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Review
. 2013 May;12(3):205-18.
doi: 10.1093/bfgp/elt002. Epub 2013 Feb 11.

Proteomics in epigenetics: new perspectives for cancer research

Till Bartke  1 , Julie Borgel, Peter A DiMaggio
Affiliations
Review

Proteomics in epigenetics: new perspectives for cancer research

Till Bartke et al. Brief Funct Genomics. 2013 May.

Abstract

The involvement of epigenetic processes in the origin and progression of cancer is now widely appreciated. Consequently, targeting the enzymatic machinery that controls the epigenetic regulation of the genome has emerged as an attractive new strategy for therapeutic intervention. The development of epigenetic drugs requires a detailed knowledge of the processes that govern chromatin regulation. Over the recent years, mass spectrometry (MS) has become an indispensable tool in epigenetics research. In this review, we will give an overview of the applications of MS-based proteomics in studying various aspects of chromatin biology. We will focus on the use of MS in the discovery and mapping of histone modifications and how novel proteomic approaches are being utilized to identify and study chromatin-associated proteins and multi-subunit complexes. Finally, we will discuss the application of proteomic methods in the diagnosis and prognosis of cancer based on epigenetic biomarkers and comment on their future impact on cancer epigenetics.

Keywords: Mass spectrometry; cancer epigenetics; chromatin; epigenetic readers; histone modifications; quantitative proteomics.

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Figures

Figure 1:
Figure 1:
Overview of MS-based proteomics workflows. Proteins can be labeled with heavy amino acids (heavy) or remain unlabeled (light) by growing cells in appropriate tissue culture media. Isolated proteins are digested into peptides which are then separated by high-performance liquid chromatography (HPLC) and electro-sprayed into the mass spectrometer. The masses of peptides are recorded in a full scan (MS1). Selected peptides are isolated and fragmented and masses determined in a MS/MS spectrum (MS2). The masses of the precursor ions and fragments are used in database searches in order to identify peptide sequences and PTMs that can be assigned to proteins.
Figure 2:
Figure 2:
Strategies for the enrichment of chromatin-bound proteins. Chromatin-bound proteins can be isolated by purifying whole chromosomes, preparing chromatin-enriched fractions or by immuno-affinity purifying specific target proteins using antibodies against DNA- or histone-binding proteins, histone variants or histone PTMs. Specific DNA domains can be isolated via hybridization with specific DNA probes.
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