NUCLEOSOME DISTRIBUTION AROUND TRANSCRIPTION FACTOR BINDING SITES ENRICHED FROM GENOME-WIDE CHIP-SEQ

The combination of chromatin immunoprecipitation with high throughput sequencing (ChIP-Seq) has been widely applied in genome-wide studies of transcription factor binding sites and epigenome which includes DNA methylation, post-translation histone modification and dynamic nucleosome positioning. They are all associated with transcription machinery. For a transcription factor, a ChIP-Seq experiment can generate thousands of enriched sites. However, it is impossible to validate each transcription factor binding sites by experiment. Similar to motif analysis, exploration nucleosome distribution through DNA sequences around these TFBSs could be a good indicator of true TFBS. Feature of Nucleosome positioning sequences can partially predict nucleosome positioning along the genome. In this work, we checked the experimental and the predicted nucleosomal distribution in NRSF enriched regions and found canonical TF motif could be both located at nucleosome locus and nucleosome free region. We proposed a nucleosome-positioned TSS method to evaluate the transcriptional relevance of an enriched region which is not located near a promoter.