Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Neuronal activity induced by BDNF prompts chromatin remodeling at regulatory elements associated with neuropsychiatric traits [mouse]

ABSTRACT: Neuronal activity induced by BDNF prompts chromatin remodeling at regulatory elements associated with neuropsychiatric traits [mouse]

PROVIDER: PRJNA702471 | ENA |

REPOSITORIES: ENA

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	SRR13732800.fastq.gz	Fastqsanger.gz
	SRR13732801.fastq.gz	Fastqsanger.gz
	SRR13732802.fastq.gz	Fastqsanger.gz
	SRR13732803.fastq.gz	Fastqsanger.gz
	SRR13732804.fastq.gz	Fastqsanger.gz

Items per page:

1 - 5 of 54

Similar Datasets

Neuronal activity induced by BDNF prompts chromatin remodeling at regulatory elements associated with neuropsychiatric traits [mouse]

Project description:Neuronal activity induced by Brain-Derived Neurotrophic Factor (BDNF) is crucial for neuronal survival, differentiation, synaptic plasticity, memory formation, and neurocognitive health. Molecular mechanisms of BDNF promoting cellular survival and synaptic plasticity have been intensely studied, yet its role in genome regulation is obscure. Here, through temporal profiling of chromatin accessibility and transcription in mouse primary cortical neurons upon BDNF treatment or depolarization (KCl), we identified BDNF-specific chromatin-to-gene expression programs. Our analyses revealed that enhancer activation is an early event in the regulatory control of BDNF treated neurons, where bZIP pioneered chromatin opening and co-regulatory transcription factors (Homeobox, EGRs, and CTCF) cooperate to induce fine-grained transcription. Deleting such cis-regulatory sequences decreased the BDNF mediated expression of Arc, a key regulator of synaptic plasticity. Furthermore, BDNF-induced accessible regions are linked to preferential exon usage of neurodevelopmental disorder related genes and heritability of neuronal complex traits. In conclusion, this work provides a comprehensive view of BDNF-mediated genome regulatory features and emphasizes the usage of genomic approaches on dissecting mammalian neuronal activity.

2022-09-01 | GSE166959 | GEO

MDGA2 constrains the BDNF/TrkB signaling

Project description:MDGA2 is an excitatory synaptic suppressor and its mutations have been associated with autism spectrum disorder (ASD). However, the detailed physiological function of MDGA2 and the mechanism underlying MDGA2 deficiency-caused ASD has yet to be elucidated. Herein, we not only confirm that Mdga2+/- mice exhibit increased excitatory synapse transmission and ASD-like behaviors, but also identify aberrant BDNF/TrkB signaling activation in these mice. We demonstrate that MDGA2 interacts with TrkB through its MAM domain, thereby competing the binding of BDNF to TrkB. Both loss of MDGA2 and the ASD-associated MDGA2 V930I mutation promote the BDNF/TrkB signaling activity. Importantly, we demonstrate that inhibiting the BDNF/TrkB signaling by both small molecular compound and MDGA2-derived peptide can attenuate the increase of AMPA receptor-mediated excitatory synaptic activity and social deficits in MDGA2 deficient mice. These results highlight a novel MDGA2-BDNF/TrkB-dependent mechanism underlying the synaptic function regulation, which may become a therapeutic target for ASD.

2025-02-06 | PXD050810 | Pride

A novel intergenic enhancer that regulates Bdnf expression in developing cortical neurons

Project description:Brain-derived Neurotrophic Factor (BDNF) promotes neuronal differentiation and survival and is implicated in the pathogenesis of many neurological disorders. Here, we identified a novel intergenic enhancer located 170 kb from the Bdnf gene, which promotes the expression of Bdnf transcript variants during mouse neuronal differentiation and activity. Following Bdnf activation, enhancer-promoter contacts increase, and the region moves away from the repressive nuclear periphery. Bdnf enhancer activity is necessary for neuronal clustering and dendritogenesis in vitro, and for cortical development in vivo. Our findings provide the first evidence of a regulatory mechanism whereby the activation of a distal enhancer promotes Bdnf expression during brain development.

2023-01-04 | GSE190306 | GEO

BDNF-AS

Project description:Homo sapiens BDNF-AS, BDNF antisense RNA [Source:HGNC Symbol;Acc:HGNC:20608], is expressed in 37 baseline experiment(s);

| ENSG00000245573 | ExpressionAtlas

BDNF-AS

Project description:Homo sapiens BDNF-AS, BDNF antisense RNA [Source:HGNC Symbol;Acc:HGNC:20608], is differentially expressed in 53 experiment(s);

| ENSG00000245573 | ExpressionAtlas

Transcriptome and chromatin accessibility landscapes across 25 human brain regions expand the susceptibility gene set for neuropsychiatric disorders [ATAC-Seq]

Project description:Brain region- and cell-specific transcriptome and epigenome molecular features are associated with heritability for neuropsychiatric traits. Here, we provide an atlas of chromatin accessibility and gene expression in neuronal and non-neuronal cells across 25 distinct regions across cortical and subcortical areas of the human brain from 6 neurotypical controls. We identified extensive gene expression and chromatin accessibility differences across brain regions. We further identified variation in alternative promoter-isoform usage and enhancer-promoter interactions across brain regions and found genes with distinct promoter-isoform usage are strongly enriched for neuropsychiatric risk variants. We identified brain region-specific chromatin co-accessibility and gene-coexpression modules that are robustly associated with genetic risk variants for neuropsychiatric disorders. Using an integrative approach, we identify a novel set of genes that is enriched for neuropsychiatric disorders risk variants but is independent of cell-type specific gene expression and annotated pathways. Our results provide a valuable multi-brain region molecular regulation resource and suggest a unique contribution of epigenetic modifications from the subcortical areas to neuropsychiatric disorders.

2022-08-25 | GSE211822 | GEO

Transcriptome and chromatin accessibility landscapes across 25 human brain regions expand the susceptibility gene set for neuropsychiatric disorders [RNA-Seq]

2022-08-25 | GSE211792 | GEO

BDNF

Project description:Monodelphis domestica BDNF, brain derived neurotrophic factor [Source:NCBI gene;Acc:554233], is expressed in 1 baseline experiment(s);

| ENSMODG00000009461 | ExpressionAtlas

Bdnf

Project description:Rattus norvegicus Bdnf, brain-derived neurotrophic factor [Source:RGD Symbol;Acc:2202], is differentially expressed in 16 experiment(s);

| ENSRNOG00000047466 | ExpressionAtlas

Bdnf

Project description:Rattus norvegicus Bdnf, brain-derived neurotrophic factor [Source:RGD Symbol;Acc:2202], is expressed in 3 baseline experiment(s);

| ENSRNOG00000047466 | ExpressionAtlas

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