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Series GSE43439 Query DataSets for GSE43439
Status Public on Jul 09, 2013
Title Genomic topography of HDACi-induced hyperacetylation of hippocampal chromatin [ChIP-Seq]
Organism Mus musculus
Experiment type Genome binding/occupancy profiling by high throughput sequencing
Summary Histone deacetylase inhibitors (HDACis) have been shown to potentiate hippocampal-dependent memory and synaptic plasticity and to ameliorate cognitive deficits and degeneration in animal models for different neuropsychiatric conditions. However, the impact of these drugs on hippocampal histone acetylation and gene expression profiles at the genomic level, and the molecular mechanisms that underlie their specificity and beneficial effects in neural tissue, remains obscure. Here, we mapped four relevant histone marks (H3K4me3, AcH3K9,14, AcH4K12 and pan-AcH2B) in hippocampal chromatin and investigated at the whole-genome level the impact of HDAC inhibition on acetylation profiles and basal and activity-driven gene expression. HDAC inhibition caused a dramatic histone hyperacetylation that was largely restricted to active loci pre-marked with H3K4me3 and AcH3K9,14. In addition, the comparison of Chromatin immunoprecipitation sequencing and gene expression profiles indicated that Trichostatin A-induced histone hyperacetylation, like histone hypoacetylation induced by histone acetyltransferase deficiency, had a modest impact on hippocampal gene expression and did not affect the transient transcriptional response to novelty exposure. However, HDAC inhibition caused the rapid induction of a homeostatic gene program related to chromatin deacetylation. These results illuminate both the relationship between hippocampal gene expression and histone acetylation and the mechanism of action of these important neuropsychiatric drugs.
Overall design Examination of 4 different histone modifications in the hippocampus of vehicle (DMSO/Saline) or HDACi TSA (2.4 mg/kg)-treated mice. Samples were obtained 30 min after intraperitoneal administration of either TSA or Vehicle. NOTE: The ChIPseq experiments described here and those presented in the series GSE44854 were performed in paralell. Therefore, some control samples are part of both datasets (GSM1062434, GSM1062437, GSM1062441 and GSM1062442).
Citation(s) 23821663
Submission date Jan 11, 2013
Last update date Sep 16, 2019
Contact name Angel Barco
Organization name Instituto de Neurociencias (UMH-CSIC)
Street address Av. Santiago Ramón y Cajal
City Sant Joan d'Alacant
State/province Alicante
ZIP/Postal code 03550
Country Spain
Platforms (2)
GPL9250 Illumina Genome Analyzer II (Mus musculus)
GPL13112 Illumina HiSeq 2000 (Mus musculus)
Samples (15)
GSM1062428 GBD1_Veh_AcH2B_ChIPseq
GSM1062429 GBD3_Veh_AcH2B_ChIPseq
GSM1062430 GBD5_TSA_AcH2B_ChIPseq
This SubSeries is part of SuperSeries:
GSE44868 Genomic targets, and histone acetylation and gene expression profiling of neural HDAC inhibition
BioProject PRJNA186421
SRA SRP017915

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Supplementary file Size Download File type/resource
GSE43439_RAW.tar 164.1 Mb (http)(custom) TAR (of WIG)
GSE43439_gbd1_3_X_SICER-W200-G600-E10-islandfiltered.wig.normalized.wig.gz 12.8 Mb (ftp)(http) WIG
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Raw data are available in SRA
Processed data provided as supplementary file
Processed data are available on Series record

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