The role of alternative splicing in regulation of macrophage inflammatory responses

Immune cells are required to function under low oxygen tensions. Tissues injured by inflammation and infection can become rapidly depleted of nutrients and oxygen. Acute foci of inflammation are extreme areas of oxygen limitation (hypoxia) due to microvascular injury, reduced blood perfusion, and increased metabolic activity of recruited inflammatory cells and replicating pathogens. These conditions are extremely challenging for macrophages and neutrophils, crucial cells of the innate immune system, which are rapidly recruited in response to tissue damage and entry of pathogens.

We have previously shown that the protein jumonji domain containing 6 (Jmjd6) is expressed in macrophages and upregulated under inflammatory and hypoxic conditions. Jmjd6 is a nuclear RNA binding protein which regulates alternative splicing by posttranslational hydroxylation of key splicing factor proteins. Alternative splicing regulation is controlled by stress response mechanisms, however, the molecular nature of these mechanisms is just beginning to emerge. Despite the importance of alternative splicing in enabling proteome complexity in eukaryotes its role in the regulation of immune responses is still very poorly understood. The aim of this PhD project is to analyse how Jmjd6 regulates the transcriptome in macrophages in response to danger signals such as oxygen stress and triggers of inflammation. We will aim to identify mRNA targets of Jmjd6 that are alternatively spliced in inflammatory activated and hypoxic macrophages. To achieve this we will use new immunoprecipitation methods coupled with RNA sequencing to identify Jmjd6 RNA binding sites and transcript targets. The project will also involve microscopic imaging of Jmjd6 nuclear shuttling mechanisms and the characterisation of host defence responses of Jmjd6 knockout macrophages to intra- and extracellular pathogens. The later will involve extensive training in mouse genetics and the use of in vivo animal models.

The PhD studies will be performed at the Roslin Institute the foremost livestock research centre in the UK. The student will have access to world-class research facilities and training.