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Genomics Inform > Volume 16(4); 2018 > Article
DOI: https://doi.org/10.5808/GI.2018.16.4.e27    Published online December 28, 2018.
A Short Report on the Markov Property of DNA Sequences on 200-bp Genomic Units of Roadmap Genomics ChromHMM Annotations: A Computational Perspective
Hyun-Seok Park1,2 
1Bioinformatics Laboratory, ELTEC College of Engineering, Ewha Womans University, Seoul 03760, Korea
2Center for Convergence Research of Advanced Technologies, Ewha Womans University, Seoul 03760, Korea
Corresponding author:  Hyun-Seok Park
Tel: +82-2-3277-3513   Fax: +82-2-3277-2306   Email: neo@ewha.ac.kr
Received: November 26, 2018   Accepted: December 13, 2018
Abstract
The non-coding DNA in eukaryotic genomes encodes a language that programs chromatin accessibility, transcription factor binding, and various other activities. The objective of this study was to determine the effect of the primary DNA sequence on the epigenomic landscape across a 200-base pair of genomic units by integrating 127 publicly available ChromHMM BED files from the Roadmap Genomics project. Nucleotide frequency profiles of 127 chromatin annotations stratified by chromatin variability were analyzed and integrative hidden Markov models were built to detect Markov properties of chromatin regions. Our aim was to identify the relationship between DNA sequence units and their chromatin variability based on integrated ChromHMM datasets of different cell and tissue types.
Keywords: chromatin maps, computational epigenetics, Markov chain, noncoding DNA, nucleotide frequency patterns


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