Enhancer RNAs in brain gene regulation and Alzheimer's disease

ABSTRACT Alzheimer's disease (AD) is the most common form of dementia in elderly population, and is the seventh leading cause of death in the US. Despite decades of efforts in understanding AD biology and in developing therapies, effective strategies to cure AD or to alleviate AD symptoms remain limited. AD poses a significant medical and socioeconomical burden to the world that requires urgent solutions to understand the basis of its pathogenesis and to develop effective means to prevent cognitive deterioration, or to improve patient lives. GWAS studies identified many risk genetic variants in the noncoding genome regions, particularly in enhancers, suggesting key roles of enhancer malfunction and gene deregulation in AD pathogenesis. Epigenetic studies of human AD brains also revealed significant changes such as histone acetylation at enhancers. Better knowledge of gene deregulation and enhancer malfunction is critical to better understand AD pathology and to identify new therapeutic targets. The recent findings that active enhancers often generate noncoding enhancer RNAs (eRNAs) have provided a new perspective to interpret enhancer malfunction in AD. This proposal aims to explore a unique direction by characterizing the molecular mechanisms underlying eRNA functions in brain and AD. Our overall hypothesis is that enhancers were aberrantly active in AD, resulting in deregulated eRNAs to assemble ribonucleoprotein complexes (RNPs) to organize a nuclear RNA compartment that can impact gene expression networks in brain cells. We have assembled a strong investigator team to test this hypothesis with three specific aims. First, we plan to identify deregulated eRNAs from both human samples and iPSC derived neuron and microglia cells, and identify functions of specific eRNAs in AD associated gene regulation. Second, we will study mechanisms of eRNAs' functions in depth, by using a robust RNA capture method that we have developed to systematically identify neuronal and microglia eRNA:protein interactomes. We will examine the mechanisms of eRNA-binding proteins (eRBPs) in regulating AD associated enhancer and gene transcription, and in impacting the three-dimensional genome architecture. Third, based on our recent findings of a critical role of RNA m6A methylation on eRNAs in enhancer activation and signal induced gene transcription, we will examine eRNA methylome in human brain samples and iPSC derived neuron/microglia in response to AD-associated signaling. This aim will uncover new knowledge to understand how chemical modifications of chromatin associated RNAs may mechanistically impact gene transcription to contribute to AD. Together, the expected results from this proposal will not only provide mechanistic insights into brain gene regulation and noncoding RNA functions in AD, but also can offer new therapeutic targets and strategies to intervene this devastating disease.