Growing evidence implicates abnormalities in chromatin regulators in a range of neuropsychiatric illnesses, including ASD and schizophrenia. However, how these chromatin regulators affect the pathophysiology of psychiatric illnesses is currently not well understood. This proposal seeks to characterize genome-wide chromatin landscape in human brains across two major epochs representing prenatal and postnatal developmental stages via Hi-C, a genome-wide chromosome conformation capture technology. Cellular heterogeneity will be delineated via fluorescence-activated nuclear sorting (FANS) to profile neurons and non- neural cells separately. Collectively, we will determine the developmental and cell-type specific 3-dimensional (3D) chromatin architecture that underlies gene regulation (Aim 1). We will leverage chromatin interaction maps to identify genes that are physically interacting with non-coding variants that predispose to neuropsychiatric disorders (Aim 2). Investigation of developmental and cell-type specific 3D chromatin architecture will specify the developmental stage and cell type that contributes to the pathophysiology of the disorders. Moreover, cross-disorder analysis will delineate shared genetic etiology and neurobiological mechanisms across psychiatric illnesses. The functional relationship between non-coding variants and Hi-C defined target genes will be interrogated by experimental validation using massive parallel reporter assays (MPRA) and CRISPR/Cas9-mediated genome editing (Aim 3). Collectively, completion of this project will unravel the folding principles of the genome underlying the psychiatric etiology. The K99 phase of this award will be essential for me to finalize my postdoctoral training. It will allow me to continue to work under supervision of Dr. Daniel H. Geschwind to finalize Aims 1 and 2, where his knowledge of neurodevelopmental biology and genetics will be instrumental. Most importantly, training with the other three members of my advisory board will be required for the experiments I want to set up as an independent researcher. Dr. Jason Ernst will help me with the integrative analysis in Aims 1 and 2, and the analysis of MPRA results in Aim 3. Dr. Eleazar Eskin will guide me in identifying causal variants in association studies of human psychiatric disorders in Aim 2. Dr. Sri Kosuri will aid me with the design and analysis of MPRA in Aim 3. Finally, the environment and opportunities at UCLA (workshops, conferences, and meetings) will provide the ideal setting for the final stages of my postdoctoral training.
Chromatin is organized into a dynamic 3-dimensional structure in the nucleus, which provides an essential basis for gene regulation. A significant proportion of genomic variation predisposing one to brain disease does not reside in genes, and is thought to exert its effects through chromatin interactions. The work proposed in this application leverages chromatin interaction profiles to permit the large-scale annotation of previously uncharacterized gene regulatory relationships relevant to brain disease, which may lead to a better understanding and treatment of brain disease.
