Competition between DNA methylation and transcription factors determines binding of NRF1

The relationship between DNA methylation and transcription factor binding was studied across the genome in mouse embryonic stem cells-the study reveals that the transcription factor NRF1 is methylation-sensitive and how physiological binding of NRF1 relies on local removal of DNA methylation. DNA methylation restricts NRF1 binding Sequence-specific transcription factors occupy only a fraction of their sequence motifs across the genome. Here, Dirk Schübeler and colleagues look at the effect of DNA methylation on transcription factor binding in mouse embryonic stem cells, and find that NRF1 (nuclear respiratory factor 1) is a methylation-sensitive transcription factor. In the absence of DNA methylation, NRF1 binds to new sites and induces aberrant transcription. The physiological binding of NRF1 relies on local removal of DNA methylation by methylation-insensitive factors. The DNA methylation sensitivity of a transcription factor can therefore be used to restrict binding specifically to regulatory regions. Eukaryotic transcription factors (TFs) are key determinants of gene activity, yet they bind only a fraction of their corresponding DNA sequence motifs in any given cell type 1 . Chromatin has the potential to restrict accessibility of binding sites; however, in which context chromatin states are instructive for TF binding remains mainly unknown 1 , 2 . To explore the contribution of DNA methylation to constrained TF binding, we mapped DNase-I-hypersensitive sites in murine stem cells in the presence and absence of DNA methylation. Methylation-restricted sites are enriched for TF motifs containing CpGs, especially for those of NRF1. In fact, the TF NRF1 occupies several thousand additional sites in the unmethylated genome, resulting in increased transcription. Restoring de novo methyltransferase activity initiates remethylation at these sites and outcompetes NRF1 binding. This suggests that binding of DNA-methylation-sensitive TFs relies on additional determinants to induce local hypomethylation. In support of this model, removal of neighbouring motifs in cis or of a TF in trans causes local hypermethylation and subsequent loss of NRF1 binding. This competition between DNA methylation and TFs in vivo reveals a case of cooperativity between TFs that acts indirectly via DNA methylation. Methylation removal by methylation-insensitive factors enables occupancy of methylation-sensitive factors, a principle that rationalizes hypomethylation of regulatory regions.