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Reduced Representation Bisulfite Sequencing (RRBS) and Cell Sorting Prior to DNA Methylation Analysis in Psychiatric Disorders

  • Wilfred C. de Vega
  • Atif Hussain
  • Patrick O. McGowanEmail author
Protocol
Part of the Methods in Pharmacology and Toxicology book series (MIPT)

Abstract

Gene-environment interactions play a major role in psychiatric disorder onset and manifestation. Environmental factors can influence gene expression in the absence of gene sequence alterations through epigenetic modifications such as DNA methylation at cytosine–guanine (CpG) dinucleotides. Due to decreasing costs associated with genomic sequencing, it is becoming more common to screen the DNA methylome to obtain comprehensive information regarding epigenetic modifications associated with phenotypes of interest. However, whole DNA methylome screening remains cost prohibitive and requires an intensive computational analysis. An economical alternative to screening the DNA methylome is Reduced Representation Bisulfite Sequencing (RRBS), which can be used to examine DNA methylation in CpG-dense regions at single-nucleotide resolution, thereby targeting gene regulatory elements. In this chapter, we detail the RRBS protocol, compare it to other techniques for DNA methylation sequencing, and outline its use in psychiatric genomics. We also describe Fluorescence-Activated Cell Sorting (FACS) and computational techniques that can be used to reduce variation associated with mixed cell populations in clinical samples, a potential confounding factor in epigenomics research.

Key words

Psychiatric disorders Epigenetics Epigenomics DNA methylation DNA methylome Reduced representation bisulfite sequencing Fluorescence-activated cell sorting Bioinformatics 

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Copyright information

© Springer Science+Business Media LLC 2017

Authors and Affiliations

  • Wilfred C. de Vega
    • 1
    • 2
  • Atif Hussain
    • 1
  • Patrick O. McGowan
    • 1
    • 2
    • 3
    • 4
    Email author
  1. 1.Department of Biological SciencesCentre for Environmental Epigenetics and Development, University of Toronto ScarboroughTorontoCanada
  2. 2.Department of Cell and Systems BiologyUniversity of TorontoTorontoCanada
  3. 3.Department of PsychologyUniversity of TorontoTorontoCanada
  4. 4.Department of PhysiologyUniversity of TorontoTorontoCanada

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