Enhancer RNAs and enhancer-centric gene regulatory networks in vascular dementia

Recent studies have reported widespread transcription of mammalian enhancers into noncoding RNAs in a stimulus-dependent manner. Growing evidence shows that these RNAs, known as enhancer RNAs (eRNAs), have essential roles in orchestrating higher-order chromatin interactions to facilitate gene expression and phenotypic outcomes during development and disease. As a result, eRNAs are emerging as an important component of the gene regulatory machinery. Due to their recent discovery, the expression, and roles of eRNAs in vascular dementia are virtually unknown. Recently, we applied a combination of genome-wide RNA- seq and genome-wide enhancer mapping using H3K27ac ChIP-seq to identify several ischemia-induced eRNAs at multiple time-points of reperfusion in the mouse cerebral cortex. This was the first study on eRNAs in brain vascular injury. We found an important role for one such eRNA in modulating post-stroke brain damage and gene expression. In the current project, we will apply our expertise in eRNA discovery and function to identify eRNAs that are expressed in the adult hippocampus specifically during the development of vascular dementia. Using a standardized bilateral carotid artery stenosis (BCAS) model of vascular dementia, we will induce hippocampal hypoperfusion in the mouse brain across a 30-day time-window. In Aim 1, we will use an unbiased, genome-wide approach incorporating H3K27ac ChIP-seq and RNA-seq to map active enhancer elements and their respective eRNAs from the earliest stages of cerebral hypoperfusion (day-3 post-BCAS) to the manifestation of vascular dementia (day-30 post-BCAS). In Aim 2, along the same timeline we will apply the cutting-edge method of Hi-C to capture genome-wide higher order chromatin interactions to pinpoint enhancer-to-gene promoter contacts and map their dynamics along the BCAS trajectory. Together, this work will identify novel enhancers and eRNAs that are activated specifically in response to BCAS-induced hypoperfusion in the hippocampus and generate a catalog of putative enhancer-gene relationships that may encompass regulatory networks. These data will lay the foundation for future mechanistic and functional studies investigating these regulatory networks and their impact on the development of the hippocampal pathophysiology and vascular dementia.