Background: DNA methylation can regulate gene expression by aiding or restricting the recruitment of transcription factors. Global genomic studies have revealed that DNA methylation changes both at CpG islands and non CpG island regions during erythroid development and differentiation. Chromatin occupancy data indicate that many transcription factors involved in erythropoiesis contain CpG within their core consensus DNA binding motifs. We hypothesise that methylation of the CpGs within these binding motifs directly influences the binding of erythropoiesis related transcription factors and thus gene regulation.
Results: Using in vitro assays we revealed that DNA methylation can either positively or negatively affect binding of important erythroid transcription factors to their DNA target sites. Based on these in vitro results, we analysed ChIP-Seq and genome-wide bisulfite sequencing datasets to find target genes of key erythroid transcription factors in vivo where DNA methylation status change significantly during erythroid differentiation. We are now validating these in vivo target genes using CRISPR/Cas9 mouse models to uncover how target site methylation modulates genetic regulation during erythroid differentiation.
Conclusion: We have shown that DNA methylation at transcription factor binding sites influences the binding affinity of key erythroid transcription factors in vitro and are extending these findings to in vivo target genes. Our study will improve the understanding of the relationship between DNA methylation, transcription factor binding and gene regulation in erythropoiesis.