Organismal Differences in Post-translational Modifications in Histones H3 and H4

Abstract

Post-translational modifications (PTMs) of histones play an important role in many cellular processes, notably gene regulation. Using a combination of mass spectrometric and immunobiochemical approaches, we show that the PTM profile of histone H3 differs significantly among the various model organisms examined. Unicellular eukaryotes, such as Saccharomyces cerevisiae (yeast) and Tetrahymena thermophila (Tet), for example, contain more activation than silencing marks as compared with mammalian cells (mouse and human), which are generally enriched in PTMs more often associated with gene silencing. Close examination reveals that many of the better-known modified lysines (Lys) can be either methylated or acetylated and that the overall modification patterns become more complex from unicellular eukaryotes to mammals. Additionally, novel species-specific H3 PTMs from wild-type asynchronously grown cells are also detected by mass spectrometry. Our results suggest that some PTMs are more conserved than previously thought, including H3K9me1 and H4K20me2 in yeast and H3K27me1, -me2, and -me3 in Tet. On histone H4, methylation at Lys-20 showed a similar pattern as H3 methylation at Lys-9, with mammals containing more methylation than the unicellular organisms. Additionally, modification profiles of H4 acetylation were very similar among the organisms examined.Cellular identity is defined by the characteristic patterns of gene expression and silencing. Inheritance of these transcription patterns through DNA replication and chromatin assembly that accompanies each cell division is crucial for cell survival, but the one or more mechanisms by which this "memory" is achieved are not well understood (reviewed in Ref. 1). A rapidly emerging literature suggests that histone proteins, which function to package genomic DNA into repeating nucleosomal units that are then further folded into higher order chromatin fibers, may be major carriers of epigenetic information (2). Each nucleosome typically contains ϳ146 bp of DNA wrapped around two copies each of histones H3, H4, H2A, and H2B. Although providing a relative constant packaging theme, subtle changes in nucleosome histone:DNA and histone:histone contacts are likely to provide variation in fiber folding that, in turn, translates into biological readout.In general, the packaging of DNA into chromatin is recognized to be a major mechanism by which the access of genomic DNA is restricted. This physical barrier to the underlying DNA is precisely regulated (and counteracted), at least in part, by the post-translational modifications (PTMs) 9 of histones. A wide number of studies has revealed that PTMs of histones, especially those located in the N-terminal tails, play a pivotal role in the regulation of chromatin structure necessary for DNA accessibility during gene expression. Remarkable diversity in the histone/nucleosome structure is generated by a variety of PTMs, such as lysine and arginine methylation, lysine acetylation, serine and threonine phosphorylation, and lysine ubiquitin...

Structural and functional insight into TAF1–TAF7, a subcomplex of transcription factor II D

“…Substitution of evolutionary conserved yTAF1 Phe493, His494, Phe480 residues, and yTAF7 Phe186 with Ala (Fig. 3D) permitted stable yTAF1/7 formation but completely abolished binding to H3K27me3 (19)(20)(21)(22)(23)(24)(25)(26)(27)(28)(29)(30)(31)(32)(33)(34)(35) peptide (Table S2). Other targeted mutations disrupted stable yTAF1/7 complex formation (Table S2).…”

The FACT Spt16 “peptidase” domain is a histone H3–H4 binding module

“…Thus, we tested the specificity of H4 tail peptide interaction by incubating Spt16-N with H4 peptides carrying known posttranslational modifications of yeast H4 (37). Diacetylation of H4 K8/K16, a mark of actively transcribed chromatin, or monomethylation of H4 K20 reduces but does not ablate the binding of H4 peptides to Spt16-N (Fig.…”

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“…Antifungal drug resistance is a major clinical problem, and few drugs are available to battle Candida infections (21). H3K56 acetylation appears to be much less abundant in mammals than in yeasts (22)(23)(24), and close homologs of Rtt109 are not detected outside of the fungal kingdom (25,26). Therefore, we hypothesized that Rtt109 might provide a unique target for antifungal therapeutics, and we began to investigate the importance of H3K56 acetylation in fungal pathogenicity.…”