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By applying novel chromatin alignment and global word search approaches, we have defined distinctive chromatin motifs for introns, origins of replication, tRNAs, antisense transcripts, double-strand-break hotspots and DNase hypersensitive sites, and can distinguish genes by expression level. We have also uncovered strong associations between transcription factor binding and specific types of nucleosomes. Our results demonstrate the uses and functionality of defining a chromatin alphabet and provide a unique and novel framework for exploring chromatin architecture.<\/jats:p>\n               <jats:p>Contact:\u2003mjbuck@buffalo.edu<\/jats:p>\n               <jats:p>Supplementary Information:\u2003Supplementary data are available at Bioinformatics online.<\/jats:p>","DOI":"10.1093\/bioinformatics\/btt382","type":"journal-article","created":{"date-parts":[[2013,7,3]],"date-time":"2013-07-03T04:27:49Z","timestamp":1372825669000},"page":"2231-2237","source":"Crossref","is-referenced-by-count":8,"title":["An integrative approach to understanding the combinatorial histone code at functional elements"],"prefix":"10.1093","volume":"29","author":[{"given":"William K. 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