DNA and histone modifications direct the functional state of chromatin and 
thereby the readout of the genome. Candidate approaches and histone peptide 
affinity purification experiments have identified several proteins that bind to 
chromatin marks. However, the complement of factors that is recruited by 
individual and combinations of DNA and histone modifications has not yet been 
defined. Here, we present a strategy based on recombinant, uniformly modified 
chromatin templates used in affinity purification experiments in conjunction 
with SILAC-based quantitative mass spectrometry for this purpose. On the 
prototypic H3K4me3 and H3K9me3 histone modification marks we compare our method 
with a histone N-terminal peptide affinity purification approach. Our analysis 
shows that only some factors associate with both, chromatin and peptide matrices 
but that a surprisingly large number of proteins differ in their association 
with these templates. Global analysis of the proteins identified implies 
specific domains mediating recruitment to the chromatin marks. Our 
proof-of-principle studies show that chromatin templates with defined 
modification patterns can be used to decipher how the histone code is read and 
translated.