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Does gene length play a role? - Transient regulation of Gcn5 histone acetyltransferase under stress conditions.

ABSTRACT: Gcn5 is a histone modification enzyme that performs its function by global or locus-specific histone acetylation. It is known that Gcn5 involves in stress responses in yeast. Our previous data showed that Gcn5 relocalized to the long genes under IM KCl stress conditions in yeast. Here we use a stress adaptation and recovery model and performed 52 microarrays. By investigating the gene regulation pattern, genome-wide localization of Gcn5, as well as histone modification, we aim to understand the regulation mechanism. The data is available in Gene Expression Omnibus (GEO: SuperSeriesGSE 36601).

SUBMITTER: Xue-Franzen Y

PROVIDER: S-EPMC4535997 | biostudies-literature | 2014 Dec

REPOSITORIES: biostudies-literature

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Does gene length play a role? - Transient regulation of Gcn5 histone acetyltransferase under stress conditions.

Xue-Franzén Yongtao Y

Genomics data 20140908

Gcn5 is a histone modification enzyme that performs its function by global or locus-specific histone acetylation. It is known that Gcn5 involves in stress responses in yeast. Our previous data showed that Gcn5 relocalized to the long genes under IM KCl stress conditions in yeast. Here we use a stress adaptation and recovery model and performed 52 microarrays. By investigating the gene regulation pattern, genome-wide localization of Gcn5, as well as histone modification, we aim to understand the ...[more]

PMID: 26484112

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Project description:The histone acetylation of post-translational modification can be highly dynamic and play a crucial role in regulating cellular proliferation, survival, differentiation and motility. Of the enzymes that mediate post-translation modifications, the GCN5 of the histone acetyltransferase (HAT) proteins family that add acetyl groups to target lysine residues within histones, has been most extensively studied. According to the mechanism studies of GCN5 related proteins, two key processes, deprotonation and acetylation, must be involved. However, as a fundamental issue, the structure of hGCN5/AcCoA/pH3 remains elusive. Although biological experiments have proved that GCN5 mediates the acetylation process through the sequential mechanism pathway, a dynamic view of the catalytic process and the molecular basis for hGCN5/AcCoA/pH3 are still not available and none of theoretical studies has been reported to other related enzymes in HAT family. To explore the molecular basis for the catalytic mechanism, computational approaches including molecular modeling, molecular dynamic (MD) simulation and quantum mechanics/molecular mechanics (QM/MM) simulation were carried out. The initial hGCN5/AcCoA/pH3 complex structure was modeled and a reasonable snapshot was extracted from the trajectory of a 20 ns MD simulation, with considering post-MD analysis and reported experimental results. Those residues playing crucial roles in binding affinity and acetylation reaction were comprehensively investigated. It demonstrated Glu80 acted as the general base for deprotonation of Lys171 from H3. Furthermore, the two-dimensional QM/MM potential energy surface was employed to study the sequential pathway acetylation mechanism. Energy barriers of addition-elimination reaction in acetylation obtained from QM/MM calculation indicated the point of the intermediate ternary complex. Our study may provide insights into the detailed mechanism for acetylation reaction of GCN5, and has important implications for the discovery of regulators against GCN5 enzymes and related HAT family enzymes.

Dataset Information

Does gene length play a role? - Transient regulation of Gcn5 histone acetyltransferase under stress conditions.

Publications

Does gene length play a role? - Transient regulation of Gcn5 histone acetyltransferase under stress conditions.

Similar Datasets

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