Identification of combinatorial patterns of post-translational modifications on individual histones in the mouse brain.

Ry Y Tweedie-Cullen,Christian Panse,David Sichau,Isabelle M Mansuy,Paolo Nanni,Andrea M Brunner,Jonas Grossmann,Safa Mohanna,Axel Imhof

doi:10.1371/journal.pone.0036980

Ry Y Tweedie-Cullen, Christian Panse + Show 7 more

Open Access

https://doi.org/10.1371/journal.pone.0036980

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Journal: PloS one	Publication Date: May 31, 2012
Citations: 191	License type: CC BY 4.0

Affiliation: University of Zurich, ETH Zurich

Abstract

Post-translational modifications (PTMs) of proteins are biochemical processes required for cellular functions and signalling that occur in every sub-cellular compartment. Multiple protein PTMs exist, and are established by specific enzymes that can act in basal conditions and upon cellular activity. In the nucleus, histone proteins are subjected to numerous PTMs that together form a histone code that contributes to regulate transcriptional activity and gene expression. Despite their importance however, histone PTMs have remained poorly characterised in most tissues, in particular the brain where they are thought to be required for complex functions such as learning and memory formation. Here, we report the comprehensive identification of histone PTMs, of their combinatorial patterns, and of the rules that govern these patterns in the adult mouse brain. Based on liquid chromatography, electron transfer, and collision-induced dissociation mass spectrometry, we generated a dataset containing a total of 10,646 peptides from H1, H2A, H2B, H3, H4, and variants in the adult brain. 1475 of these peptides carried one or more PTMs, including 141 unique sites and a total of 58 novel sites not described before. We observed that these PTMs are not only classical modifications such as serine/threonine (Ser/Thr) phosphorylation, lysine (Lys) acetylation, and Lys/arginine (Arg) methylation, but also include several atypical modifications such as Ser/Thr acetylation, and Lys butyrylation, crotonylation, and propionylation. Using synthetic peptides, we validated the presence of these atypical novel PTMs in the mouse brain. The application of data-mining algorithms further revealed that histone PTMs occur in specific combinations with different ratios. Overall, the present data newly identify a specific histone code in the mouse brain and reveal its level of complexity, suggesting its potential relevance for higher-order brain functions.

Highlights

The acquisition and storage of information in memory require specific long-lasting changes in gene expression
Using a ‘bottom-up’ approach, we recently generated a map of post-translational modifications (PTMs) that exist on histone proteins in the adult mouse brain [2]
electron transfer dissociation (ETD) was used on a hybrid LTQ-Orbitrap-XL machine, which records the mass of each eluting peptide with high accuracy, and makes the assignment of overall PTM states possible

Summary

Introduction

The acquisition and storage of information in memory require specific long-lasting changes in gene expression. These changes have been proposed to depend upon chromatin remodelling, and on site-specific and dynamic post-translational modifications (PTMs) of histone proteins in brain cells. Nucleosomes are separated from each other by a short stretch of internucleosomal DNA bound to the linker histone H1. All core histones, their variants and linker H1 are known to be subjected to PTMs [2], which are covalent modifications that can occur on selective amino acids and that can be induced and erased by complexes of chromatin-modifying enzymes.

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