Deciphering the cis-regulatory logic of circadian reprogramming in a mouse model of Alzheimer's Disease

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PROJECT SUMMARY Alzheimer’s Disease (AD), the most common origin of dementia, is frequently accompanied by circadian rhythm disruption. It is not clear how circadian function relates to neurodegeneration, but deletion of the core circadian transcription factor (TF) BMAL1 in astrocytes causes both an AD-like cellular phenotype and increased neuron loss after oxidative stress. Within astrocytes of a mouse model of AD, we have observed a phenomenon known as circadian reprogramming, in which some genes lose circadian expression while other genes gain circadian expression. The goal of this proposal is to determine how circadian reprogramming is regulated in astrocytes of our AD mouse model. I hypothesize that within AD-model astrocytes, BMAL1 interacts with disease-specific TFs to bind to new genomic locations and cause new genes to become rhythmic. To test this hypothesis, I will 1) determine whether BMAL1 changes in astrocytes of our AD mouse model to bind to reprogrammed genes (Aim 1), and 2) identify TF motif combinations sufficient to produce circadian gene expression and reprogramming in astrocytes of our AD mouse model (Aim 2). To characterize BMAL1 binding in Aim 1, I have preliminary data that FLEXCCs, a technology to record TF binding on a cell type specific level, can be used to record BMAL1 binding. For this project, I will use FLEXCCs to record BMAL1 binding in astrocytes of both wildtype mice and in our AD mouse model. In Aim 2, I will identify TF motif combinations that drive circadian expression in our AD mouse model using a Massively Parallel Reporter Assay (MPRA) and capture astrocytic transcripts with translating ribosome affinity purification and RNA-sequencing (TRAP-seq). This proposal will begin to determine how the cellular environment of AD-like astrocytes generates circadian reprogramming. By establishing a mechanism of circadian reprogramming in astrocytes in a mouse model of AD, I will help elucidate how circadian disruption progresses in AD and uncover new pathways to potentially alter disease course.