CTCF delimits a DNA methylation transition at the intergenic region between the embryonic and adult α-globin genes

Abstract

ABSTRACT Transcriptional activation of cell-type-specific genes is achieved by multiple mechanisms that guarantee chromatin accessibility at cis-regulatory elements and the long-range interactions between them. Generally, DNA methylation counteracts these processes and promotes gene silencing in vertebrates. CTCF is a conserved and essential multifunctional transcription factor relevant for establishing and maintaining chromatin architecture and accessibility, while its precise role in regulating DNA methylation remains to be determined. We focused on the highly abundant and previously studied erythroid-specific αD gene (HBAD) to systematically investigate the role of CTCF binding on DNA methylation, chromatin accessibility, and gene expression using a chicken erythroid cell differentiation system. The perturbation of CTCF binding at the intergenic region between the embryonic π and the adult αD gene resulted in DNA methylation propagation towards the αD gene, which was accompanied by decreased chromatin accessibility, GATA-1 binding, and gene expression. Notably, chromatin conformation analyses revealed that CTCF binding enables αD transcriptional activation independently of its architectural function. We observed a similar role of CTCF on DNA methylation and gene expression in the human orthologous gene HBA2. Our findings support a conserved role of CTCF in preventing DNA methylation spreading and gene silencing of cell-type-specific genes along differentiation.