Histone H1-mediated inhibition of transcription initiation of methylated templates in vitro

The detailed mechanism underlying the inhibition of transcription by DNA methylation is still obscure. Chromatin structure has frequently been proposed as a role player in this mechanism. Histone H1 is a known key element in the formation and stabilization of chromatin fibers. We describe here experiments designed to examine the effect of DNA methylation on the binding of histone H1 to DNA and the consequent inhibitory effect of the bound histone H1 on in vitro transcription. The results of these experiments showed a clear preferential binding of histone H1 to methylated DNA as compared with unmethylated DNA. The in vitro transcription assay indicated that transcription of methylated templates was inhibited at a lower histone H1/DNA ratio than of unmethylated templates, and that the extent of inhibition depends on the density of methyl groups in the promoter region. This inhibition of in vitro transcription was alleviated efficiently by methylated competitor DNA, whereas, under similar conditions, almost no effect was observed with unmethylated competitor. Experiments designed to pinpoint the stage in the transcription process that was suppressed by the preferred binding of histone H1 to methylated template revealed that inhibition occurred at the initiation and not at the elongation level.