Biological processes including development, differentiation, and disease are regulated at the level of gene expression – a process that is tightly modulated by transcription factors. These proteins are often regarded as having two distinct components: a DNA binding domain (DBD) to allow binding to the regulatory region of a target gene and a trans-acting functional domain (FD) to modulate gene expression. However, it is becoming clear that the DBDs of transcription factors alone are incapable of providing sufficient specificity to account for the highly complex genomic structures in eukaryotes.

Our recent publications revealed the importance of the FD of an archetypal zinc finger transcription factor, Krüppel-like factor 3 (KLF3) for in vivo DNA binding specificity. KLF3 is one of the 17 members of KLF family of transcription factors. All KLFs have highly conserved C-terminal C₂H₂ zinc finger DBD and variable N-terminal FDs. Despite highly homologous DNA binding domains, each member regulates different sets of target genes and thus biological processes in vivo ranging from regulation of proliferation and cell growth, differentiation, development, survival and responses to external stress. We hypothesised that the variable FDs between the KLF members may play a role in determining the sets of genes regulated by different KLF proteins. To test this hypothesis, in this current study, we are assessing in vivo genome-wide occupancy of various fusion proteins consisting of different KLF FD fused to the KLF3 DBD via Chromatin Immunoprecipitation followed by high throughput DNA sequencing (ChIP-seq).

These analyses will provide an unprecedented view of the role of regions outside the DBD in in vivo DNA-binding specificity within an important transcription factor family.