Purification and characterization of two porcine liver nuclear histone acetyltransferases

HAT discovery: Heading toward an elusive goal with a key biological assist

Eukaryotic genomes are maintained within DNA-protein complexes called chromatin. Post-translational modification of chromatin proteins, and especially acetylation of the core histone amino-terminal tails, has long been associated with chromatin assembly and the regulation of gene expression. It is now well accepted that an elaborate array of enzymes are responsible for posttranslational chromatin marks including acetylation and methylation among others and that together they have profound effects on gene regulation. However, this was not always the case. Here we describe the events surrounding the initial identification of GCN5 as a histone acetyltransferase from Tetrahymena thermophila and the discovery that it is an ortholog of a transcription co-activator complex in yeast. This discovery was the first to directly link a well-described transcription factor and histone modifying activity.

Association with the origin recognition complex suggests a novel role for histone acetyltransferase Hat1p/Hat2p

Background

Histone modifications have been implicated in the regulation of transcription and, more recently, in DNA replication and repair. In yeast, a major conserved histone acetyltransferase, Hat1p, preferentially acetylates lysine residues 5 and 12 on histone H4.

Results

Here, we report that a nuclear sub-complex consisting of Hat1p and its partner Hat2p interacts physically and functionally with the origin recognition complex (ORC). While mutational inactivation of the histone acetyltransferase (HAT) gene HAT1 alone does not compromise origin firing or initiation of DNA replication, a deletion in HAT1 (or HAT2) exacerbates the growth defects of conditional orc-ts mutants. Thus, the ORC-associated Hat1p-dependent histone acetyltransferase activity suggests a novel linkage between histone modification and DNA replication. Additional genetic and biochemical evidence points to the existence of partly overlapping histone H3 acetyltransferase activities in addition to Hat1p/Hat2p for proper DNA replication efficiency. Furthermore, we demonstrated a dynamic association of Hat1p with chromatin during S-phase that suggests a role of this enzyme at the replication fork.

Conclusion

We have found an intriguing new association of the Hat1p-dependent histone acetyltransferase in addition to its previously known role in nuclear chromatin assembly (Hat1p/Hat2p-Hif1p). The participation of a distinct Hat1p/Hat2p sub-complex suggests a linkage of histone H4 modification with ORC-dependent DNA replication.

Epstein-Barr virus nuclear protein 2 interacts with p300, CBP, and PCAF histone acetyltransferases in activation of the LMP1 promoter

The Epstein-Barr virus (EBV) nuclear protein 2 (EBNA2) and herpes simplex virion protein 16 (VP16) acidic domains that mediate transcriptional activation now are found to have affinity for p300, CBP, and PCAF histone acetyltransferases (HATs). Transcriptionally inactive point mutations in these domains lack affinity for p300, CBP, or PCAF. P300 and CBP copurify with the principal HAT activities that bind to EBNA2 or VP16 acidic domains through velocity sedimentation and anion-exchange chromatography. EBNA2 binds to both the N- and C-terminal domains of p300 and coimmune-precipitates from transfected 293T cells with p300. In EBV-infected Akata Burkitt's tumor cells that do not express the EBV encoded oncoproteins EBNA2 or LMP1, p300 expression enhances the ability of EBNA2 to up-regulate LMP1 expression. Through its intrinsic HAT activity, PCAF can further potentiate the p300 effect. In 293 T cells, P300 and CBP (but not PCAF) can also coactivate transcription mediated by the EBNA2 or VP16 acidic domains and HAT-negative mutants of p300 have partial activity. Thus, the EBNA2 and VP16 acidic domains can utilize the intrinsic HAT or scaffolding properties of p300 to activate transcription.

Purification and characterization of the cytoplasmic histone acetyltransferase B of maize embryos

From a soluble cellular fraction of maize embryos we purified to apparent homogeneity a cytoplasmic histone acetyltransferase, which matches all criteria for a B-type enzyme. Using 8 chromatographic steps, we achieved a 6700-fold purification of an enzymatically active protein with a molecular weight of approximately 90 kDa. Under denaturing conditions the protein split into 2 components which migrated at 45 and 50 kDa in SDS-PAGE, suggesting that the native enzyme is a heterodimer. The purified enzyme was characterized in terms of physicochemical and kinetic properties, and substrate specificity. It was specific for histone H4, leading to acetylation of non-acetylated H4 subspecies into the di-acetylated state in vitro. Its activity was coincident with the intensity of DNA replication in meristematic cells during embryo germination. We established an electrophoretic system under non-denaturing conditions for detection of enzyme activity within the gel matrix; in combination with second dimension SDS-PAGE the procedure allowed the unambiguous identification of histone acetyltransferase, even in crude enzyme preparations.

Special HATs for special occasions: linking histone acetylation to chromatin assembly and gene activation

Post-translational acetylation of the core histone amino-terminal tails has long been associated with both chromatin assembly and the regulation of gene expression. The recent identification and cloning of histone acetyltransferase genes represents a significant breakthrough in our understanding of how specific acetylation states are established. Ongoing characterization of these enzymes and their molecular cohorts supports a direct role for acetylation in a signaling pathway that modulates chromatin structure to create new patterns of transcription.

Differential immunostaining of plant chromosomes by antibodies recognizing acetylated histone H4 variants

Metaphase chromosomes of Vicia faba were exposed to antibodies recognizing defined acetylated isoforms of histone H4. After indirect immunostaining with antibodies directed against H4 acetylated on lysines 5, 8 and 12 respectively, the entire chromosome complement was labelled. The brightest signal appeared at the nucleolus organizing region (NOR). The large genetically inert heterochromatic regions, which are composed of late replicating tandemly repetitive DNA sequences, remained unlabelled. Thus, the chromosomal distribution of histones H4 acetylated at positions of lysine 5, 8 and 12 is broadly correlated with the intensity of transcription and the sequence of replication of the field bean chromatin during interphase. Antibodies against H4 acetylated at lysine 16 also caused a strong signal at the NOR but otherwise a uniform fluorescence along the chromosome.

The nuclear matrix and the regulation of chromatin organization and function

Nuclear DNA is organized into loop domains, with the base of the loop being bound to the nuclear matrix. Loops with transcriptionally active and/or potentially active genes have a DNase I-sensitive chromatin structure, while repressed chromatin loops have a condensed configuration that is essentially invisible to the transcription machinery. Core histone acetylation and torsional stress appear to be responsible for the generation and/or maintenance of the open potentially active chromatin loops. The transcriptionally active region of the loop makes several dynamic attachments with the nuclear matrix and is associated with core histones that are dynamically acetylated. Histone acetyltransferase and deacetylase, which catalyze this rapid acetylation and deacetylation, are bound to the nuclear matrix. Several transcription factors are components of the nuclear matrix. Histone acetyltransferase, deacetylase, and transcription factors may contribute to the dynamic attachment of the active chromatin domains with the nuclear matrix at sites of ongoing transcription.

Identification of a gene encoding a yeast histone H4 acetyltransferase

A collection of yeast temperature-sensitive mutants was screened by an enzymatic assay to find a mutant defective in the acetylation of histone H4. The assay used a fractionated cell extract and measured acetylation of a peptide corresponding to amino acids 1-28 of H4. There are at least two activities in this fraction that acetylate the peptide. A mutation, hat1-1, that eliminates one of the activities was identified and mapped to a locus near the centromere of chromosome XVI. The HAT1 gene was cloned and found to encode a protein of 374 amino acids. Analysis of the peptide used in the assay demonstrated that the HAT1 enzyme acetylates lysine 12 of histone H4. hat1 mutants have no obvious growth defects or phenotypes other than the enzyme defect itself. The HAT1 protein expressed in Escherichia coli gave histone acetyltransferase activity in vitro, demonstrating that HAT1 is the structural gene for the enzyme.