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

Yongjun Piao, Seong Keon Lee, Eun Joon Lee, Keith D Robertson, Huidong Shi, Keun Ho Ryu, Jeong Hyeon Choi

Research output: Contribution to journalArticle

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.

Original languageEnglish (US)
Pages (from-to)1139-1146
Number of pages8
JournalBioinformatics
Volume33
Issue number8
DOIs
StatePublished - Apr 15 2017

Fingerprint

Methylation
Nucleosomes
Chromatin
Accessibility
Sequencing
Genes
Transcription factors
Computational methods
Gene expression
Machinery
Seed
Chemical activation
Methyltransferases
Molecules
Template
Genome
Nucleic Acid Regulatory Sequences
Gene Silencing
DNA Methylation
Transcription Factor

ASJC Scopus subject areas

  • Statistics and Probability
  • Biochemistry
  • Molecular Biology
  • Computer Science Applications
  • Computational Theory and Mathematics
  • Computational Mathematics

Cite this

CAME : Identification of chromatin accessibility from nucleosome occupancy and methylome sequencing. / Piao, Yongjun; Lee, Seong Keon; Lee, Eun Joon; Robertson, Keith D; Shi, Huidong; Ryu, Keun Ho; Choi, Jeong Hyeon.

In: Bioinformatics, Vol. 33, No. 8, 15.04.2017, p. 1139-1146.

Research output: Contribution to journalArticle

Piao, Yongjun ; Lee, Seong Keon ; Lee, Eun Joon ; Robertson, Keith D ; Shi, Huidong ; Ryu, Keun Ho ; Choi, Jeong Hyeon. / CAME : Identification of chromatin accessibility from nucleosome occupancy and methylome sequencing. In: Bioinformatics. 2017 ; Vol. 33, No. 8. pp. 1139-1146.
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