Combinatorial patterns of histone modifications in Saccharomyces cerevisiae.

Histone modification is an important subject of epigenetics that plays an intrinsic role in transcriptional regulation. It has been suggested that multiple histone modifications act in a combinatorial fashion to form a 'histone code'. In this study, the combinatorial patterns of histone modifications were studied by using a Bayesian network at the level of individual nucleosomes in S. cerevisiae. Our results indicated that there were 23 combinatorial patterns for 12 histone modifications investigated when a general Bayesian network was constructed. Meanwhile, different networks were also constructed for the genes with high transcript levels (H-network) and low transcript levels (L-network), respectively. Comparison among the general network, H-network and L-network illustrated four conserved combinations: H2BK16Ac → H3K4me3; H3K14Ac → H3K4me3; H2AK7Ac → H3K14Ac; and H4K12Ac → H3K18Ac. The detailed analysis for some combinations demonstrated that the combinations were ascribed to some histone-modifying enzymes.