Regulation of inducible immune gene expression in T cells compared to macrophages

The initiation, duration and resolution of an appropriate immune response is vital for defending the host against invading pathogens, toxins and cancerous cells. Such immune responses are reliant on the cooperative action of multiple cell types and the co-ordinated regulation of gene expression programs, which direct immune function. Inducible gene expression upon immune activation is determined by the complex interaction between transcription factors, the chromatin structure and chromatin modifying/remodelling factors at the regulatory regions of immune genes. The NF-˜í‚à´B transcription factor c-Rel is a key regulator of gene expression programs within the immune system. c-Rel regulates expression of cytokines and transcription factors during immune cell activation and is essential for the correct function of immune cells from divergent cell lineages. These differentiated cells are highly specialised and have a diverse range of functions requiring precise regulation of their gene expression profiles for targeted responses. This study explores the role of c-Rel in divergent lymphocyte and macrophage lineages. c-Rel has previously been shown to instigate chromatin remodelling events required for activation of the GM-CSF gene in T cells. Activation involves the depletion of hyper-acetylated histones from the promoter region of the gene, mediated by the chromatin remodelling protein BRG1. This study shows that activation of the GM-CSF gene is also c-Rel dependent in macrophages, however the gene promoter is not marked by acetylated chromatin and no loss of H3 is detected in association with activation. These findings suggest that whilst the GM-CSF gene is expressed in both T cells and macrophages, activation is regulated by fundamentally different mechanisms in the two cell types. The hypothesis underlying this study is that during the process of differentiation lineage specific chromatin structure is established at inducible gene promoters and that this chromatin structure largely dictates the cooperative regulation of gene expression through interaction with transcription factors, structural proteins and chromatin remodelling enzymes. Using genome-wide data sets, a cohort of immune genes which are regulated by c-Rel were identified. These genes were further categorised into BRG1 independent and dependent genes. The activation requirements of these genes were examined in both T cells and macrophages to determine whether the switch in regulatory control identified for the GM-CSF gene is a common feature of genes that are co-expressed by these cell types, and to characterise the mechanisms underlying this fundamental difference in regulation. Data presented in this thesis demonstrates that several genes undergo switches in the requirements for gene expression between the two cell types. The analysis of chromatin structure indicates that these differences in activation kinetics are reflective of the basal chromatin accessibility established at the genes promoter regions. Furthermore, the extent of chromatin remodelling across promoter regions correlates with the magnitude of the gene transcription response. Additionally, gene expression analysis of macrophage and T cells derived from c-Rel-/- mice suggest that c-Rel can act as a represser as well as an activator of gene transcription.