title: CAME: identification of chromatin accessibility from nucleosome occupancy and methylome sequencing.
abstract: Chromatin accessibility plays a key role in epigenetic regulation of gene activation and silencing. Open chromatin regions allow regulatory elements such as transcription factors and polymerases to bind for gene expression while closed chromatin regions prevent the activity of transcriptional machinery. Recently, Methyltransferase Accessibility Protocol for individual templates-Bisulfite Genome Sequencing (MAPit-BGS) and nucleosome occupancy and methylome sequencing (NOMe-seq) have been developed for simultaneously profiling chromatin accessibility and DNA methylation on single molecules. Therefore, there is a great demand in developing computational methods to identify chromatin accessibility from MAPit-BGS and NOMe-seq.
  
  
  
  In this article, we present CAME (Chromatin Accessibility and Methylation), a seed-extension based approach that identifies chromatin accessibility from NOMe-seq. The efficiency and effectiveness of CAME were demonstrated through comparisons with other existing techniques on both simulated and real data, and the results show that our method not only can precisely identify chromatin accessibility but also outperforms other methods.
  
  
  
  CAME is implemented in java and the program is freely available online at http://sourceforge.net/projects/came/.
  
  
  
  jechoi@gru.edu or khryu@dblab.chungbuk.ac.kr.
  
  
  
  Supplementary data are available at Bioinformatics online.
authors.affiliation: Cancer Center, Georgia Regents University, Augusta, GA, USA.|College of Electrical and Computer Engineering, Chungbuk National University, Cheongju, Republic of Korea.
authors.forename: Yongjun
authors.initials: Y
authors.lastname: Piao
authors.affiliation: Department of Statistics, Sungshin Women's University, Seoul, Republic of Korea.
authors.forename: Seong Keon
authors.initials: SK
authors.lastname: Lee
authors.affiliation: Cancer Center, Georgia Regents University, Augusta, GA, USA.
authors.forename: Eun-Joon
authors.initials: EJ
authors.lastname: Lee
authors.affiliation: Department of Molecular Pharmacology and Experimental Therapeutics, Center for Individualized Medicine, Mayo Clinic, Rochester, MN, USA.
authors.forename: Keith D
authors.initials: KD
authors.lastname: Robertson
authors.affiliation: Cancer Center, Georgia Regents University, Augusta, GA, USA.|Department of Biochemistry and Molecular Biology.
authors.forename: Huidong
authors.initials: H
authors.lastname: Shi
authors.affiliation: College of Electrical and Computer Engineering, Chungbuk National University, Cheongju, Republic of Korea.
authors.forename: Keun Ho
authors.initials: KH
authors.lastname: Ryu
authors.affiliation: Cancer Center, Georgia Regents University, Augusta, GA, USA.|Department of Biostatistics and Epidemiology, Georgia Regents University, Augusta, GA, USA.|Department of Applied Research, Marine Biodiversity Institute of Korea, Seocheon, Republic of Korea.
authors.forename: Jeong-Hyeon
authors.initials: JH
authors.lastname: Choi
mesh_terms: D000465:Algorithms; D001483:Base Sequence; D003110:Colonic Neoplasms / Q000235:genetics; D003198:Computer Simulation; D018899:CpG Islands / Q000235:genetics; D019175:DNA Methylation / Q000235:genetics*; D030541:Databases, Genetic; D044127:Epigenesis, Genetic; D045325:HCT116 Cells; D006801:Humans; D009690:Nucleic Acid Conformation; D009707:Nucleosomes / Q000378:metabolism*; D012372:ROC Curve; D012015:Reference Standards; D017422:Sequence Analysis, DNA / Q000379:methods*; D012984:Software
chemical_list: D009707:Nucleosomes