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Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

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Genome-wide activity-dependent MeCP2 phosphorylation regulates nervous system development and function [cultured cortical neurons]

ABSTRACT: To examine potential differences in activity-dependent gene expression, we analyzed mRNA expression in cultured neurons isolated from Wild-type vs MeCP2 S421A mice at 0 (unstimulated), 1 or 6 hours after membrane depolarization by exposure to high extracellular KCl (55mM) All mice were male littermates from one of three litters. We isolated RNA from dissociated cortical cultures (E16+7DIV) isolated from Wild-Type or MeCP2 S421A knock-in mice littermates. Cells were either left unstimulated or depolarized for 1 or 6 hours by addition of 55mM KCl to the media. mRNA expression was analyzed using the Affymetrix GeneChip Mouse Expression Set 430 2.0 microarray platform.

ORGANISM(S): Mus musculus

SUBMITTER: Harrison Gabel

PROVIDER: E-GEOD-31849 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Genome-wide activity-dependent MeCP2 phosphorylation regulates nervous system development and function.

Cohen Sonia S Gabel Harrison W HW Hemberg Martin M Hutchinson Ashley N AN Sadacca L Amanda LA Ebert Daniel H DH Harmin David A DA Greenberg Rachel S RS Verdine Vanessa K VK Zhou Zhaolan Z Wetsel William C WC West Anne E AE Greenberg Michael E ME

Neuron 20111001 1

Autism spectrum disorders such as Rett syndrome (RTT) have been hypothesized to arise from defects in experience-dependent synapse maturation. RTT is caused by mutations in MECP2, a nuclear protein that becomes phosphorylated at S421 in response to neuronal activation. We show here that disruption of MeCP2 S421 phosphorylation in vivo results in defects in synapse development and behavior, implicating activity-dependent regulation of MeCP2 in brain development and RTT. We investigated the mechan ...[more]

PMID: 21982370

Similar Datasets

Genome-wide activity-dependent MeCP2 phosphorylation regulates nervous system development and function [ChIP-Seq]

Project description:Autism spectrum disorders such as Rett syndrome (RTT) have been hypothesized to arise from defects in experience-dependent synapse maturation. RTT is caused by mutations in MECP2, a nuclear protein that becomes phosphorylated at S421 in response to neuronal activation. We show here that disruption of MeCP2 S421 phosphorylation in vivo results in defects in synapse development and behavior, implicating activity-dependent regulation of MeCP2 in brain development and RTT. We investigated the mechanism by which S421 phosphorylation regulates MeCP2 function and show by chromatin immunoprecipitation-sequencing that this modification occurs on MeCP2 bound across the genome. The phosphorylation of MeCP2 S421 appears not to regulate the expression of specific genes; rather, MeCP2 functions as a histone-like factor whose phosphorylation may facilitateM-CM-^BM-BM- a genome-wide response of chromatin to neuronal activity during nervous system development. We propose that RTT results in part from a loss of this experience-dependent chromatin remodeling. To examine MeCP2 binding across the neuronal genome and where on the genome MeCP2 is phosphorylated at Serine 421 in response to neuronal activity we performed anti-total MeCP2 and anti-phospho-Serine 421 specific Chromatin immunoprecipitation from cultured cortical neurons that were either left unstimulated or membrane depolarized for 2 hours by addition of 55mM KCl to the media. ChIP DNA was verified for successful IP by qPCR then cloned and sequenced using ABI SOLiD system 4. ChIP was performed from E16 +7DIV disociated cortical cultures from one or two independent dissections using an anti-c-terminal antiserum recognizing MeCP2 independent of its phosphorylation state or with an anti-pS421 antiserum that specifically immunoprecipitates MeCP2 phosphorylated at serine 421. Samples were qPCR validated and sequenced using ABI SOLiD system 4 library preparation and sequencing.

2011-09-08 | E-GEOD-31951 | biostudies-arrayexpress

Genome-wide activity-dependent MeCP2 phosphorylation regulates nervous system development and function [cultured cortical neurons]

Project description:To examine potential differences in activity-dependent gene expression, we analyzed mRNA expression in cultured neurons isolated from Wild-type vs MeCP2 S421A mice at 0 (unstimulated), 1 or 6 hours after membrane depolarization by exposure to high extracellular KCl (55mM) All mice were male littermates from one of three litters.

2011-09-08 | GSE31849 | GEO

Identification of activity-induced Npas4-regulated genes in cortical inhibitory and excitatory neurons (array)

Project description:To identify the activity-induced gene expression programs in inhibitory and excitatory neurons, we analyzed RNA extracted from cultured E14 mouse MGE- and CTX-derived neurons (DIV 10) after these cultures were membrane-depolarized for 0, 1 and 6 hrs with 55mM extracellular KCl. To identify the gene programs regulated in these cells by the activity-induced early-response transcription factor Npas4, we repeated the same experiment in the MGE- and CTX-cultures lacking Npas4 (Npas4-KO). Littermate mouse E14 MGE- or CTX-derived neurons (WT or KO for Npas4) were cultured for 9 days, quieted overnight with TTX and AP-5 and then membrane-depolarized for 0, 1 or 6 hours by raising the extracellular KCl-concentration to 55mM. RNA was then extracted and analyzed using Affymetrix GeneChip Mouse Expression Set 430 2.0 microarray platform.

2015-06-04 | E-GEOD-55588 | biostudies-arrayexpress

Identification of activity-induced genes in cortical inhibitory neurons (RNA-Seq)

Project description:To identify the activity-induced gene expression programs in inhibitory neurons, we analyzed RNA extracted from cultured E14 mouse MGE-derived neurons (DIV 10) after these cultures were membrane-depolarized for 0, 1 and 6 hrs with 55mM extracellular KCl. Mouse E14 MGE-derived neurons were cultured for 9 days, quieted overnight with TTX and AP-5 and then membrane-depolarized for 0, 1 or 6 hours by raising the extracellular KCl-concentration to 55mM. RNA was then extracted and WT RNA-Seq was performed on ABi SOLiD

2014-05-22 | E-GEOD-55590 | biostudies-arrayexpress

MEF2D binding sites in rat hippocampal neurons

Project description:We analyzed the binding profiles of MEF2D, a member of MEF2 family transcription factors, in rat hippocampal neurons. Keywords: ChIP-chip We used custom-designed rat genome tiling array manufactured by Nimblegen Systems, Inc . This array contains probes that represent the following rat genomic regions: 182 genes identified by mRNA profiling experiments, 86 genes whose expression was decreased by both KCl-mediated depolarization and MEF2 RNAi, and 40 control genes whose expression was not altered by MEF2 RNAi or MEF2-VP16-ER. The array not only covers the entire gene regions but also contains probes that correspond to the 40 kb 5â²and 3â² to each gene. Repeatmasking was conducted by Nimblegen to ensure that repetitive elements were not tiled on the microarray. Probe length and spacing between the probes were 50-75mer and 50 bp, respectively.

2010-05-06 | E-GEOD-13551 | biostudies-arrayexpress

Genome-wide activity-dependent MeCP2 phosphorylation regulates nervous system development and function [ChIP-Seq]

Project description:Autism spectrum disorders such as Rett syndrome (RTT) have been hypothesized to arise from defects in experience-dependent synapse maturation. RTT is caused by mutations in MECP2, a nuclear protein that becomes phosphorylated at S421 in response to neuronal activation. We show here that disruption of MeCP2 S421 phosphorylation in vivo results in defects in synapse development and behavior, implicating activity-dependent regulation of MeCP2 in brain development and RTT. We investigated the mechanism by which S421 phosphorylation regulates MeCP2 function and show by chromatin immunoprecipitation-sequencing that this modification occurs on MeCP2 bound across the genome. The phosphorylation of MeCP2 S421 appears not to regulate the expression of specific genes; rather, MeCP2 functions as a histone-like factor whose phosphorylation may facilitateÂ a genome-wide response of chromatin to neuronal activity during nervous system development. We propose that RTT results in part from a loss of this experience-dependent chromatin remodeling. To examine MeCP2 binding across the neuronal genome and where on the genome MeCP2 is phosphorylated at Serine 421 in response to neuronal activity we performed anti-total MeCP2 and anti-phospho-Serine 421 specific Chromatin immunoprecipitation from cultured cortical neurons that were either left unstimulated or membrane depolarized for 2 hours by addition of 55mM KCl to the media. ChIP DNA was verified for successful IP by qPCR then cloned and sequenced using ABI SOLiD system 4.

2011-09-08 | GSE31951 | GEO

RNA-seq of E16.5 mouse cortical neurons depolarized with 55mM KCl for 0h, 2h and 6h.

Project description:We performed RNA-seq of E16.5 mouse cortical neurons depolarized with 55mM KCl for 0h, 2h and 6h.

2022-11-02 | GSE201636 | GEO

shRNA profiling of rat neurons to identify MEF2 Regulated Genes

Project description:Expression profiling in hippocampal neurons to identify activity-regulated genes controlled by MEF2; Experiments were conducted to identify activity-regulated MEF2 target genes. Experiment Overall Design: Neurons were depolarized with 55mM extracellular KCl for one or six hours in the presence of control or MEF2-specific shRNAs

2009-01-17 | E-GEOD-13537 | biostudies-arrayexpress