Abstract
Significant advances in circuit-level analyses of the brain require tools that allow for labeling, modulation of gene expression, and monitoring and manipulation of cellular activity in specific cell types and/or anatomical regions. Large-scale projects and individual laboratories have produced hundreds of gene-specific promoter-driven Cre mouse lines invaluable for enabling genetic access to subpopulations of cells in the brain. However, the potential utility of each line may not be fully realized without systematic whole brain characterization of transgene expression patterns. We established a high-throughput in situ hybridization (ISH), imaging and data processing pipeline to describe whole brain gene expression patterns in Cre driver mice. Currently, anatomical data from over 100 Cre driver lines are publicly available via the Allen Institute's Transgenic Characterization database, which can be used to assist researchers in choosing the appropriate Cre drivers for functional, molecular, or connectional studies of different regions and/or cell types in the brain.
Highlights
Experimental access to neural components, i.e., the specific cell types and neuronal populations which constitute a circuit, is critical for understanding the complexity of network connectivity and functional roles in perception and behavior
The online Transgenic Characterization database contains data from lines with Cre driven by enhancer elements, a small number of other driver lines (Flp, Dre, tTA, GFP), and reporter lines, which were excluded from the analyses here
COMPARISON OF WHOLE BRAIN Cre EXPRESSION PATTERNS WITH ENDOGENOUS GENE EXPRESSION To compare expression patterns across the entire brain between genes and the same gene promoter-driven Cre expression, we identified in situ hybridization (ISH) datasets from postnatal day 56 (P56) mice generated as part of the Allen Mouse Brain Atlas (ABA) (Lein et al, 2007), which corresponded to the specific promoters of Cre lines in the Transgenic Characterization pipeline
Summary
Experimental access to neural components, i.e., the specific cell types and neuronal populations which constitute a circuit, is critical for understanding the complexity of network connectivity and functional roles in perception and behavior. This genetic strategy is highly flexible, enabling cell type-specific and regional control of Cre expression by unique gene promoters combined with an increasing variety of reporter genes, including fluorescent proteins, optogenetic molecules, and calcium indicators that become active in the presence of Cre (Madisen et al, 2010, 2012; Zariwala et al, 2012; Zeng and Madisen, 2012) Using this binary system, cell-specific transgene expression is accomplished practically through breeding of Cre driver and reporter transgenic mouse lines, co-injection of Cre driver and reporter engineered recombinant viruses into wild type mice, or the injection of recombinant viruses into transgenic mouse lines, which allows for additional spatial and temporal control of reporter gene expression. These approaches are becoming common tools in many neuroscience laboratories and have contributed to significant advances in understanding a variety of specific functional circuits (O’Connor et al, 2013; Ramirez et al, 2013; Anthony et al, 2014)
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