Laboratory of Protein and DNA Interactions

All living organisms must be able to control expression of their genes with great precision. Within cells, proteins known as transcription factors interact with DNA to control the on-off switches that are found in the regulatory regions of genes. The interaction between these proteins and their specific DNA binding sites is crucial for the correct temporal and spacial control of gene expression networks.

The basic Helix-Loop-Helix (bHLH) domain defines an extensive transcription factor family. This domain consists of a basic DNA binding sequence adjacent to the helix-loop-helix dimerisation region, which allows homo- or hetero-dimerisation amongst bHLH proteins to form functional DNA binding complexes.

The bHLH.PAS sub-group of bHLH proteins has the bHLH domain contiguous with a second domain, termed the PAS (Per-Arnt-Sim homology) domain, which also regulates dimerisation. PAS domains are a widespread protein/protein interaction module forming a highly conserved structure, despite having low sequence homology. PAS protein interactions are often regulated in response to signals detected by the PAS domain, where PAS-bound small molecules produce conformational changes that regulate activity, and subtle conformational changes have large biological consequences.

We and others have shown that, in addition to functioning in dimerization, the PAS domains of bHLH.PAS proteins have a critical influence on DNA binding, contributing to affinity and protein-bound DNA conformation, as well as defining partner choice and target gene specificity.

• The molecular mechanisms that drive these functions of the PAS domain are not known. In fact, although aspects of bHLH.PAS biology are the subject of much research, few of the molecular events underlying gene regulation by these essential proteins are understood.

The bHLH.PAS transcription factors are often coexpressed and their dimerisation behaviour is tightly regulated. The various protein dimers in the family bind to closely related DNA sequences, yet are functionally distinct, being able to activate specific and discrete sets of target genes.

• The focus of our research is to understand the specificity of the bHLH.PAS transcription factors, that is, to decipher the amino acids and structural elements of the bHLH and PAS domains that control their protein-protein and protein-DNA interactions.

The bHLH.PAS proteins we study have significant functions in biology:

Aryl hydrocarbon Receptor (AhR) mediates the severe toxicity associated with the environmental pollutants dioxin, benzopyrenes, and structurally related halogenated aromatic hydrocarbons.

Hypoxia Inducible Factors, HIF-1α and HIF-2α direct genomic responses to oxygen deficiency by controlling genes that increase oxygen supply to tissues and facilitate metabolic adaption to hypoxia. The HIFαs are important in anoxic human disease states, such as ischaemia and myocardial infarction, and in cancer, where cellular responses to reduced oxygen are a crucial component of tumour progression.

Single Minded proteins, Sim1 and Sim2 are involved in control of neural development and, like the HIFαs, are both biologically essential and non-redundant.
Neural specific NPAS4, a stress induced bHLH.PAS transcription factor, has been found to be active in rodents during chemically initiated epileptic seizure and may have a role in autism.

These bHLH.PAS proteins must dimerize with the common partner Aryl hydrocarbon Receptor Nuclear Translocator (Arnt) for transcriptional function.