Dataset Information

Histone hyperacetylation in the coding region of chromatin undergoing transcription in SV40 minichromosomes is a dynamic process regulated directly by the presence of RNA polymerase II.

ABSTRACT: SV40 chromosomes undergoing transcription operationally defined by the presence of RNA polymerase II (RNAPII) were immune-selected with antibody to RNAPII and subjected to secondary chromatin immunoprecipitation with antibodies to hyperacetylated or unacetylated H4 or H3. Immune selection fragmentation and immunoprecipitation was used to determine the hyperacetylation status of histones independent of the location of the RNAPII and Re chromatin immunoprecipitation was used to determine their hyperacetylation status when associated with RNAPII. While hyperacetylated H4 and H3 were found in the coding regions regardless of the location of RNAPII, unacetylated H4 and H3 were found only at sites lacking RNAPII. The absence of unacetylated H4 and H3 at sites containing RNAPII was correlated with the specific association of the histone acetyl transferase p300 with the RNAPII. In contrast, the presence of unacetylated H4 and H3 at sites lacking RNAPII was shown to result from the action of a histone deacetylase based upon the effects of the inhibitor sodium butyrate. These results suggest that the extent of hyperacetylation of H4 and H3 during transcription alternates between hyperacetylation directed by an RNAPII associated histone acetyl transferase and deacetylation directed by a histone deacetylase at other sites.

SUBMITTER: Balakrishnan L

PROVIDER: S-EPMC1847586 | biostudies-literature | 2007 Jan

REPOSITORIES: biostudies-literature

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Histone hyperacetylation in the coding region of chromatin undergoing transcription in SV40 minichromosomes is a dynamic process regulated directly by the presence of RNA polymerase II.

Balakrishnan Lata L Milavetz Barry B

Journal of molecular biology 20060920 1

SV40 chromosomes undergoing transcription operationally defined by the presence of RNA polymerase II (RNAPII) were immune-selected with antibody to RNAPII and subjected to secondary chromatin immunoprecipitation with antibodies to hyperacetylated or unacetylated H4 or H3. Immune selection fragmentation and immunoprecipitation was used to determine the hyperacetylation status of histones independent of the location of the RNAPII and Re chromatin immunoprecipitation was used to determine their hyp ...[more]

PMID: 17055528

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Project description: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. 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).

Dataset Information

Histone hyperacetylation in the coding region of chromatin undergoing transcription in SV40 minichromosomes is a dynamic process regulated directly by the presence of RNA polymerase II.

Publications

Histone hyperacetylation in the coding region of chromatin undergoing transcription in SV40 minichromosomes is a dynamic process regulated directly by the presence of RNA polymerase II.

Similar Datasets

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