Establishment, Maintenance and Modulation of heterochromatin domains

The DNA of our genome contains the instructions, or code, to make cells and to make a person. Some of the DNA sequences (genes) in our cells code for making proteins. However, much of our DNA is made up of repeat sequences that do not code for proteins. For example, the human genome contains 46% repeat sequences. Other genomes contain even higher proportions of repeats (e.g. 65% for maize). The function of these repeats is not well understood. However, it is understood that repetitive sequences spell trouble for the cell. This is because repetitive sequences tend to be 'unstable' and can interact and fuse with other repeat sequences in other places in the genome. This means the genome can become rearranged, causing loss of some sequences and duplication of others. It can also bring two separate sections of the genome together which can mess up the instructions for making the right amounts of proteins. Genome rearrangements are a hallmark of cancer and birth defects. To counteract the potential threat to the genome by DNA repeats, organisms have developed strategies to fight against the instability of DNA repeats. One strategy is to coat the repetitive sequences in protective proteins that prevent them from interacting with other repetitive sequences. This protective protein structure is called 'heterochromatin'.
In fact, our DNA is packaged in proteins called histones - the DNA and histones together make 'chromatin'. The chromatin structure allows the DNA to be wrapped up so that it fits inside cells, and it also controls how often and how quickly the instructions coded by DNA are released to make proteins. Repeat sequences are packaged in specialised heterochromatin which is more tightly packaged in histones. This means that it's harder for repeats to find each other and harder for the proteins that might join up different parts of the genome to find the repeats. Therefore, heterochromatin acts to prevent genome rearrangements. For this reason it is important to know how DNA repeats are packaged into heterochromatin. This is one of the questions that we aim to answer in this proposal. We will study heterochromatin formation in a simple model organism, the unicellular yeast Schizosaccharomyces pombe. We study S. pombe because its heterochromatin is similar to what is found in humans but simpler. In S. pombe, we have recently developed systems to take apart and build up the process of heterochromatin assembly to understand how it is put together. Using this system we aim to identify the DNA sequences and the proteins that allow heterochromatin to be assembled and maintained on DNA repeats. For certain organisms, such as microbial pathogens, it could be convenient in certain environmental conditions to rearrange their genomes and therefore to temporarily erase heterochromatin from DNA repeats. One of such organism is the fungal pathogen Candida albicans. C. albicans is the most important human fungal pathogen. It normally lives inside our body without problem, but in certain situations (e.g. immunocompromised patients), it can cause life-threatening diseases. Pathogenic C. albicans adapts efficiently to different environments and it can acquire resistance to anti-fungal drugs. This is because, in contrast to most organisms, C. albicans can live and thrive without the normal, correct ratios of genes and even missing part of a chromosome (a phenomenon called genome plasticity). It was discovered that DNA repeats (called MRS) play an important role into the transformation of C. albicans into a dangerous pathogen. Rearrangements of the genome often occur at the MRS repeats. We will ask whether the MRS repeats are usually kept in a 'safe' state by being coated in heterochromatin and whether the type of chromatin at MRS changes to allow the genome rearrangements that cause C. albicans to become a pathogen. We will ask whether the type of chromatin at MRS repeats controls C. albicans pathogenicity.

The genomes of most organisms are composed in major part of repetitive DNA. The repetitive nature of these sequences threatens genome stability and organisms have evolved mechanisms to protect themselves against the harmful effects of repeats. One such mechanism is the assembly of a repressive chromatin structure inhibitory to recombination: heterochromatin. Heterochromatin assembly needs to be a faithful process and heterochromatin mis-targeting as well as failure to assemble heterochromatin domains on DNA repeats, is at the basis of several important pathologies, such as neurodegenerative diseases and cancer. It is still unknown how heterochromatin is established on DNA repeats and how it is maintained at this location through cell division. Once assembled, the chromatin status associated with DNA repeats could be modulated. Partial assembly and disassembly of heterochromatin could be particularly advantageous for organisms, such as microbial pathogens, that have to adapt rapidly to different or changing environmental niches.
In this project, we will define the mechanism(s) regulating heterochromatin establishment, maintenance and modulation. We will investigate mechanisms of heterochromatin establishment and maintenance in the model system Schizosaccharomyces pombe. To study mechanisms and consequences of heterochromatin modulation, we will investigate how the chromatin status associated with DNA repeats is modulated in the fungal pathogen Candida albicans. This pathogen undergoes dramatic morphological transitions in response to environmental changes and it is therefore an ideal system in which to study the underlying modulation of chromatin. This study will advance our understanding of heterochromatin assembly on DNA repeats and will provide insight into mechanisms and consequences of epigenetic regulation in response to environmental changes.

Who will benefit from this research?
The proposed research is basic in nature and the immediate impact of this work will be on the bioscience research community with interest in epigenetics and fungal biology. In the longer term, this research has the potential to impact in areas of healthcare and pharmaceutical industries. Beneficiaries beyond academia are the biopharmaceutical sector with interest in anti-cancer and anti-fungal drug discovery, the biotechnology sector involved in live-stock production and the wider general public.

How will they benefit from this research?
The Bioscience research community.
Scientists interested in epigenetics and global regulation of gene expression will benefit from our discoveries of mechanisms underlying establishment, maintenance and modulation of chromatin domain at DNA repeats. Chromatin biology in the fungal pathogen Candida albicans is a surprisingly poorly explored area. Our research will deliver increased capacity and capability in this area of biology through the provision of training and further development of key methodologies.

The biopharmaceutical sector with interest in anti-cancer drug discovery.
We will elucidate the role of six novel proteins in heterochromatin assembly. Proteins involved in heterochromatin formation (such as HDACs) have been already successfully used as targets for anti-cancer drug development. Our research will generate new potential targets for development of drugs effective in oncology.

The biopharmaceutical sector with interest in anti-fungal drug discovery.
C. albicans is the main human fungal pathogen. One of the major obstacles in defeating this pathogen is the high occurrence of anti-fungal drug resistance, creating an urgent need for innovative anti-fungal drugs. Our research has identified new potential anti-fungal targets and this proposal could exploit their potential commercial application.

The biotechnology sector involved in live-stock production. C. albicans is a major pathogen of poultry and cattle. Our research will have a major impact on reducing financial losses and improve animal welfare.

The wider general public.
Non-functional establishment of heterochromatin domains can lead to important diseases such as cancer, ageing-related diseases and neurodegenerative disorders. C. albicans infection is at the basis of important life-threating diseases with mortality rates up to 71%. These diseases have huge cost implications and our research, in the longer term, will benefit the National Health Service, the patient and ultimately the UK economy by the development of new drugs.

In synthesis, our research will provide substantial and widespread benefit to our society with respect to scientific output, the economy, quality of life and health.