Structural identification, quantitation, and mapping of DNA epigenetic marks are
critical for our understanding of epigenetic control in healthy cells and to allow for
insight into epigenetic deregulation in human disease and the efficacy of epigenetic
therapies. This review focuses on experimental techniques and methodologies that
can be used to study epigenetic modifications of DNA, including methods for
quantifying global levels of epigenetically modified nucleosides and sequencing
techniques for mapping the locations of various epigenetic marks along the genome,
leading to better understanding of their biological functions and dynamics.
Keywords Direct detection, Epigenetics, Mass spectrometry, Microarray,
Quantitation, Sequencing
Abbreviations
2D-LC
Two-dimensional HPLC
4mC
N
4 -methyl-2
0 -deoxyadenosine
5caC
5-Carboxylcytosine
5fC
5-Formylcytosine
5hmC
5-Hydroxymethylcytosine
5mC
5-Methylcytosine
6mA-RE-Seq
N6MedA restriction enzyme sequencing
anti-CMS-Seq Anti-cytosine-5-methylenesulfonate sequencing
ARP
Aldehyde reactive probe
caMAB-Seq
Carboxylcytosine modification-assisted bisulfite sequencing
CGIs
CpG islands
CMS
Cytosine-5-methylenesulfonate
DNMT
DNA methyltransferase
ELISA
Enzyme-linked immunosorbent assay
ESI
Electrospray ionization
fCAB-Seq
Formylcytosine chemical-assisted bisulfite sequencing
GLIB-Seq
Glucosylation, periodate oxidation, biotinylation sequencing
hMeSeal-Seq
Hydroxymethyl selective chemical labeling sequencing
HPLC
High-performance liquid chromatography
IP
Immunoprecipitation
LOD
Limit of detection
LOQ
Limit of quantitation
MAB-Seq
Modification-assisted bisulfite sequencing
MeDIP
Methylated DNA immunoprecipitation
MS
Mass spectrometry
MS/MS
Tandem mass spectrometry
MSO
Methylation-specific oligonucleotide
N6MedA
N
6 -methyl-2
0 -deoxyadenosine
488
C. L. Seiler et al.