Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Neuronal Activity Suppresses NEUROD-Dependent Transcription and Genome Organization [Hi-C]

ABSTRACT: Neuronal activity induces gene expression programs associated with plasticity in the brain, but it also transiently suppresses gene expression through poorly understood mechanisms. Here, we report that neuronal activity downregulates NEUROD-dependent gene expression in cerebellar granule neurons in adult mice. Using NEUROD1/2 double conditional knockout mice of both sexes, we show that NEUROD binds and activates its target gene enhancers and establishes a three-dimensional genome architecture that facilitates transcription when neuronal activity is low. Moreover, NEUROD antagonizes activity-dependent gene expression programs, including those regulated by MEF2. However, when granule neurons are activated, NEUROD-dependent transcriptional and genome organizing functions are disrupted. Together, these findings reveal NEUROD as a key regulator of transcriptional programs associated with inactive neurons. Our study provides new insights into how neuronal activity reshapes gene transcription and genome architecture in the brain.

ORGANISM(S): Mus musculus

PROVIDER: GSE310752 | GEO | 2026/01/09

REPOSITORIES: GEO

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
		Other

Items per page:

1 - 1 of 1

Similar Datasets

Neuronal Activity Suppresses NEUROD-Dependent Transcription and Genome Organization [RNA-Seq]

Project description:Neuronal activity induces gene expression programs associated with plasticity in the brain, but it also transiently suppresses gene expression through poorly understood mechanisms. Here, we report that neuronal activity downregulates NEUROD-dependent gene expression in cerebellar granule neurons in adult mice. Using NEUROD1/2 double conditional knockout mice of both sexes, we show that NEUROD binds and activates its target gene enhancers and establishes a three-dimensional genome architecture that facilitates transcription when neuronal activity is low. Moreover, NEUROD antagonizes activity-dependent gene expression programs, including those regulated by MEF2. However, when granule neurons are activated, NEUROD-dependent transcriptional and genome organizing functions are disrupted. Together, these findings reveal NEUROD as a key regulator of transcriptional programs associated with inactive neurons. Our study provides new insights into how neuronal activity reshapes gene transcription and genome architecture in the brain.

2026-01-09 | GSE310753 | GEO

Neuronal Activity Suppresses NEUROD-Dependent Transcription and Genome Organization [ChIP-Seq]

2026-01-09 | GSE310749 | GEO

Sensory experience remodels genome architecture in neural circuit to drive motor learning

Project description:Neuronal activity-dependent transcription couples sensory experience to adaptive responses of the brain including learning and memory. Mechanisms of activity-dependent gene expression including alterations of the epigenome have been characterized. However, the fundamental question of whether and how sensory experience remodels chromatin architecture in the adult brain in vivo to induce neural code transformations and learning and memory remains to be addressed. Here, in vivo calcium imaging, optogenetics, and pharmacological approaches reveal that granule neuron activation in the anterior dorsal cerebellar vermis (ADCV) plays a crucial role in a novel delay tactile startle learning paradigm in mice. Strikingly, using large-scale transcriptome and chromatin profiling, we have discovered that activation of the motor learning-linked granule neuron circuit reorganizes neuronal chromatin including through long-distance enhancer-promoter and transcriptionally active compartment interactions to orchestrate distinct granule neuron gene expression modules. Conditional CRISPR knockout of the chromatin architecture regulator Cohesin in ADCV granule neurons in adult mice disrupts activity-dependent transcription and motor learning. These findings define how sensory experience patterns chromatin architecture and neural circuit coding in the brain to drive motor learning.

2019-05-09 | GSE127995 | GEO

Transcription profiling of mouse beta cells lacking NeuroD

Project description:The goal: Investigate NeuroD function in the mature beta cells. The model: Cross RIP-Cre to NeuroD flox/flox mouse to delete neuroD when insulin gene is activated; The methods: Islets are purified and RNA is extracted to see how the profile of gene expression is altered after neuroD is deleted from the beta cells. The comparison: Compare control with mutant; The hypothesis: Since neuroD is deleted, I would expect that neuroD mRNA will be decreased in the mutant samples; The samples: two types of samples will be submitted including control and conditional knockout (mutant); Flox/+,Ins (F/+,I) is the control and labled as group B; and Flox/-,Ins (F/-,I) is the conditional knockout and labled as group A

2010-03-03 | E-MTAB-152 | biostudies-arrayexpress

Gene expression profiling of wild-type, Nkx2.2 null, NeuroD null and Nkx2.2/NeuroD double KO E13.5 pancreata

Project description:The experiment consist of 16 one channel assays for analyzing embryonic pancreas at E13. There are four replicates per condition. We are looking at differential gene expression across four mouse lines: WT, Nkx2.2, NeuroD and Nkx2.2/NeuroD double mutants at E13.5.

2015-02-03 | E-MTAB-3350 | biostudies-arrayexpress

Genome-wide analysis of the therapeutic effect of NeuroD on irradiation-induced intestinal injury

2015-09-16 | GSE73068 | GEO

Sox11 - a novel activity-regulated gene with dentate gyrus-specific expression

Project description:Neuronal activity initiates transcriptional programs that shape long-term changes in plasticity. Although neuron subtypes differ in their plasticity response, most activity-dependent transcription factors are broadly expressed across different neuron subtypes and brain regions. Thus, how regional and neuronal subtype-specific plasticity are established on the transcriptional level remains poorly understood. Here, we report that the developmental transcription factor Sox11 is induced in mature neurons upon hippocampal circuit activity and that this activity-dependent expression occurs exclusively in the dentate gyrus (DG) of the hippocampus. In addition, we show that Sox11 can modify synaptic plasticity and intrinsic excitability of DG granule cell neurons as well as the expression of plasticity-related genes. We propose that Sox11 is a DG-specific activity-dependent gene and might play a role in fine tuning regional plasticity in the hippocampal circuit.

2019-11-10 | GSE140180 | GEO

Chromatin Remodeling Inactivates Activity Genes and Regulates Neural Coding

2016-07-18 | GSE83253 | GEO

Genome-wide analysis of the therapeutic effect of NeuroD on irradiation-induced intestinal injury

Project description:The objective was to investigate the therapeutic effect of NeuroD on irradiation-induced intestinal injury at gene expression level. Gene expression profilings between NeuroD and EGFP treated mice which were received 9 Gy total body irradiation were compared. All mice were given 9 Gy radiation and divided into two groups (3 mice per group). After radiation, mice were immediately administered with an intraperitoneal injection of 0.1 mM EGFP or NeuroD-EGFP. EGFP treated mice were served as controls. 12 hours post radiation, mice jejunum tissues were isolated. Total RNA obtained from jejunum tissues and subjected to gene expression profiling assays.

2015-09-16 | E-GEOD-73068 | biostudies-arrayexpress

Chromatin Remodeling Inactivates Activity Genes and Regulates Neural Coding

Project description:Activity-dependent transcription influences neuronal connectivity, but the roles and mechanisms of inactivation of activity-dependent genes have remained poorly understood. Genome-wide analyses in the mouse cerebellum revealed that the nucleosome remodeling and deacetylase (NuRD) complex deposits the histone variant H2A.z at promoters of activity-dependent genes, thereby triggering their inactivation. Purification of translating mRNAs from synchronously developing granule neurons (Sync-TRAP) showed that conditional knockout of the core NuRD subunit Chd4 impairs inactivation of activity-dependent genes when neurons undergo dendrite pruning. Chd4 knockout or expression of NuRD-regulated activity genes impairs dendrite pruning. Imaging of behaving mice revealed hyperresponsivity of granule neurons to sensorimotor stimuli upon Chd4 knockout. Our findings define an epigenetic mechanism that inactivates activity-dependent transcription and regulates dendrite patterning and sensorimotor encoding in the brain. One or two replicates of the histone modifications (H3K27me3 and H2A.z), total histone proteins (H2A.z and H3), and ATPase Chd4 using postnatal day 22 cerebella from wild type (WT) or Chd4 conditional knockout (cKO) mice were examined using libraries prepared with the Illumina ChIP-Seq DNA Sample Prep Kit. Four replicates of total RNA were extracted from postnatal day 27-28 cerebella from rotarod-trained or control homecage mice, or Chd4 cKO or WT mice using Trizol and reverse-transcribed with oligo-dT priming. Three replicates of immunoprecipitated Sync-TRAP RNA or the input control using postnatal day 12 Chd4 cKO or WT cerebella were purified and amplified with Ovation RNA-Seq System V2 (NuGEN). All samples were sequenced on the Illumina HiSeq 2000 platform.

2016-07-18 | E-GEOD-83253 | biostudies-arrayexpress

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