Abstract
During gene expression, histone acetylation by histone acetyltransferase (HAT) loosens the chromatin structure around the promoter to allow RNA polymerase II (Pol II) to initiate transcription, while de-acetylation by histone deacetylase (HDAC) tightens the structure in the transcribing region to repress false initiation. Histone acetylation is also regulated by intracellular pH (pHi) with global hypoacetylation observed at low pHi, and hyperacetylation, causing proliferation, observed at high pHi. However, the mechanism underlying the pHi-dependent regulation of gene expression remains elusive. Here, we have explored the role of the chromodomain (CD) of budding yeast Eaf3, a common subunit of both HAT and HDAC that is thought to recognize methylated lysine residues on histone H3. We found that Eaf3 CD interacts with histone H3 peptides methylated at Lys4 (H3K4me, a promoter epigenetic marker) and Lys36 (H3K36me, a coding region epigenetic marker), as well as with many dimethyl-lysine peptides and even arginine-asymmetrically dimethylated peptides, but not with unmethylated, phosphorylated or acetylated peptides. The Eaf3 CD structure revealed an unexpected histidine residue in the aromatic cage essential for binding H3K4me and H3K36me. pH titration experiments showed that protonation of the histidine residue around physiological pH controls the charge state of the aromatic cage to regulate binding to H3K4me and H3K36me. Histidine substitution and NMR experiments confirmed the correlation of histidine pKa with binding affinity. Collectively, our findings suggest that Eaf3 CD functions as a pHi sensor and a regulator of gene expression via its pHi-dependent interaction with methylated nucleosomes.
Highlights
Post-translational modifications of histones play an essential role in the regulation of transcription, DNA repair, replication and heterochromatin formation by changing the chromatin structure
It has been reported that essential Sas2-related acetyltransferase1-associated factor 3 (Eaf3) CD binds weakly to the H3K4me peptide as well as the H3K36me peptide [9,10,14,33]
As described above and in previous studies [9,10,14,33], Eaf3 CD itself has high methylation specificity but low sequence specificity; combinatorial actions with the plant homeodomain (PHD) of Yng2 in NuA4 and with the PHD of Rco1 in Rpd3S are necessary for the overall affinity and specificity of the H3K4me- and H3K36me-nucleosome interaction [12,16], and activation [15,38,39] of the complexes (Figure 7)
Summary
Post-translational modifications of histones play an essential role in the regulation of transcription, DNA repair, replication and heterochromatin formation by changing the chromatin structure. Acetylation loosens the chromatin structure, allowing RNA polymerase II (Pol II) to access the promoter; in transcribing regions, by contrast, de-acetylation tightens the chromatin structure, meaning that Pol II can read the gene information but cannot access the gene to start transcription from a cryptic site. Similar to these patterns of acetylation, lysine 4 of histone H3 (H3K4) is methylated by Set methyltransferase at promoter sites, whereas Set methyltransferase mediates H3K36 methylation in coding regions [5].
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