An Sp1/Sp3 binding polymorphism confers methylation protection

Authors

Yanis A. Boumber, Department of Leukemia, M. D. Anderson Cancer Center, University of Texas, Houston, Texas, United States of America; Program in Cancer Biology, Graduate School of Biomedical Sciences, University of Texas, Houston, Texas, United States of America
Yutaka Kondo, Department of Leukemia, M. D. Anderson Cancer Center, University of Texas, Houston, Texas, United States of America
Xuqi Chen, Department of Leukemia, M. D. Anderson Cancer Center, University of Texas, Houston, Texas, United States of America
Lanlan Shen, Department of Leukemia, M. D. Anderson Cancer Center, University of Texas, Houston, Texas, United States of America
Yi Guo, Department of Leukemia, M. D. Anderson Cancer Center, University of Texas, Houston, Texas, United States of America
Carmen Tellez, Department of Leukemia, M. D. Anderson Cancer Center, University of Texas, Houston, Texas, United States of America
Marcos R H Estécio, Department of Leukemia, M. D. Anderson Cancer Center, University of Texas, Houston, Texas, United States of America
Saira Ahmed, Department of Leukemia, M. D. Anderson Cancer Center, University of Texas, Houston, Texas, United States of America
Jean-Pierre J. Issa, Department of Leukemia, M. D. Anderson Cancer Center, University of Texas, Houston, Texas, United States of America; Program in Cancer Biology, Graduate School of Biomedical Sciences, University of Texas, Houston, Texas, United States of America

Publication Date

8-22-2008

Journal

PLoS Genetics

Abstract

Hundreds of genes show aberrant DNA hypermethylation in cancer, yet little is known about the causes of this hypermethylation. We identified RIL as a frequent methylation target in cancer. In search for factors that influence RIL hypermethylation, we found a 12-bp polymorphic sequence around its transcription start site that creates a long allele. Pyrosequencing of homozygous tumors revealed a 2.1-fold higher methylation for the short alleles (P<0.001). Bisulfite sequencing of cancers heterozygous for RIL showed that the short alleles are 3.1-fold more methylated than the long (P<0.001). The comparison of expression levels between unmethylated long and short EBV-transformed cell lines showed no difference in expression in vivo. Electrophorectic mobility shift assay showed that the inserted region of the long allele binds Sp1 and Sp3 transcription factors, a binding that is absent in the short allele. Transient transfection of RIL allele-specific transgenes showed no effects of the additional Sp1 site on transcription early on. However, stable transfection of methylation-seeded constructs showed gradually decreasing transcription levels from the short allele with eventual spreading of de novo methylation. In contrast, the long allele showed stable levels of expression over time as measured by luciferase and approximately 2-3-fold lower levels of methylation by bisulfite sequencing (P<0.001), suggesting that the polymorphic Sp1 site protects against time-dependent silencing. Our finding demonstrates that, in some genes, hypermethylation in cancer is dictated by protein-DNA interactions at the promoters and provides a novel mechanism by which genetic polymorphisms can influence an epigenetic state.

Keywords

Animals, Base Sequence, Binding Sites, Cell Line, Transformed, Colonic Neoplasms, DNA Methylation, DNA-Binding Proteins, Humans, Leukemia, Mice, NIH 3T3 Cells, Polymorphism, Genetic, Promoter Regions, Genetic, Rats, Sp1 Transcription Factor, Sp3 Transcription Factor, Transcription Initiation Site

Comments

PMC2515197

Link to article in PLoS