Switching mammalian genes on and off during development, lineage specification, and differentiation, and its impact on human genetic disease

In animals, life starts with the fertilisation of an egg by a sperm to produce a single cell that will divide and change to produce a fully formed organism. An adult human being is made up of 30 trillion cells that have specialised roles, for example, in the brain, liver, kidney, and blood. All these cells originate from that first single cell.

The instructions that tell each cell what to do are contained in DNA. Our DNA is inherited from our parents, and contains 3 billion 'letters' (called bases) organised in 20,000 'words' (called genes). The complete order of letters within the code was established by the Human Genome Project in 2003.

Each of our 30 trillion cells contains a copy of the same code and the same 20,000 genes. So how do tissues differ, and perform different roles? Cells behave differently in different tissues in our body because different combinations of genes are switched on and off in different cell types. It is this variation that determines which type of cell (e.g. brain or blood) is made.

Imagine that each of your cells was an iPhone: in each case the hardware is identical but, depending on which programmes you switch on, what appears on your screen is quite different. Therefore, one of the major aims in biology at the moment is to understand how a cell decides to switch a particular gene on or off. To do this we must decipher the DNA code, rather like the scientists at Bletchley Park cracked the German 'Enigma' code during the second world war.

Our laboratory is trying to crack this code using one particular gene as a model. We know that this gene has the instructions to make haemoglobin, the pigment inside red blood cells. We want to understand how this gene is switched on or off in the bone marrow stem cells. These stem cells can become both red and white blood cells. When a cell makes haemoglobin (turning the gene on) it has decided to become a red blood cell. When it doesn't make haemoglobin (turning the gene off) it has decided to become a white blood cell. Understanding how this process works for one gene will help us understand how it works for many of the other 20,000 genes.

Over the last few years we and others have identified three fundamental signals in the code, each comprising 50-300 letters. The first signal is called the gene promoter and it marks the location of the gene and where it starts. This is rather like tuning in to your favourite radio station. The second class of signal is called an enhancer, which acts by modifying the tone and volume of the station into which you have tuned. The third type of signals are called boundary elements and they help the enhancer focus on the chosen station and prevent them drifting off to another station. All three elements work together to make sure that a gene is switched on or off at the right time in development.

We are trying to understand how these enhancers, promoters and boundary elements, work together to regulate the production of haemoglobin. We also want to understand how errors in the DNA code can sometimes mean that this control doesn't work properly, leading to human genetic diseases related to anaemia. Our ultimate aim is to use a newly developed technology called genome editing to correct these mistakes in the DNA code.

Although our work concentrates on a single gene and the diseases associated with it, understanding the principles behind gene regulation will help us understand how many of the 20,000 genes in our cells are normally switched on and off to form a full human body, and how this goes wrong in inherited diseases such as haemophilia or acquired genetic diseases such as cancer.

This programme addresses a key question in biomedical research: how are genes switched on and off during development, lineage commitment, differentiation and maturation? To date we know that this involves the three fundamental regulatory elements of the genome: enhancers, promoters and boundary elements. Here we investigate how these elements interact to regulate gene expression in three-dimensional space and time.

To address this, we study how the human and mouse alpha-globin multi-gene clusters are switched on and off as haematopoietic stem cells differentiate into mature erythroid cells. Past lessons from studying globin gene expression have elucidated many of the general principles underpinning our understanding of mammalian gene regulation. Using newly developed synthetic biology, and proteomics approaches, together with new experimental models, the unanswered questions we address here are: how do promoters and enhancers come into close physical contact; how do enhancers interact specifically with their cognate promoters; what specifically does the enhancer bring to the promoter and how does this alter the transcription cycle; what is the role of CTCF binding sites in this process?

While elucidating the normal process of gene regulation we will also examine how this process is perturbed in human genetic diseases. Studying globin gene disorders has elucidated many general principles underlying human genetic disease. While some single gene disorders are known to result from mutations in promoters and enhancers, it seems likely that variations in gene expression underlying complex diseases and variable human traits mainly affect the regulatory landscape. Our programme will address in detail, how changes in intergenic DNA may influence gene expression. Finally, we are using this information to develop new approaches to regulating gene expression via genome editing in pre-clinical and eventually clinical studies by manipulating haematopoietic stem cells

The aims of our work are to understand how the 20,000 genes in each mammalian cell are switched on and off as stem cells decide which specialised cells they will eventually become. Our work uses the blood system to address this. Understanding gene regulation is a major question in current biology and if solved would answer how an organism develops from a single cell to a full organism comprising 30 trillion cells in the case of a human being. The academic and practical impact of solving this issue is enormous and wide reaching.

Our contribution to this field, via this programme, will continue to advance scientific knowledge by elucidating the basic principles underlying gene expression. As in the past we will also advance the field by developing new methods by which to address the mechanisms underpinning gene expression and make these available to the scientific community to promote and facilitate the science of others.

A related aim is to understand how gene expression is perturbed in inherited and acquired human genetic diseases. As in the past our work will provide new insights into the mechanism of disease and will be used to accurately diagnose and classify these disorders within genetic laboratories throughout the world who use this information to improve public health and wellbeing. On the basis of our research on the haemoglobinopathies we will advise such health providers in developing their policies for implementing this knowledge and discuss and explain these findings to the affected individuals and families in the context of patient/scientific meetings.

The third aim of our programme is to use state-of-the-art gene editing technology together with our understanding of gene regulation to correct genetic defects that occur in inherited forms of anaemia. Again, the impact of this will be to improve the health and wellbeing of affected patients with these conditions.

Our research laboratory will continue to train basic scientists and clinician scientists providing scientifically skilled academics and clinicians to the UK work force adding economic competitiveness to our universities, the health service, the pharmaceutical industry, publishers and many more.

The topics of this programme have attracted extremely talented young researchers to our laboratory and we anticipate that these key questions in current biology will continue to inspire the next generation of scientists interested in this problem which will take many more years of focussed research to solve in full.