dissecting nucleosome free regions by a segmental semi-markov model解剖核小体自由区域由一个节段半马尔科夫模型.pdfVIP

Dissecting Nucleosome Free Regions by a Segmental Semi-Markov Model 1,2. 3,4. 3 3 4,5 Wei Sun , Wei Xie , Feng Xu , Michael Grunstein *, Ker-Chau Li * 1 Department of Biostatistics, Carolina Center for Genome Science, University of North Carolina, Chapel Hill, North Carolina, United States of America, 2 Department of Genetics, Carolina Center for Genome Science, University of North Carolina, Chapel Hill, North Carolina, United States of America, 3 Department of Biological Chemistry, University of California Los Angeles, Los Angeles, California, United States of America, 4 Department of Statistics, University of California Los Angeles, Los Angeles, California, United States of America, 5 Institute of Statistical Science, Genomics Research Center, Academia Sinica, Taipei, Taiwan Abstract Background: Nucleosome free regions (NFRs) play important roles in diverse biological processes including gene regulation. A genome-wide quantitative portrait of each individual NFR, with their starting and ending positions, lengths, and degrees of nucleosome depletion is critical for revealing the heterogeneity of gene regulation and chromatin organization. By averaging nucleosome occupancy levels, previous studies have identified the presence of NFRs in the promoter regions across many genes. However, evaluation of the quantitative characteristics of individual NFRs requires an NFR calling method. Methodology: In this study, we propose a statistical method to identify the patterns of NFRs from a genome-wide measurement of nucleosome occupancy. This method is based on an appropriately designed segmental semi-Markov model, which can capture each NFR pattern and output its quantitative characterizations. Our results