Transcriptional regulation is crucial for a number of biological processes and involves the binding of sequence-specific transcription factors (TFs) which in turn effect the recruitment of RNA polymerase II and the rate of gene expression. These TFs are able to each regulate a specific set of genes, however it is still difficult to predict exactly where these factors bind and which genes they regulate. While it has generally been accepted that each TF has a specific DNA binding motif, these motifs occur very commonly throughout the genome. Through ChIP-seq and other genomic studies, it has been shown that TFs bind only a fraction of these motifs and regulate even a smaller fraction of genes.
We are investigating how TFs achieve this specificity and why they may bind certain sites and not others despite both having the consensus binding motif. To investigate this, we are approaching the question from two different angles, one looking at the structure of DNA and the other looking at the TF itself.
Genomic DNA can adopt many different structures apart from the usual B-form double-stranded DNA (dsDNA) such as G-quadruplexes, Z-DNA, H-DNA and R-loops. The recent development of techniques such as DNA-RNA immunoprecipitation (DRIP) and ssDNA-seq have shown that these structures are abundant throughout the mammalian genome. Furthermore, specific Non-B DNA structures have been shown to act as mediators of transcriptional regulation and cellular differentiation. Using erythroid cells as a model, we are investigating how these structures may play a role in transcriptional regulation, and more specifically, in modulation of TF binding.
We are also investigating how the non DNA-binding domain (i.e. the functional domain) affects genomic localisation in a family of TFs, the Krüppel like factor (KLF) family which all share the same DNA-binding domain but have different genome-wide binding profiles and gene regulatory functions.