Combinatorial effects of epigenetic modifications on transcription activity have 
been proposed as "histone codes". However, it is unclear whether there also 
exist inter-nucleosomal communications among epigenetic modifications at single 
nucleosome level, and if so, what functional roles they play. Meanwhile, how 
clear nucleosome patterns, such as nucleosome phasing and depletion, are formed 
at functional regions remains an intriguing enigma. To address these questions, 
we developed a Bayesian network model for interactions among different histone 
modifications across neighboring nucleosomes, based on the framework of dynamic 
Bayesian network (DBN). From this model, we found that robust inter-nucleosomal 
interactions exist around transcription start site (TSS), transcription 
termination sites (TTS) or around CTCF binding sites; and these 
inter-nucleosomal interactions are often involved in transcription regulation. 
In addition to these general principles, DBN also uncovered a novel specific 
epigenetic interaction between H2A.Z and H4K20me1 on neighboring nucleosomes, 
involved in nucleosome free region (NFR) and nucleosome phasing establishment or 
maintenance. The level of negative correlation between neighboring H2A.Z and 
H4K20me1 strongly correlate with the size of NFR and the strength of nucleosome 
phasing around TSS. Our study revealed inter-nucleosomal communications as 
important players in signal propagation, chromatin remodeling and transcription 
regulation.