Measuring RNA from a defined subset of cells derived from a complex tissue is an important challenge that has confounded the field. Two recently developed tools have simplified this issue. The RiboTag and BacTRAP (Translating Ribosome Affinity Purification) methods allow for immunoprecipitation of ribosome-associated RNA from specific cells within complex tissues by expressing tagged ribosomal protein in desired cell types (GFP-tagged RPL10 for TRAP and hemagglutinin-tagged RPL22 for RiboTag) (Doyle et al, 2008; Heiman et al, 2008; Sanz et al, 2009). More specifically, these methods allow analysis of the ‘translatome’—ribosome-associated mRNA—which may be particularly sensitive to event-dependent regulation of protein translation. For example, RiboTag-expressing transgenic mice were recently used to compare differential gene expression responses to cocaine in striatal neurons expressing D1 and D2 dopamine receptors (Chandra et al, 2015).

Because RiboTag and BacTRAP allow the measurement of ribosome-associated mRNA, it is not a direct reflection of the pool of total RNA but can provide intriguing insights into regulatory shifts in protein synthesis in response to a stimulus. Conditional expression using either Cre-dependent viral vectors or transgenic breeding strategies allows highly specific expression of RiboTag in desired cells, and the RNA enriched from the immunopurification can be efficiently harvested and interrogated using RT-PCR, microarrays, or RNA-seq. For example, we have used dual-virus transduction approaches to analyze the molecular phenotype of distinct output pathways in lateral habenula and have utilized transgenic mice that express RiboTag in Pet1-positive neurons to investigate how stress alters the translatome in serotonin neurons.

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