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Determining Epigenetic Targets: A Beginner’s Guide to Identifying Genome Functionality Through Database Analysis

  • Elizabeth A. Hay
  • Philip Cowie
  • Alasdair MacKenzie
Protocol
Part of the Methods in Molecular Biology book series (MIMB, volume 1589)

Abstract

There can now be little doubt that the cis-regulatory genome represents the largest information source within the human genome essential for health. In addition to containing up to five times more information than the coding genome, the cis-regulatory genome also acts as a major reservoir of disease-associated polymorphic variation. The cis-regulatory genome, which is comprised of enhancers, silencers, promoters, and insulators, also acts as a major functional target for epigenetic modification including DNA methylation and chromatin modifications. These epigenetic modifications impact the ability of cis-regulatory sequences to maintain tissue-specific and inducible expression of genes that preserve health. There has been limited ability to identify and characterize the functional components of this huge and largely misunderstood part of the human genome that, for decades, was ignored as “Junk” DNA. In an attempt to address this deficit, the current chapter will first describe methods of identifying and characterizing functional elements of the cis-regulatory genome at a genome-wide level using databases such as ENCODE, the UCSC browser, and NCBI. We will then explore the databases on the UCSC genome browser, which provides access to DNA methylation and chromatin modification datasets. Finally, we will describe how we can superimpose the huge volume of study data contained in the NCBI archives onto that contained within the UCSC browser in order to glean relevant in vivo study data for any locus within the genome. An ability to access and utilize these information sources will become essential to informing the future design of experiments and subsequent determination of the role of epigenetics in health and disease and will form a critical step in our development of personalized medicine.

Keywords:

Cis-regulatory genome Polymorphic variation Epigenetics DNA methylation Chromatin modification Genome databases Bioinformatics 

Notes

Acknowledgements

We would like to thank Dr. Susan Fairley from the University of Aberdeen for providing information about other genome browsers and databases mentioned in Section 3.8. Elizabeth A. Hay is funded by Medical Research Scotland (PhD-719-2013) and GW Pharmaceuticals. Philip Cowie was funded by the Scottish Universities Life Science Alliance (SULCA).

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Copyright information

© Springer Science+Business Media New York 2015

Authors and Affiliations

  • Elizabeth A. Hay
    • 1
  • Philip Cowie
    • 1
  • Alasdair MacKenzie
    • 1
  1. 1.Institute of Medical Sciences, School of Medical SciencesUniversity of AberdeenAberdeenUK

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