Enriched transcription factor binding sites in hypermethylated gene promoters in drug resistant cancer cells.
BACKGROUND
In the human genome, 'CpG islands', CG-rich regions located in or near gene promoters, are normally unmethylated. However, in cancer cells, CpG islands frequently gain methylation, resulting in silencing of growth-limiting tumor suppressor genes. To our knowledge, the potential relationship between CpG island hypermethylation, transcription factor (TF) binding in local promoter regions and transcriptional control has not been previously explored in a genome-wide context.


RESULTS
In this study, we utilized bioinformatics tools and TF binding site(TFBs) databases to globally analyze sequences methylated in a laboratory model for the development of drug-resistant cancer. Our results demonstrated that four TFBS were enriched in hypermethylated sequences. More interestingly, overrepresentation of these TFBS was observed in hyper-/hypo-methylated sequences where signi.cant changes in methylation levels were observed in drug-resistant cancer cells. In summary, we believe that these.ndings offer a means to further explore the relationship between DNA methylation and gene expression in drug resistance and tumorigenesis.
Li
Meng
M
Medical Sciences, School of Medicine, Indiana University, Bloomington, IN 47404, USA.
Paik
Hyun-il Henry
HI
Balch
Curt
C
Kim
Yoosung
Y
Li
Lang
L
Huang
Tim H-M
TH
Nephew
Kenneth P
KP
Kim
Sun
S
D000818:Animals; D001665:Binding Sites; D019175:DNA Methylation; D019008:Drug Resistance, Neoplasm / Q000235:genetics*; D015972:Gene Expression Regulation, Neoplastic / Q000235:genetics*; D006801:Humans; D009369:Neoplasms / Q000188:drug therapy* / Q000235:genetics*; D011401:Promoter Regions, Genetic / Q000235:genetics*; D011485:Protein Binding; D017422:Sequence Analysis, DNA / Q000379:methods*; D014157:Transcription Factors / Q000235:genetics*
D014157:Transcription Factors