A simple algorithm for quantifying DNA methylation levels on multiple independent CpG sites in bisulfite genomic sequencing electropherograms.
DNA methylation at cytosines is a widely studied epigenetic modification. Methylation is commonly detected using bisulfite modification of DNA followed by PCR and additional techniques such as restriction digestion or sequencing. These additional techniques are either laborious, require specialized equipment, or are not quantitative. Here we describe a simple algorithm that yields quantitative results from analysis of conventional four-dye-trace sequencing. We call this method Mquant and we compare it with the established laboratory method of combined bisulfite restriction assay (COBRA). This analysis of sequencing electropherograms provides a simple, easily applied method to quantify DNA methylation at specific CpG sites.
Leakey
Tatiana I
TI
Department of Biochemistry and Molecular Biology, The University of Arkansas for Medical Sciences, Central Arkansas Veterans Health Care Systems, Little Rock AR, USA.
Zielinski
Jerzy
J
Siegfried
Rachel N
RN
Siegel
Eric R
ER
Fan
Chun-Yang
CY
Cooney
Craig A
CA
D000465:Algorithms; D000818:Animals; D018899:CpG Islands; D019175:DNA Methylation; D004587:Electrophoresis, Agar Gel; D005456:Fluorescent Dyes; D023281:Genomics / Q000379:methods*; D051379:Mice; D016133:Polymerase Chain Reaction; D013447:Sulfites / Q000737:chemistry*; D013941:Thymine / Q000032:analysis
D005456:Fluorescent Dyes; D013447:Sulfites; C042345:hydrogen sulfite; D013941:Thymine