Marked Diversity of Unique Cortical Enhancers Enables Neuron-Specific Tools by Enhancer-Driven Gene Expression

Understanding neural circuit function requires individually addressing their component parts: specific neuronal cell types. However, not only do the precise genetic mechanisms specifying neuronal cell types remain obscure, access to these neuronal cell types by transgenic techniques also remains elusive. Whereas most genes are expressed in the brain, the vast majority are expressed in many different kinds of neurons, suggesting that promoters alone are not sufficiently specific to distinguish cell types. However, there are orders of magnitude more distal genetic cis-regulatory elements controlling transcription (i.e., enhancers), so we screened for enhancer activity in microdissected samples of mouse cortical subregions. This identified thousands of novel putative enhancers, many unique to particular cortical subregions. Pronuclear injection of expression constructs containing such region-specific enhancers resulted in transgenic lines driving expression in distinct sets of cells specifically in the targeted cortical subregions, even though the parent gene’s promoter was relatively non-specific. These data showcase the promise of utilizing the genetic mechanisms underlying the specification of diverse neuronal cell types for the development of genetic tools potentially capable of targeting any neuronal circuit of interest, an approach we call enhancer-driven gene expression (EDGE). •Enhancer ChIP-seq of cortical subregions reveals 59,372 putative enhancers•3,740 of these are specific to particular cortical subregions•This reflects the remarkable anatomical diversity of the adult cortex•Unique enhancers provide a means to make targeted cell-type-specific genetic tools Blankvoort et al. identify the enhancers active in microdissected cortical subregions, finding similar numbers of novel and unique putative enhancers as found in entire organs. They use such enhancers to make transgenic mice with expression specific to neurons of the targeted brain region, obtaining specific genetic tools from non-specific genes.