Molecular mechanisms of gene regulation
Eukaryotic transcriptional control is a complex process involving multiple cis-acting DNA control elements and trans-acting protein components. Chromatin unravelling is an essential component of this. The whole process is dynamic and is regulated by external signals mediated by signal transduction cascades and protein kinases. The importance of maintaining correctly controlled transcription is emphasised by the observation that many tumours arise due to the mutation of genes encoding components of the transcription machinery, chromatin regulating complexes or the pathways which modify their activity. We are studying how transcription factors function at the molecular level and how they link to cellular signalling pathways to generate dynamic transcriptional events in the context of a changing chromatin environment. Current projects:
1. Mechanisms of signal-mediated gene regulation: The receptor tyrosine kinase (RTK) driven pathways are some of the best studied signalling systems, partly due to their frequent deregulation in cancer. However, we know very little about how they impact on gene regulation. We are focussing on the ERK pathway and how this promotes changes in the regulatory chromatin landscape and subsequently on the underlying gene expression programmes. Current projects are focussing on changes to the 3D architecture surrounding growth factor regulated genes and the mechanisms through which promoters are “reset” to respond to activated signalling pathways. This work is closely integrated with our work on studying enhancer function and how they are formed in a temporally choreographed manner during differentiation (see below).
2. Transcriptional control modules in oesophageal cancer: Oesophageal cancer is highly prevalent and yet has poor survival rates, due to a lack of suitable treatments and poor diagnostic and prognostic markers. We are interested in how transcription factors contribute to oesophageal cancer and their relationships to signalling pathways in this context (Mol Cancer, 2015, 14, 69). More recently, we have begun to focus on the regulatory chromatin landscape of oesophageal adenocarcinoma and how this is established and maintained (Plos Genetics, 2017, 13, e1006879). Current projects are focussed on how the regulatory chromatin landscape is re-sculpted through the action of transcription factors during cell fate changes that accompany cancer progression.
3. Signal-mediated transcriptional drivers of stem cell differentiation: Stem cell differentiation is controlled by the interplay of signalling pathways and transcriptional regulators. These in turn impact on the regulatory chromatin landscape and the underlying transcriptional programmes. Current projects in the lab are designed to understand the control mechanisms involved, including the role of chromatin remodelling complexes and their interplay with transcription factors like FOXK2 (NAR, 2014, 42, 6232). Other projects are studying the formation of enhancers within the changing chromatin environment and how transcription factors direct their formation (Cell Rep, 2014, 7, 1968).
Our approach: The multitude of transcription factors and signalling pathways in the cell and the complex nature of DNA regulatory elements, means that extensive regulatory networks exist for controlling gene transcription. We are using a balanced approach which melds genome and proteome-wide studies with deep mechanistic investigation to understand how these events are orchestrated. We are using a "systems analysis" approach using a combination of single cell, in silico, and sequencing-based techniques (eg RNAseq, ChIPseq and ATACseq) to probe the networks controlled by transcription factors and coactivators in response to different signalling events (PLoS Genetics, 2012, 8, e1002694). Incorporated into these studies, are mechanistic approaches aimed at understanding how transcription factors orchestrate changes in chromatin structure in response to signalling cues, and particularly how promoters are re-set following temporal activation in response to signalling. These include classical molecular and biochemical techniques, including the latest CRISPR Cas9-based genome editing and manipulation approaches.
….and a jargon-free summary for the general public…..
Recent technological advances have enabled us to discover the genetic blueprint for life- DNA- in many different organisms. DNA contains all the information required to form a fully functioning organism. However, this information must be accessed and decoded to enable the building blocks of life to be assembled. The basic initial process involved in decoding the genome is called transcription. This is in turn facilitated by chromatin remodelling, which is a process that allows the DNA to become accessible to the transcription machinery. Transcription does not occur constantly and at the same rate throughout the DNA in our genomes, and instead is controlled by molecular switches called transcription factors which themselves are turned on or off in response to signals. The overall aim of the work in my lab is to understand how transcription factors function as molecular switches and respond to signals, and hence are able to control the decoding of specific parts of the genome. Cancer is a disease primarily caused by errors in the genome-decoding process. Furthermore, future disease therapies are being developed based on the utility of stem cells for regenerating damaged tissues. Our work harnesses the latest technologies to focus on transcription factor switches in both these areas.