It is clear that transcription factors which recognise specific DNA sequences in gene regulatory elements play a central role in defining gene expression outcome. However the vertebrate genome is vast, containing all the coding and structural information required to make gene products and effectively segregate chromosomes following cell division. Therefore only a small percentage of the total genome sequence is utilized to directly specify whether genes should be expressed or not. Recognizing this small fraction of the genome represents a formidable task for the gene expression machinery. This is complicated by the fact that DNA is not simply found as naked template but is instead wrapped into a structural entity called chromatin that consists of both DNA and protein encoded histone molecules. Recently it has become clear that gene regulatory elements in vertebrate genomes have a very specific chromatin modification architecture that differs from surrounding non-regulatory regions of the genome. Importantly this chromatin architecture can be specific to individual cell types, suggesting that this may play an important role in allowing individual cell types to achieve defined gene expression outcomes.
In understanding how chromatin and epigenetics contributes to gene regulation, the Klose lab has recently discovered that a ZF-CxxC DNA binding domain can recognize an epigenetically distinct state of DNA at gene regulatory elements called CpG islands. This DNA binding domain recruits a further set of chromatin modifying enzymes that alter the post-translational state of histone molecules in chromatin. This fundamental discovery places ZF-CxxC domain containing proteins as central players in chromatin modification at the majority of genes throughout the genome.
Building on this discovery the Lab is now focussed on understanding three central questions related to how this interesting system works to regulate gene expression:
(1) How do the family of ZF-CxxC domain containing proteins recognize and modify chromatin at gene regulatory elements?
(2) What does the chromatin architecture at gene promoters contribute to gene regulation?
(3) Why do CpG islands remain free of DNA methylation when the majority of the genome is densely methylated?
Our motivation for understanding these fundamental questions about gene regulation is to ultimately inform therapeutic approaches to counteract these processes when they malfunction in cancer and other human diseases.