A Mammalian enhancer trap resource for discovering and manipulating neuronal cell types

Abstract

There is a continuing need for driver strains to enable cell-type-specific manipulation in the nervous system. Each cell type expresses a unique set of genes, and recapitulating expression of marker genes by BAC transgenesis or knock-in has generated useful transgenic mouse lines. However, since genes are often expressed in many cell types, many of these lines have relatively broad expression patterns. We report an alternative transgenic approach capturing distal enhancers for more focused expression. We identified an enhancer trap probe often producing restricted reporter expression and developed efficient enhancer trap screening with the PiggyBac transposon. We established more than 200 lines and found many lines that label small subsets of neurons in brain substructures, including known and novel cell types. Images and other information about each line are available online (enhancertrap.bio.brandeis.edu).DOI: http://dx.doi.org/10.7554/eLife.13503.001

Variation in Activity State, Axonal Projection, and Position Define the Transcriptional Identity of Individual Neocortical Projection Neurons

“…Interestingly, the gene expression pooled across the two BC L6CThN subtypes identified here is consistent with previously observed aggregate gene expression signatures of Ntsr1-Cre-expressing neurons (Figures S3B and S3C; Shima et al, 2016). The two subtypes also share some transcriptional similarity with two recently defined subtypes in primary visual cortex (Figure S3A; Tasic et al, 2016).…”

“…The two subtypes also shared transcriptional similarities with highlighted genes expressed in two recently defined subtypes of L6CThNs in primary visual cortex (Figure S3A; Tasic et al, 2016). When we pooled our data across the two types, we also found a close correspondence between our data and a recent study which assessed the gene expression of small pools of Ntsr1-Cre-expressing L6CThNs using bulk RNA-seq (Figures S3B and S3C; Shima et al, 2016). …”

“…Studies of primary sensory cortex demonstrate that L6CThNs are heterogeneous (Bourassa and Deschênes, 1995; Bourassa et al, 1995; Briggs et al, 2016; Katz, 1987; Killackey and Sherman, 2003; Kwegyir-Afful and Simons, 2009; Shima et al, 2016; Tasic et al, 2016; Zhang and Deschênes, 1997). In rat barrel cortex (BC), L6CThNs in upper L6 project to the ventral posterior medial nucleus (VPM) of the thalamus, while L6CThNs in lower L6 project primarily to both VPM and the posterior medial nucleus (POm; Bourassa et al, 1995; Killackey and Sherman, 2003).…”

“…These data reinforce the importance of measuring response variables at single-cell resolution, as they may not be uniform in retrogradely or genetically labeled populations. Profiling a greater number of neurons or selecting the profiled neurons differently may reveal additional subtypes of L6CThNs (Bourassa and Deschênes, 1995; Bourassa et al, 1995; Shima et al, 2016). Alternatively, such studies may reveal that subtle variations in axonal projection pattern seen in some anatomical studies are not apparent in the neurons’ expression profiles.…”

“…We compared expression profiles of layer 6 corticothalamic neurons (L6CThNs), a heterogeneous population of cortical projection neurons defined by anatomical, functional, and gene expression studies, making them ideally suited for investigating relationships between transcriptional subtypes and other cellular properties (Bourassa and Deschênes, 1995; Bourassa et al, 1995; Briggs et al, 2016; Katz, 1987; Killackey and Sherman, 2003; Kwegyir-Afful and Simons, 2009; Shima et al, 2016; Sorensen et al, 2015; Tasic et al, 2016; Zhang and Deschênes, 1997). By combining scRNA-seq with an enrichment strategy that preserved axonal target information, we identified two transcriptionally distinct L6CThN subtypes whose transcriptional profiles reflected their long-range projection targets and laminar position within layer 6 (L6).…”