Enhancers define cortical interneuron types

Principal Investigator: John L. R. Rubenstein
UCSF Neuroscience
Title: “Identification of enhancers whose activity defines cortical interneuron types”
BRAIN Category: Tools for Cells and Circuits (RFA MH-14-216)

Dr. Rubenstein and colleagues plan to identify enhancer molecules specific to particular types of interneurons – that relay neural signals – and use this information to profile distinct cell types and new ways to manipulate genes.

NIH Webpages

Cortical Circuits: Projection Neurons and Interneurons

Cortical Circuits: Projection Neurons and Interneurons

Project Description

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 is 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.

Public Health Relevance Statement

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.

NIH Spending Category

Eye Disease and Disorders of Vision; Genetics; Neurosciences

Project Terms

Adult; Agreement; Alleles; Autistic Disorder; Automobile Driving; base; behavior measurement; Behavioral; Binding (Molecular Function); Biological Assay; Brain; Cell Transplants; cell type; Cells; Cerebral cortex; Chip seq; Development; Disease; Electrophysiology (science); Embryo; Enhancer Elements (Genetics); Enhancers; Epilepsy; Funding; Gene Expression; Genes; Genetic Transcription; Genomics; Histones; Human; Image; Immunohistochemistry; In Situ Hybridization; in vivo; Interneuron function; Interneurons; Knowledge; Label; Lentivirus Vector; Maps; Medial; Methods; Molecular; Molecular Genetics; Morphology; Mus; Nature; Neonatal; neurogenetics; Neurons; Neurophysiology – biologic function; neuropsychiatry; novel; optogenetics; Pattern; Phenotype; Physiological; Physiology; Play; Positioning Attribute; Process; progenitor; Property; Proteins; public health relevance; ranpirnase; Regulatory Element; Reporter; Research; research study; Rhodopsin; RNA; Role; Schizophrenia; Series; Slice; Staging; Taxonomy; Time; tool; transcription factor; Transplantation; Viral; Whole-Cell Recordings

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