Post-transcriptional Regulation of Gene Expression in Innate Immunity

Abstract

Gene expression can be regulated from transcriptional initiation to RNA processing and turnover time and post translational modification of a protein. The majority of studies of gene expression have focussed on transcription. However, it is also important to understand how post-transcriptional pathways are regulated in response to inflammatory stimuli. Chapter 1 introduces background to gene expression during post transcriptional regulation and its regulation related to inflammatory diseases. The innate immune response to LPS is highly dynamic yet tightly regulated. RNA decay pathways include nonsense-mediated decay, the RNA decay exosome, P-body localised deadenylation, decapping and degradation and AU-rich element targeted decay mediated by tristetraprolin. Chapter 2, we examined the regulation of RNA degradation pathways during the lipopolysaccharide response in macrophages and these results have been published. Alternative splicing has been identified as a key process in post-transcriptional regulation of gene expression in higher eukaryotes. In the immune system, alternative splicing provides a major role in regulating gene expression and generating the diverse mRNA transcripts and protein isoforms, therefore giving rise to protein diversity.Intron retention (IR) is a form of alternative splicing where an intron is not removed during transcription coupled splicing and is considered a widely regulated process during gene expression. Chapter 3 we examined its regulation during inflammation. Also, gene expression can be regulated via nonsense-mediated decay, which can precisely control the timing and level of gene expression as well as eliminating unstable or toxic protein production. SMG1 is a member of the PIKK (phosphoinisitide 3-kinase related kinases) family and plays an important role in NMD. For Chapter 4 we investigated the role of SMG1 in the regulating in response to inflammatory stimuli. We generated a novel animal model of total SMG1 loss in macrophages to address this question. For Chapter 5, we showed how to analyse RNA-seq. of BMM from LysM+/CreSmg1fl/fl (Cre) and Smg1fl/fl (wild-type) mice treated with LPS treatment at dedicated time points by gene ontology tools to discover gene enriched clusters during an LPS treatment between LysM+/CreSmg1fl/fl (Cre) and Smg1fl/fl (wild-type) mice. A final discussion and future directions for this field of study are provided in Chapter 6.