BANP opens chromatin and activates CpG island regulated genes [RNA-Seq]

In mammalian genomes, the vast majority of RNA polymerase II initiation events take place at CpG island promoters. Despite their relevance our understanding of their regulation remains limited. Here we identify Banp as the long sought-after TF that binds the orphan CGCG element in CpG islands by combining single-molecule footprinting with interaction proteomics. We show that Banp drives activity of CpG islands that control essential metabolic genes in the mouse and human genome. Banp binding is strongly repelled by DNA methylation of its motif in vitro and in vivo, which restricts most binding to CpG islands and accounts for its absence at aberrantly methylated CpG islands in cancer cells. Upon binding to an unmethylated motif, Banp opens chromatin and positions nucleosomes. These findings expand our understanding of CpG island gene regulation and put forth a model whereby CpG islands rely for their activity on methylation sensitive TFs capable of opening and organizing chromatin. RNA-seq in mouse ESCs and neurons: ESC wt, DNMT triple-ko (tko) and tko dTag untreated and treated for 1h, 2h, 4h and 6h, neurons dTag untreated and treated for 1h, 2h, 4h and 6h. All conditions in triplicates, except for ESC wt and tko (6 replicates) and ESC tko dTag 1h (2 replicates). Batch 1: ESC wt replicates 1-3 and ESC tko replicates 1-3. Batch 2: ESC tko replicates 4-6 and ESC tko degron time course. Batch 3: ESC wt replicates 4-6, ESC with Ngn2 construct uninduced and all neuron samples.