ABSTRACT
Escape from X inactivation results in expression of genes embedded within inactive chromatin, suggesting the existence of boundary elements between domains. We report that the 5' end of Jarid1c, a mouse escape gene adjacent to an inactivated gene, binds CTCF, displays high levels of histone H3 acetylation, and functions as a CTCF-dependent chromatin insulator. CpG island methylation at Jarid1c was very low during development and virtually absent at the CTCF sites, signifying that CTCF may influence DNA methylation and chromatin modifications. CTCF binding sites were also present at the 5' end of two other escape genes, mouse Eif2s3x and human EIF2S3, each adjacent to an inactivated gene, but not at genes embedded within large escape domains. Thus, CTCF was specifically bound to transition regions, suggesting a role in maintaining both X inactivation and escape domains. Furthermore, the evolution of X chromosome domains appears to be associated with repositioning of chromatin boundary elements.
Subject(s)
Chromatin/metabolism , CpG Islands/physiology , DNA-Binding Proteins/metabolism , Dosage Compensation, Genetic , Gene Expression Regulation, Developmental/physiology , Repressor Proteins/metabolism , Acetylation , Animals , Binding Sites , CCCTC-Binding Factor , Cells, Cultured , DNA Methylation , Electrophoretic Mobility Shift Assay/methods , Embryo, Mammalian , Eukaryotic Initiation Factor-2/metabolism , Histone Demethylases , Humans , Immunoprecipitation/methods , Mice , Mice, Inbred C57BL , Models, Molecular , Molecular Sequence Data , Mutagenesis/physiology , Oxidoreductases, N-Demethylating , Proteins/metabolism , X ChromosomeABSTRACT
CTCF is a widely expressed 11-zinc finger (ZF) transcription factor that is involved in different aspects of gene regulation including promoter activation or repression, hormone-responsive gene silencing, methylation-dependent chromatin insulation, and genomic imprinting. Because CTCF targets include oncogenes and tumor suppressor genes, we screened over 100 human tumor samples for mutations that might disrupt CTCF activity. We did not observe any CTCF mutations leading to truncations/premature stops. Rather, in breast, prostate, and Wilms' tumors, we observed four different CTCF somatic missense mutations involving amino acids within the ZF domain. Each ZF mutation abrogated CTCF binding to a subset of target sites within the promoters/insulators of certain genes involved in regulating cell proliferation but did not alter binding to the regulatory sequences of other genes. These observations suggest that CTCF may represent a novel tumor suppressor gene that displays tumor-specific "change of function" rather than complete "loss of function."
