The Sas3p and Gcn5p histone acetyltransferases are recruited to similar genes

Abstract

Background: Specific histone modifications can perform several cellular functions, for example, as signals to recruit trans-acting factors and as modulators of chromatin structure. Acetylation of Lys14 of histone H3 is the main target of many histone acetyltransferases in vitro and may play a central role in the stability of the nucleosome. This study is focused on the genome-wide binding of Saccharomyces cerevisiae histone acetyltransferases that are specific for Lys14 of histone H3.

Results: We have used a variation of the genome-wide location analysis method, based on a macroarray platform, to identify binding sites of yeast histone acetyltransferase catalytic subunits and to correlate their positions with acetylation of Lys14 of histone H3. Our results revealed that the histone acetyltransferases Sas3p and Gcn5p are recruited to a pool of intensely transcribed genes and that there is considerable overlap between the two cohorts of Sas3p and Gcn5p bound gene pools. We also demonstrate a positive correlation between binding sites of both proteins and the acetylation state of Lys14 of histone H3. Finally, a positive correlation between the decrease of H3 Lys14 acetylation in a GCN5 deleted strain and the Gcn5p genome occupancy is shown.

Conclusion: Our data support a model in which both Gcn5p and Sas3p act as general activators of an overlapping pool of intensely transcribed genes. Since both proteins preferentially acetylate Lys14 of histone H3, our data support the hypothesis that acetylation of this specific residue facilitates the action of the transcriptional apparatus.

Figure 1

Distribution of intergenic (coding or non-coding genes) and ORF-tRNA distances. The frequency of every intergenic distance in S. cerevisisae is plotted [31]. Coordinates of all tRNA genes were collected and distances from adjacent genes were calculated. The frequency of each distance is plotted.

Figure 2

Correlations between several histone acetyltransferase occupancies and transcription rates. The occupancy was obtained by calculating the moving median of the binding ratio over a sliding window of 100 genes across all genes ordered by transcription rate. The binding ratio was calculated as the ratio of chromatin-immunoprecipitated signals between the epitope-tagged strain and the untagged parent, using the same antibodies. Transcription rate data [36] were also transformed as a moving median of values for each gene over a sliding window of 100 genes across all of them.

Figure 3

Correlation between Sas3p and Gcn5p histone acetyltransferase occupancies. The occupancy of both HATs was calculated as in Figure 2. Only ORFs that showed binding ratios higher than one were plotted. Sas3p occupancies were plotted as a function of Gcn5p occupancies and a correlation coefficient (r) of 0.91 was obtained.

Figure 4

Correlation between Gcn5p, Sas3p, Sas2 and Hpa2 occupancies and acetylated H3K14 enriched regions. Occupancies from (a) Gcn5p, (b) Sas3p, (c) Sas2p and (d) Hpa2p were calculated as in Figure 2. Acetylation at Lys14 of histone H3 was obtained by two ChIP-chip experiments. The first was performed by immunoprecipitating WCE with an antibody that recognizes the carboxyl termini of histone H3 (α-H3Ct) and the other one by immunoprecipitating with α-K14acH3. Ratios from the α-K14acH3 ChIP-chip experiment and the control from the α-H3Ct ChIP-chip experiment were calculated, and their moving median was obtained over a sliding window of 100 ORFs ordered by Gcn5p, Sas3p, Sas2p or Hpa2 occupancy.

Figure 5

Correlation between Gcn5p and Sas3p occupancies and acetylation of K14H3 in gcn5Δ or sas3Δ strains. Correlation between (a) Gcn5p and (b) Sas3p occupancies and acetylated K14H3 enriched regions in their respective deletion mutants. Occupancies from Gcn5p and Sas3p were calculated as in Figure 4, and the same was done for acetylated regions at gcn5Δ or sas3Δ.