Introduction

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.

Publications

  1. CAME: identification of chromatin accessibility from nucleosome occupancy and methylome sequencing.
    Cite this
    Piao Y, Lee SK, Lee EJ, Robertson KD, Shi H, Ryu KH, Choi JH, 2017-04-01 - Bioinformatics (Oxford, England)

Credits

  1. Yongjun Piao
    Developer

    College of Electrical and Computer Engineering, Chungbuk National University

  2. Seong Keon Lee
    Developer

    Department of Statistics, Sungshin Women's University

  3. Eun-Joon Lee
    Developer

    Cancer Center, Georgia Regents University, United States of America

  4. Keith D Robertson
    Developer

    Department of Molecular Pharmacology and Experimental Therapeutics, Center for Individualized Medicine, United States of America

  5. Huidong Shi
    Developer

  6. Keun Ho Ryu
    Developer

    College of Electrical and Computer Engineering, Chungbuk National University

  7. Jeong-Hyeon Choi
    Investigator

    Department of Applied Research, Marine Biodiversity Institute of Korea

Community Ratings

UsabilityEfficiencyReliabilityRated By
0 user
Sign in to rate
Summary
AccessionBT006710
Tool TypeApplication
Category
PlatformsLinux/Unix
Technologies
User InterfaceTerminal Command Line
Download Count0
Submitted ByJeong-Hyeon Choi