During haematopoiesis, widespread changes to the DNA methylome accompany the activation and repression of critical lineage-specific genes. Whilst it is well-established that DNA methylation is closely correlated with gene repression, whether it is the direct cause of this repression is the subject of ongoing debate. However, one mechanism by which methylation may directly coordinate changes in haematopoietic transcription is by directly obstructing the binding of methyl-sensitive transcription factors. This prompts the question: are such methylation-sensitive transcription factors important in the regulation of haematopoiesis?
We have previously shown that GATA1, a key mediator of haematopoiesis, is sensitive to DNA methylation. To investigate the effect of methylation on GATA1 binding genome-wide, structural modelling was employed to engineer a mutant methyl-binding (MB)-GATA1 which, unlike its WT counterpart, binds methylated CGATA motifs. We performed parallel RNA-seq and ChIP-seq on erythroid HUDEP2 cells, expressing either WT-GATA1 or MB-GATA1, to profile in vivo binding and resultant changes to the transcriptome.
Compared to WT, MB-GATA1 exhibited higher binding at only 0.03% of CGATA motifs genome-wide. This is strikingly low given the global hypermethylation expected. MB-GATA1 binding at these sites correlated with significant upregulation of the nearest gene for 16 genes. Together, this suggests that methylation-regulated GATA1 binding is a mechanism that is rarely employed across the genome. However, KLF13 emerged saliently from the selection of candidate genes given its established indispensable role in regulating erythropoiesis, as demonstrated in knockout mice models. KIT, another key hematopoietic regulatory gene, is the only other gene that has been previously demonstrated to be regulated in this way.
Whilst previously the influence of DNA methylation on transcription factor binding has been questioned, here we paint a nuanced picture of its importance: GATA1 binding regulation via DNA methylation is rare, however the cases where it does occur are of vital importance to haematopoiesis.