Computational Approaches in Next-Generation Sequencing Data Analysis for Genome-Wide DNA Methylation Studies

Jeong Hyeon Choi, Huidong Shi

Research output: Chapter in Book/Report/Conference proceedingChapter


DNA methylation is one of the most important epigenetic mechanisms that ensures the maintenance and inheritance of gene-expression programs in mammalian cells. Three highly conserved DNA methyltransferase (DNMT) proteins (DNMT1, DNMT3A, and DNMT3B), which complex together in vivo, establish and maintain the DNA methylation landscape within the human genome. These novel next-generation sequencing (NGS) platforms also have many other advantages over the current platforms such as less bias during template preparation, possible longer read length, lower cost, higher speed, and better accuracy. The chapter presents the enrichment-based sequencing and bisulfite treatment-based approaches have successfully profiled DNA methylation and identified genome-wide differential methylation. The DMRs are segregated based on the location to a gene: promoter, downstream, body, exon, or intron. They are also intergrated into epigenomic marks for histone modification, transcription factors, chromatin structure, and nucleosome positioning in ENCODE, epigenome ATLS, and TCGA by overlapping or distance using BEDTools or FeatureCount.

Original languageEnglish (US)
Title of host publicationComputational Methods for Next Generation Sequencing Data Analysis
Number of pages30
ISBN (Electronic)9781119272182
ISBN (Print)9781118169483
StatePublished - Sep 6 2016


  • Bisulfite treatment-based approaches
  • Computational approaches
  • DNA methyltransferase
  • Enrichment-based sequencing
  • Gene-expression programs
  • Genome-wide DNA methylation studies
  • Next-generation sequencing data analysis

ASJC Scopus subject areas

  • Computer Science(all)


Dive into the research topics of 'Computational Approaches in Next-Generation Sequencing Data Analysis for Genome-Wide DNA Methylation Studies'. Together they form a unique fingerprint.

Cite this