|Professor Anjana Rao’s research in the field of epigenetics has shaped global understanding and current opinion regarding the role of DNA modification in human health and disease. Here, Professor Rao discusses her role on the Cambridge Epigenetix Scientific Advisory Board (SAB), her research and the challenges of epigenetic research.|
Bringing research insights and expertise to the Scientific Advisory Board
The Cambridge Epigenetix SAB provides an excellent opportunity to interact with a group of bright industry and academic colleagues with a common interest in epigenetics research. My experience in this field allows me to offer advice and insights concerning regulation of gene expression through epigenetic modifications of DNA and histones, and transcription factors. In 2009, our research group was the first to show that the Ten-Eleven Translocation (TET) family of enzymes converts 5-methylcytosine (5mc) to 5-hydroxymethylcytosine (5hmC) in DNA. Since then, it has been shown that loss of TET function is associated with aggressive cancers and we are working to understand the mechanisms involved.
A great deal of our current work focuses on gaining a better understanding of the biological effects of TET proteins. We are specifically examining the relationship between TET-mediated methylcytosine oxidation, chromatin accessibility and transcriptional regulation in the context of cell lineage specification and cancer. We are also studying transcriptional mechanisms in different types of blood cells – haematopoietic stem cells, B cells and several T cell subtypes – during different states of activation or differentiation.
Epigenetic research: understanding mammalian development and disease
My interest in epigenetics began when we discovered that the induction of interleukin-4 (IL-4) gene expression is coupled to DNA demethylation at the IL-4 promoter in activated T cells. This process was clearly replication-dependent. However, our interest in potential ‘active’ (replication-independent) mechanisms of DNA demethylation was sparked when we noticed a study published in Nature in 2000, showing an apparent replication-independent demethylation of the paternal genome in zygotes very soon after fertilisation.
Epigenetics is an exciting field of research with important implications concerning disease. DNA methyltransferases and TET proteins both modify cytosine in DNA. The modified DNA created by both classes of enzymes seems to play important roles in gene regulation, cell lineage specification and repression of transposable elements. These processes are involved in the functioning of many mammalian systems, including embryonic development and the haematopoietic, immune and nervous systems. Dysfunction of these pathways is associated with a number of diseases including autism spectrum disorders and cancers.
Current challenges in research
Mapping the kinetics of changes at a single-cell/single-allele level in living cells is a major challenge. While there are established methods that enable gene transcription to be followed in real time in living cells, our understanding is still limited regarding epigenetic changes and coupling of enhancers with promoters occurring during this process. For example, it is possible that histone modifications and enhancer-promoter coupling occur dynamically, before and after transit of RNA polymerase II through a gene body, but it is not clear whether and how this may occur.
Once all the static genome-wide information has been collated, I predict that the field will go back to trying to understand, at a highly molecular level, the kinetics of how DNA and histone modifications are coupled to gene expression, especially of genes that are induced in primary cells during development and differentiation.
The continued study of 5hmC, 5mC and other oxidised methylcytosines is essential. To advance research more rapidly, we need to develop a technology that can decode long DNA sequences without prior amplification, using techniques that can accurately detect these types of DNA modification.
Data analysis and bioinformatics: opportunities for industry partnerships
Data analysis is an ongoing challenge for epigeneticists. Our excellent bioinformatics students have played a key role in analysing data and we have collaborated with many skilled computational biologists across the world.
Vast amounts of data have been generated globally concerning epigenetic modifications. These data have been captured in the genomes of many different cell types (e.g. embryos, cancer cells, neurons) and across a range of time points during development, often from humans with diverse genetic makeup. To move research forward, we need to develop practical systems that enable this information to be used effectively to draw simple and powerful conclusions. This is an area where industry partners such as Cambridge Epigenetix could help us to reach a solution.
Advice for young researchers
Young researchers beginning their work should be encouraged to enter this very exciting field, but be warned to prepare themselves for the frustrations associated with gathering data that will often be correlative and that may not always enable them to reach definitive conclusions.
Professor Rao’s laboratory uses a wide range of techniques to study epigenetics, including:
- RNA sequencing (total, polyA+ and nascent RNA) - single-cell and bulk population level
- ATAC-seq - single-cell and bulk population level
- Whole-genome sequencing
- Whole-genome bisulfite sequencing
- Oxidative bisulfite sequencing (on amplicons)
- Chromatin immunoprecipitation for DNA and histone modifications
Recommended reading – epigenetics papers of interest
- Tahiliani et al. Conversion of 5-methylcytosine to 5-hydroxymethylcytosine in mammalian DNA by MLL partner TET1. Science. 2009;15;324(5929):930-5.
- Pastor et al. Genome-wide mapping of 5-hydroxymethylcytosine in embryonic stem cells. Nature. 2011;19;473(7347):394-7.
- L. Bintu et al. Dynamics of epigenetic regulation at the single-cell level, Science 2016; 35: 720-724.
- Scott-Browne et al. Dynamic Changes in Chromatin Accessibility Occur in CD8+ T Cells Responding to Viral Infection. Immunity. 2016;20;45(6):1327-1340.
Professor Rao has kindly made available a presentation detailing her group's groundbreaking research and providing the latest information about 5hmC and cancer.
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