Histone H4 lysine 91 acetylation a core domain modification associated with chromatin assembly

Abstract

The acetylation of the NH2-terminal tail of histone H4 by type B histone acetyltransferases (HATs) is involved in the process of chromatin assembly. Histone H4 associated with a nuclear type B HAT complex contains modifications in its globular core domain as well. In particular, acetylation was found at lysine 91. A mutation that alters this residue, which lies in the interface between histone H3/H4 tetramers and H2A/H2B dimers, confers phenotypes consistent with defects in chromatin assembly such as sensitivity to DNA damaging agents and derepression and alteration of silent chromatin structure. In addition, this mutation destabilizes the histone octamer, leading to defects in chromatin structure. These results indicate an important role for histone modifications outside the NH2-tail domains in the processes of chromatin assembly, DNA repair, and transcriptional silencing.

Figure 1. Histone H4 Associated with the Hat1p-Hat2p-Hif1p Complex Is Acetylated on Lysine 91, a Residue Important for DNA Damage Repair

(A) Histone H4 resolved by SDS-PAGE was proteolytically digested, and the indicated modified peptides were identified by mass spectrometry. (B) Crystal structure of the nucleosome showing the full histone octamer (left) or the H3/H4 tetramer (right). Histone H4 K 91 is highlighted in pink. Structure was generated with MOLSCRIPT and RASTER 3D by using PDB code 1ID3. (C) 10-fold serial dilutions of cells, containing the indicated allele of histone H4, were plated on synthetic complete plates (HC) ± the indicated DNA damaging agent. (D) For the analysis of UV sensitivity, cells were plated on HC plates and then subjected to the indicated doses of UV radiation. (E–H) The indicated histone H4 alleles were introduced into strains deleted for factors involved in the DNA damage checkpoint (E), NHEJ (F), recombinational repair (G), or chromatin assembly (H).

Figure 2. Histone H4 Lysine 91 Is Important for Gene Silencing

(A) The indicated alleles of histone H4 were transformed into strains carrying the URA3 reporter gene at a telomere (UCC1111), the silent mating loci HML (UCC7266) and HMR (UCC7262), or the rDNA repeat (UCC1188) (van Leeuwen et al., 2002). Transcriptional silencing of URA3 was assayed by comparing growth of cells on plates containing synthetic complete media (HC) ± 5-FOA (5-FOA). (B) The number of genes that are upregulated in H4 K91A mutant, identified by microarray analysis, is plotted versus their distance to the telomere. (C) The fraction of the total ORFs within each distance range from the telomere that are upregulated greater than 1.5- or 2-fold. (D) The number of genes that are downregulated in H4 K91A mutant, identified by microarray analysis, is plotted versus their distance to the telomere.

Figure 3. H4 K 91 Acetylation Is Important for Maintaining Silent Chromatin Structure and Is Enriched in Active Chromatin Regions

(A) Schematic representation of chromosomal regions assayed by ChIP. (B–D) ChIP assays measuring the presence of Sir2p (B), acetylated histone H4 (C), and histone H3 lysine 79 methylation (D) at the indicated loci. (E) A Western blot containing histones isolated from either sodium butyrate-treated HeLa cells or E. coli-expressing recombinant H4 was probed with immunodepleted anti-acetylated H4 K 91 antibodies. (F) Either unmodified (even numbered lanes) or modified (odd numbered lanes) peptides encompassing sites of histone H4 acetylation (lanes 1 and 2, K 12; lanes 3 and 4, K 16; lanes 5 and 6, K 91; lanes 7 and 8, K 5; and lanes 9 and 10, K 8) were spotted in the concentrations indicated. Dot blots were then probed with immunodepleted anti-acetylated H4 K 91 antibodies. (G) ChIP assays were performed with anti-acetylated H4 K 91 antibody to measure the relative abundance of this modification at the indicated loci. (H) Abundance of acetyl-H4 K 91 at the indicated loci was determined in wild-type (wt) and H3 K79A cells by ChIP. Bar graphs give the average of three independent trials with the SD represented by error bars.

Figure 4. Histone H4 Lysine 91 Is Important for Dimer/Tetramer Interactions and the Proper Formation of Chromatin Structure

(A) Equal quantities of nuclei from wt and H4 K91A cells (lanes K and A, respectively) were digested with MNase for the indicated times. After deproteination, DNA was analyzed by agarose gel electrophoresis. (B) An equal quantity of chromatin from wt and H4 K91A cells was applied to a hydroxyapatite column and step eluted with buffer containing the indicated concentrations of NaCl (lanes labeled IP indicate the input samples). Fractions were analyzed by Western blots probed with an antibody recognizing histone H2B. All lanes shown were from a single blot. This experiment was performed three times with identical results. (C) Plasmids containing the indicated alleles of H4 were transformed into UCC1111 and telomeric silencing assayed as in Figure 2. (D) Strains containing the indicated alleles of H4 were assayed for sensitivity to MMS as described in Figure 1.