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

Judith Recht,Robert L. Diaz,Jeffrey Shabanowitz,C. David Allis,Stephanie A. Morris,Benjamin A. Garcia,Brian D. Strahl,Donald F. Hunt,Monika Kauer,Nilamadhab Mishra,Sandra B. Hake

doi:10.1074/jbc.m607900200

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.

Highlights

Cellular identity is defined by the characteristic patterns of gene expression and silencing
We sought to examine the extent to which the histone code is universal, focusing on H3 and H4 from a limited, but select, number of popular organisms as an entry point for our studies. Using both mass spectrometry (MS) and immunobiochemical approaches, we show that the post-translational modifications (PTMs) profile of histone H3 greatly differs among species and that the PTM pattern is more complex in mammals as compared with “simple” eukaryotes, such as Saccharomyces cerevisiae and Tetrahymena thermophila (Tet)
Summed mass spectra that record the ion abundances for [M ϩ 2H]2ϩ ions corresponding to residues 3– 8 of H3 from human, mouse, Tet, and yeast are presented in Fig. 1, As indicated in Fig. 1 (A–D), respectively

Summary

Histone Modification Differences among Organisms

Histone PTMs occur on multiple but specific sites, suggesting that histone PTMs can act as signaling platforms for proteins that “read” these marks [10]. We sought to examine the extent to which the histone code is universal, focusing on H3 and H4 from a limited, but select, number of popular organisms as an entry point for our studies Using both mass spectrometry (MS) and immunobiochemical approaches, we show that the PTM profile of histone H3 greatly differs among species and that the PTM pattern is more complex in mammals as compared with “simple” eukaryotes, such as Saccharomyces cerevisiae (yeast) and Tetrahymena thermophila (Tet). Our data reveal a diverse pattern of modification usage on histone H3 that is fundamentally different among unicellular organisms and mammals We suggest that these differences may be due to the co-development of additional histone-modifying enzymes and histone H3 variants, allowing for additional regulation of more complex genomes

EXPERIMENTAL PROCEDURES

RESULTS

Acetyl ϩ dimethyl

Comparison of PTMs on Histone

NDb ϩc ϩc ϩ

DISCUSSION