title: A co-localization model of paired ChIP-seq data using a large ENCODE data set enables comparison of multiple samples.
abstract: Deep sequencing approaches, such as chromatin immunoprecipitation by sequencing (ChIP-seq), have been successful in detecting transcription factor-binding sites and histone modification in the whole genome. An approach for comparing two different ChIP-seq data would be beneficial for predicting unknown functions of a factor. We propose a model to represent co-localization of two different ChIP-seq data. We showed that a meaningful overlapping signal and a meaningless background signal can be separated by this model. We applied this model to compare ChIP-seq data of RNA polymerase II C-terminal domain (CTD) serine 2 phosphorylation with a large amount of peak-called data, including ChIP-seq and other deep sequencing data in the Encyclopedia of DNA Elements (ENCODE) project, and then extracted factors that were related to RNA polymerase II CTD serine 2 in HeLa cells. We further analyzed RNA polymerase II CTD serine 7 phosphorylation, of which their function is still unclear in HeLa cells. Our results were characterized by the similarity of localization for transcription factor/histone modification in the ENCODE data set, and this suggests that our model is appropriate for understanding ChIP-seq data for factors where their function is unknown.
authors.affiliation: Department of Advanced Initiative Medicine, Faculty of Medicine, Kyushu University, JST-CREST, Fukuoka 812-8582, Japan.
authors.forename: Kazumitsu
authors.initials: K
authors.lastname: Maehara
authors.forename: Jun
authors.initials: J
authors.lastname: Odawara
authors.forename: Akihito
authors.initials: A
authors.lastname: Harada
authors.forename: Tomohiko
authors.initials: T
authors.lastname: Yoshimi
authors.forename: Koji
authors.initials: K
authors.lastname: Nagao
authors.forename: Chikashi
authors.initials: C
authors.lastname: Obuse
authors.forename: Koichi
authors.initials: K
authors.lastname: Akashi
authors.forename: Taro
authors.initials: T
authors.lastname: Tachibana
authors.forename: Toshio
authors.initials: T
authors.lastname: Sakata
authors.forename: Yasuyuki
authors.initials: Y
authors.lastname: Ohkawa
mesh_terms: D047369:Chromatin Immunoprecipitation; D044127:Epigenesis, Genetic; D006367:HeLa Cells; D059014:High-Throughput Nucleotide Sequencing; D006657:Histones / Q000378:metabolism; D006801:Humans; D008957:Models, Genetic; D010766:Phosphorylation; D012319:RNA Polymerase II / Q000378:metabolism; D012694:Serine / Q000378:metabolism; D012984:Software; D024363:Transcription Initiation Site
chemical_list: D006657:Histones; D012694:Serine; D012319:RNA Polymerase II