How do the cells of an organism, all of which have exactly the same genetic code, adopt such different fates, morphologies and functions? And how do they then respond to the signals and stresses around them in order to make up a living, growing, healthy organism that can adapt to its environment?
Seminal work in the field of Epigenetics has taught us that the answer to the first question lies in the fact that our genome is subject to epigenetic regulation, which ensures its stability and determines when and where genes produce their transcript and protein products. And the answer to the second question lies largely within the fact that these proteins, which then go on to execute most of the cell’s functions, are themselves subject to regulatory mechanisms which determine when, where and how a protein will function. Our lab combines these two fascinating biological questions to understand how genome-regulating proteins are themselves regulated during development.
We employ biochemistry, cell and molecular biology, genomic and epigenetic approaches and mouse model systems to understand the mechanisms that modulate the function of epigenetic regulators, how these mechanisms are perturbed in disease and how they may be targeted for therapeutic effect. We have a particular interest in protein post-translational modifications (PTMs). These are small chemical changes that happen on proteins as a result of cell signalling changes and can quickly alter the activity, stability and sub-cellular localisation of these proteins, as well as their affinity for other molecules. As a result, PTMs add an enormous degree of sophistication to biological systems, beyond what can be achieved by gene regulation.
Our favourite PTM is citrullination, the conversion of an arginine residue to the non-coded amino acid citrulline. Exciting developments in this classically under-explored field have shown that citrullination and the enzymes that catalyse it, the peptidylarginine deiminases (PADIs or PADs), regulate many aspects of cell physiology, while their deregulation contributes to the development of pathologies such as autoimmunity, neurodegeneration and cancer. Understanding the mechanisms that control PADIs and other epigenetic regulators in response to developmental cues and cellular stresses can offer valuable insights into human health, which can be exploited towards therapeutic benefit in a variety of disease conditions.
During mammalian embryo development, pluripotent epiblast cells diversify into the three primary germ layers, which will later give rise to all fetal and adult tissues. These processes involve profound transcriptional and epigenetic changes that require precise coordination. Peptidylarginine deiminase IV (PADI4) is a transcriptional regulator that is strongly associated with inflammation and carcinogenesis but whose physiological roles are less well understood. We previously found that expression is associated with pluripotency. Here, we examined the role of PADI4 in maintaining the multi-lineage differentiation potential of mouse embryonic stem (ES) cells. Using bulk and single-cell transcriptomic analyses of embryoid bodies (EBs) derived from knock-out () mouse ES cells, we find that PADI4 loss impairs mesoderm diversification and differentiation of cardimyocytes and endothelial cells. Additionally, deletion leads to concerted downregulation of genes associated with polarized growth, sterol metabolism and the extracellular matrix (ECM). This study indicates a requirement for in the specification of the mesodermal lineage and reports the associated transcriptome, providing a platform for understanding the physiological functions of in development and homeostasis. This article is part of the Theo Murphy meeting issue 'The virtues and vices of protein citrullination'.
The post-translational modification of proteins expands the regulatory scope of the proteome far beyond what is achievable through genome regulation. The field of protein citrullination has seen significant progress in the last two decades. The small family of peptidylarginine deiminase (PADI or PAD) enzymes, which catalyse citrullination, have been implicated in virtually all facets of molecular and cell biology, from gene transcription and epigenetics to cell signalling and metabolism. We have learned about their association with a remarkable array of disease states and we are beginning to understand how they mediate normal physiological functions. However, while the biochemistry of PADI activation has been worked out in exquisite detail , we still lack a clear mechanistic understanding of the processes that regulate PADIs within cells, under physiological and pathophysiological conditions. This review summarizes and discusses the current knowledge, highlights some of the unanswered questions of immediate importance and gives a perspective on the outlook of the citrullination field.