CAME: identification of chromatin accessibility from nucleosome occupancy and methylome sequencing

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 machin...

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Published in:Bioinformatics (Oxford, England) England), 2017-04, Vol.33 (8), p.1139-1146
Main Authors: Piao, Yongjun, Lee, Seong Keon, Lee, Eun-Joon, Robertson, Keith D, Shi, Huidong, Ryu, Keun Ho, Choi, Jeong-Hyeon
Format: Article
Language:English
Subjects:
Algorithms
Base Sequence
bioinformatics
Colonic Neoplasms - genetics
computational methodology
Computer Simulation
CpG Islands - genetics
Databases, Genetic
DNA methylation
DNA Methylation - genetics
Epigenesis, Genetic
epigenetics
gene activation
gene expression
HCT116 Cells
Humans
methyltransferases
Nucleic Acid Conformation
nucleosomes
Nucleosomes - metabolism
Original Papers
Reference Standards
regulatory sequences
ROC Curve
sequence analysis
Sequence Analysis, DNA - methods
Software
transcription (genetics)
transcription factors
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Summary: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.
ISSN:1367-4803
1460-2059
1367-4811
DOI:10.1093/bioinformatics/btw785