MEASURING THE EPIGENOME
Clearly, changes to the epigenome play a fundamental role in the development, baseline regulation, and experience-
dependent alteration of the nervous system as a whole. However, this invites another question: How can we begin
to understand which epigenetic modifications are important and which modifications we would seek to manipulate
as part of a pharmacoepigenomic strategy? In essence, the answer to this question lies in our ability to link specific
epigenetic modifications to discrete transcriptional outcomes, as defined in the section titled Druggable Epigenome.
Single-nucleotide resolution: The language of the DNA methylome is dominated by modifications that oc-
cur at single cytosine nucleotides. Therefore, it is necessary to measure epigenetic changes with techniques that
capture this resolution. Scientists investigating the epigenome have long used bisulfite sequencing to investigate
modifications at individual cytosine bases in DNA. This approach has proved to be useful for interrogating the
methylation status of individual cytosine bases in DNA (32, 34, 36). Although bisulfite sequencing was once limited
by the fact that both mC and hmC are preserved during bisulfite treatment (44), recent methodologies have built
upon this approach to enable separate hydroxymethylation and methylation characterization (45, 46). A second,
largely complementary method for estimation of global DNA methylation or hydroxymethylation involves high-
performance liquid chromatography in tandem with mass spectrometry, which allows quantitative measurement of
each modification in comparison to total cytosine (41, 47). However, this technique is limited by its inability to map
cytosine modifications to any specific genomic locus.
MEASURING THE EPIGENOMEClearly, changes to the epigenome play a fundamental role in the development, baseline regulation, and experience-dependent alteration of the nervous system as a whole. However, this invites another question: How can we beginto understand which epigenetic modifications are important and which modifications we would seek to manipulateas part of a pharmacoepigenomic strategy? In essence, the answer to this question lies in our ability to link specificepigenetic modifications to discrete transcriptional outcomes, as defined in the section titled Druggable Epigenome.Single-nucleotide resolution: The language of the DNA methylome is dominated by modifications that oc-cur at single cytosine nucleotides. Therefore, it is necessary to measure epigenetic changes with techniques thatcapture this resolution. Scientists investigating the epigenome have long used bisulfite sequencing to investigatemodifications at individual cytosine bases in DNA. This approach has proved to be useful for interrogating themethylation status of individual cytosine bases in DNA (32, 34, 36). Although bisulfite sequencing was once limitedby the fact that both mC and hmC are preserved during bisulfite treatment (44), recent methodologies have builtupon this approach to enable separate hydroxymethylation and methylation characterization (45, 46). A second,largely complementary method for estimation of global DNA methylation or hydroxymethylation involves high-performance liquid chromatography in tandem with mass spectrometry, which allows quantitative measurement ofeach modification in comparison to total cytosine (41, 47). However, this technique is limited by its inability to mapcytosine modifications to any specific genomic locus.
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