTP 90 minutes was induced using field electrophysiology and compares them with control, unstimulated slices. Thius allowed us to identify wich genes are modulated in the hippocampus in order to promote and sustain LTP.

2018-10-02 | GSE120712 | GEO

Branch point evolution controls species-specific alternative splicing and regulates long term potentiation

2022-12-02 | GSE208181 | GEO

Smolen2018 - Paradoxical LTP maintenance with inhibition of protein synthesis and the proteasome

Project description:This is a mathematical model describing the formation of long-term potentiation (LTP) at the Schaffer collateral of CA1 pyramidal cell synapse. The model consists of nine ordinary differential equations that denote synaptic states associated with different degrees of LTP, as well as the levels of regulatory proteins involved in the formation and maintenance of LTP.

2024-09-02 | BIOMD0000000853 | BioModels

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