Online resources for studies of genome biology and epigenetics

Paul J. Lee, Mayank NK Choudhary, Ting Wang

Research output: Contribution to journalReview articlepeer-review

Abstract

Environmental exposure to chemical toxins alters epigenetic modifications that culminate in altered cellular gene expression without changing the underlying DNA sequence. The complex interplay between the layers of epigenetic regulators ultimately results in observed cellular phenotype. This review highlights epigenetics annotations assayed in the Encyclopedia of DNA Elements (ENCODE) community resource project—a publically accessible database for understanding genomic function, development and disease etiologies. We outline the multiple levels of epigenetic control (DNA methylation, chromatin accessibility, histone modifications, genome topology) with their associated interrogation methodology. We explore the limitations and strengths of each methodology at every epigenetic checkpoint. This review points readers to epigenetic resources that have gathered focused scientific data and directs them toward data visualization tools that can help answer questions related to epigenetic controls. The purpose of this review is to highlight online resources available to toxicological epigenetic researchers that can help fast track novel insights using already curated reference epigenome datasets.

Original languageEnglish
Pages (from-to)34-41
Number of pages8
JournalCurrent Opinion in Toxicology
Volume6
DOIs
StatePublished - Oct 2017

Keywords

  • 3D genome
  • Chromatin accessibility
  • ENCODE
  • Epigenome
  • Histone modifications
  • Methylation
  • Methylome
  • Next generation sequencing
  • Online database
  • ROADMAP
  • TADs

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