Transcriptional regulation in mouse macrophages : the role of enhancers in macrophage activation and infection

The results presented in Chapter 3 of this thesis were published as (the Authors retain copyright): Denisenko, E., Guler, R., Mhlanga, M. M., Suzuki, H., Brombacher, F., & Schmeier, S. (2017). Genome-wide profiling of transcribed enhancers during macrophage activation. Epigenetics & Chromatin, 10(1), 50. doi: 10.1186/s13072-017-0158-9Macrophages are sentinel cells essential for tissue homeostasis and host defence. Owing to their plasticity, macrophages acquire a range of functional phenotypes in response to microenvironmental stimuli. Of those, M(IFN-γ) and M(IL-4/IL-13) macrophage activation states are well known for their opposing pro- and anti-inflammatory roles. Imbalance in these populations of macrophages has been implicated in progression of various diseases. Macrophages also comprise the first line of an organism’s defence against Mycobacterium tuberculosis, the causative agent of tuberculosis; interactions between the bacteria and host macrophages define the infection outcome. The area of mammalian transcriptional regulation progressed remarkably with recent advances in high-throughput technologies. Enhancers emerged as crucial regulatory DNA elements capable of activating transcription of target genes at distance in an orientation-independent manner. A recent discovery revealed that enhancers can be transcribed themselves into enhancer RNAs, or eRNAs. Enhancers were shown to be pervasive, yet the associated regulatory patterns remain largely unknown and require further research. In this thesis, we investigated in silico transcribed enhancers in mouse tissues and cell lines, with a particular focus on macrophages. We have performed a large-scale study to identify transcribed enhancers across multiple tissues and to characterise their properties. In macrophages, we have established the most accurate, to our knowledge, genome-wide catalogue of transcribed enhancers and enhancer-gene regulatory interactions. We have inferred enhancers that might drive transcriptional responses of protein-coding genes upon M(IFN-γ) and M(IL-4/IL-13) macrophage activation, and demonstrated stimuli specificity of regulatory associations. We have conducted the first to our knowledge study of the role of transcribed enhancers in macrophage response to Mycobacterium tuberculosis infection. Taken together, the present work provides new insights into genome-wide enhancer-mediated transcriptional control of macrophage protein-coding genes in different conditions. Given the increasing promise for enhancer and chromatin-directed therapy, this work paves the way for further studies towards hostdirected therapies and novel treatments for tuberculosis and immune diseases associated with macrophage dysfunction