Identification of genes with consistent methylation levels across different human tissues
Journal
Scientific Reports
Journal Volume
4
Date Issued
2014
Author(s)
Abstract
DNA methylation plays an important role in regulating cell growth and disease development. Methylation profiles are examined by bisulfite conversion; however, the lack of markers for bisulfite conversion efficiency and appropriate internal control genes remains a major challenge. To address these issues, we utilized two bioinformatics approaches, coefficients of variances and resampling tests, to identify probes showing stable methylation levels from several independent microarray datasets. Mass spectrometry validated the consistently high methylation levels of the five probes (N4BP2, EGFL8, CTRB1, TSPAN3, and ZNF690) in 13 human tissue types from 24 cell lines. Linear associations between detected methylation levels and methyl concentrations of DNA samples were further demonstrated in three genes (N4BP2, EGFL8, and CTRB1). To summarize, we identified five genes which may serve as internal controls for methylation studies by analyzing large-scale microarray data, and three of them can be used as markers for evaluating the efficiency of bisulfite conversion.
Other Subjects
apoptosis regulatory protein; BCL 3 binding protein, human; BCL-3-binding protein, human; biological marker; carrier protein; chymotrypsin; chymotrypsin b; EGFL8 protein, human; endothelial cell growth factor; tetraspanin; article; biology; DNA methylation; DNA microarray; genetics; human; mass spectrometry; metabolism; protein processing; standard; Apoptosis Regulatory Proteins; Biological Markers; Carrier Proteins; Chymotrypsin; Computational Biology; DNA Methylation; Endothelial Growth Factors; Humans; Mass Spectrometry; Oligonucleotide Array Sequence Analysis; Protein Processing, Post-Translational; Reference Standards; Tetraspanins
Publisher
Nature Publishing Groups
Type
journal article