It is critical to understand how transcription factor (TF) genome localisation guides a cell’s fate and response to the cellular environment. TFs contain two separable components: a DNA binding domain and a functional domain. It was historically believed that the DNA binding domain was the only region that determined the genomic localisation of transcription factors. However, evidence has emerged that the functional domain can also play a crucial role in determining the genomic localisation of transcription factors.
Based on extensive preliminary data, we hypothesise that the functional domains of a TF can recruit histone reader proteins which direct the TF to target sites. We aimed to explore the impact of histone reader recruitment on the genomic localisation of transcription factors, by directly fusing histone reader domains to an artificial zinc finger (AZF) protein.
We fused a bromodomain histone reader domain to an AZF to investigate whether a histone reader is sufficient to direct the AZF to new target genes. We have generated stable overexpression of these constructs in different mammalian cell lines to investigate how the epigenetic state can impact the genome wide localisation of the AZF. We confirmed that binding to the AZF recognition motif was not disrupted by the bromodomain using electrophoretic mobility shift assays. We then performed ChIPseq to test whether the fused histone reader altered the genomic localisation of the AZF.
We found that the bromodomain histone reader domain remarkably redirects the AZF to new genes. These newly bound sites include those enriched for histone 3 lysine acetylation marks which are known as marks that the bromodomain can read. This knowledge could be applied to harness histone readers to design superior artificial transcription factors that can be used to reprogram gene expression and control cell differentiation.