1. CAME: identification of chromatin accessibility from nucleosome occupancy and methylome sequencing
- Author
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Seong Keon Lee, Huidong Shi, Keith D. Robertson, Eun Joon Lee, Keun Ho Ryu, Yongjun Piao, and Jeong Hyeon Choi
- Subjects
0301 basic medicine ,Statistics and Probability ,Computational biology ,Biology ,Biochemistry ,DNA sequencing ,Epigenesis, Genetic ,03 medical and health sciences ,Databases, Genetic ,Humans ,Nucleosome ,Computer Simulation ,Epigenetics ,Molecular Biology ,Transcription factor ,Regulation of gene expression ,Base Sequence ,Sequence Analysis, DNA ,DNA Methylation ,Reference Standards ,HCT116 Cells ,Original Papers ,Nucleosomes ,Computer Science Applications ,Chromatin ,Computational Mathematics ,030104 developmental biology ,ROC Curve ,Computational Theory and Mathematics ,CpG site ,Colonic Neoplasms ,DNA methylation ,Nucleic Acid Conformation ,CpG Islands ,Algorithms ,Software - Abstract
Motivation 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. Results 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. Availability and Implementation CAME is implemented in java and the program is freely available online at http://sourceforge.net/projects/came/ Supplementary information Supplementary data are available at Bioinformatics online.
- Published
- 2016