Predicting nucleosome binding motif set and analyzing their distributions around functional sites of human genes.

Nucleosome positioning and remodeling correlate closely with the DNA sequence bias. It is possible that DNA motifs, interacted preferentially with histone octamers, direct the nucleosome positioning. Exploring the complete set of nucleosome binding motifs is of crucial importance for our understanding of the roles of nucleosomes in gene regulation. Based on the 8-mer multimodal spectra of the human genome, a systematic nucleosome binding motif set is inferred. Its structural features and density distributions for different types of sequences are consistent with the published data. Distributions of these motifs around several functional sites could describe the ground state of nucleosome distribution of these regions. Our results strongly support that the predicted nucleosome binding motif set is reliable. Our findings indicate that the recognition of distinct functional sites or sequences could be greatly improved by the help of a nucleosome array.