Nuclear receptors (NR) constitute a large transcription factor (TF) family with ~50 NRs identified in human or mouse. NRs have crucial roles in multiple tissues and biological processes. Consequently, misregulation of NR gene expression has been linked to several severe pathologies including cancer and neurodegenerative diseases. Despite their pathological importance, the core NR gene regulatory network (i.e. the protein-DNA interactions or PDIs controlling the expression of NR genes) has been very poorly studied. We will initiate the elucidation of the NR gene regulatory network by focusing on primary microglial cells as a non-transformed, and homogeneous model system. Microglia are poorly characterized macrophage-like brain immune cells, which may have both neurotoxic and neuroprotective properties. The majority of NRs exhibit a very dynamic expression profile in activated macrophages. Together with our preliminary data, this suggests that NRs may play a central role in microglial gene regulatory networks as well. The biological question of this proposal is to understand “which, when, and how NRs are expressed in microglia in response to neurotoxic stimuli”. We will (1) identify the temporal gene expression profiles of NRs in activated microglia; (2) identify the TFs controlling differentially expressed microglial NRs by uniquely combining two novel technologies (chromosome conformation capture and high-throughput PDI screening), whose respective co-inventors will both be involved in the project; and (3) experimentally validate the detected PDIs in microglia using siRNA and ChIP. The resulting list of high-confidence PDIs will be used to generate a first microglial NR gene regulatory network. The latter can be used for future modeling efforts to predict how the network will behave under distinct physiological conditions, or how to manipulate the network such that the neuroprotective properties of microglia are stimulated and its neurotoxic properties suppressed.
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