Analysis of methylation in the 5' region of the human alpha-galactosidase A gene containing a binding site for methylated DNA-binding protein/RFX1-4

We examined methylation in the 5' untranslated region and surrounding sequences of the X-linked human alpha-galactosidase A gene. This region includes a methylation-dependent binding site for the MDBP/RFX1-4 transcription factor family. By bisulfite-based genomic sequencing, we determined the distribution of 5-methylcytosine residues from position +28 to +143 relative to the major transcription start site of the gene in almost 500 molecular clones from different tissues and individuals. The CpG methylation patterns in DNA from females differed from molecule to molecule with no indication of tissue-specificity or age-dependence. In contrast, the CG dinucleotides within this region were completely unmethylated in almost all of the DNA molecules cloned from male tissues. In female eutherian mammals, 50% of the molecules are expected to be methylated in an X-linked gene region in which methylation is coupled to gene silencing. Of the cloned DNA molecules from female tissues, 40% had 4 or more of the 9 CpG's methylated and the MDBP site was methylated in about one-fifth of the female tissue-derived DNA molecules.

The major histocompatibility complex class II promoter-binding protein RFX (NF-X) is a methylated DNA-binding protein

A mammalian protein called RFX or NF-X binds to the X box (or X1 box) in the promoters of a number of major histocompatibility (MHC) class II genes. In this study, RFX was shown to have the same DNA-binding specificity as methylated DNA-binding protein (MDBP), and its own cDNA was found to contain a binding site for MDBP in the leader region. MDBP is a ubiquitous mammalian protein that binds to certain DNA sequences preferentially when they are CpG methylated and to other related sequences, like the X box, irrespective of DNA methylation. MDBP from HeLa and Raji cells formed DNA-protein complexes with X-box oligonucleotides that coelectrophoresed with those containing standard MDBP sites. Furthermore, MDBP and X-box oligonucleotides cross-competed for the formation of these DNA-protein complexes. DNA-protein complexes obtained with MDBP sites displayed the same partial supershifting with an antiserum directed to the N terminus of RFX seen for complexes containing an X-box oligonucleotide. Also, the in vitro-transcribed-translated product of a recombinant RFX cDNA bound specifically to MDBP ligands and displayed the DNA methylation-dependent binding of MDBP. RFX therefore contains MDBP activity and thereby also EF-C, EP, and MIF activities that are indistinguishable from MDBP and that bind to methylation-independent sites in the transcriptional enhancers of polyomavirus and hepatitis B virus and to an intron of c-myc.