Molecular definitions of neural cell types largely depend on the expression of RNAs or proteins as assessed by in situ hybridization, RNA array and sequencing, and immunohistochemistry. However, recent studies are demonstrating that gene regulatory elements, such as enhancers, can have highly specific spatial and temporal activity patterns in the developing brain. Thus, enhancer activity can be used to define neural cell types, and importantly, also have other broad applications. First, they can be used as tools to drive gene expression in specific cell types, which can then be used to visualize and/or purify the cells (GFP), modify gene expression in the cells (Cre), modify electrical activity (channel rhodopsin), and visualize electrical activity in the cells (GCaMP). Secondly, knowledge about the nature and position of enhancers enables geneticists to identify disease alleles that map in extra-exonic genomic space. Herein, we will focus on identifying enhancers that are active in cortical interneurons, during development and in the mature state. We choose to study cortical GABAergic interneurons because of their central role in cortical function and diseases. We will focus on these GABAergic neurons derived from the medial ganglionic eminence (MGE), which generates the majority of cortical interneurons.
Our aim i s to identify novel enhancers that are active in cortical interneurons using three assays: 1) histone (H3K27Ac) ChIP-seq (marker of active enhancers);2) transcription factor (TF) ChIP- seq using TFs that regulate cortical interneurons development and function (Arx, Dlx2 and Lhx6);3) a newly developed in vivo assay of enhancer function based on viral transduction of the enhancer driving Cre and GFP in immature cortical interneurons. We will then use a series of methods to define the interneuron subtypes that have enhancer activity. Together, our unique approach should define interneuronal cell types (developmental and adult), and simultaneously generate a powerful toolkit that will enable new ways to assess neural function and disease.
Identification of new neural cell types, especially cortical interneurons, will be important for understanding diseases of the cerebral cortex, such as epilepsy, autism and schizophrenia. Furthermore, identification of enhancer elements will aid in mapping of disease genes causing human neurogenetic disorders.