Gene regulation within the human genome relies on the interaction of transcription factors with regulatory elements that influence transcription rates. Transcription factors are typically composed of a DNA binding domain and an effector domain, with the DNA binding domain predominantly dictating where in the genome the transcription factor can bind, and therefore which genes it will regulate. Given the large number of potential binding motifs throughout a genome, a question remains of how transcription factors select specific genomic binding sites.
We have studied this in the context of the KLF transcription factor family, which has 17 members with highly conserved DNA binding domains but divergent effector domains and unique sets of genome binding sites and gene targets. We have previously shown that when the effector domain of KLF3 was fused to an artificial zinc finger, it directed the fusion protein to many regions which correlated to where KLF3 natively binds within the genome. This suggests that effector domains play a crucial role in determining genome localisation and that the divergent functional domains within the KLF family may drive the unique genome binding sites and targets for members of this family. We have performed effector domain swaps between members of the KLF family followed by ChIP-seq and our findings support this hypothesis.
To understand this further we explored whether differential binding to partner proteins is responsible for the role of effector domains in genome occupancy. Previous work on KLF3 has shown that the effector domain interactions with CtBP2 and other partner proteins impact genome localisation. To identify partner proteins for other KLF family effector domain, we have performed co-immunoprecipitation coupled with mass spectrometry. These studies have provided us with insights about the important role of transcription factor effector domains in genome localisation.