Nr4a1 regulates cell-specific transcriptional programs in inhibitory GABAergic interneurons

The patterns of synaptic connectivity and physiological properties of diverse neuron types are shaped by distinct gene sets. Our study demonstrates that, in the mouse forebrain, the transcriptional profiles of inhibitory GABAergic interneurons are regulated by Nr4a1, an orphan nuclear receptor whose expression is transiently induced by sensory experiences and is required for normal learning. Nr4a1 exerts contrasting effects on the local axonal wiring of Parvalbumin- and Somatostatin-positive interneurons, which innervate different subcellular domains of their postsynaptic partners. The loss of Nr4a1 activity in these interneurons results in bidirectional, cell-type-specific transcriptional switches across multiple gene families, including those involved in surface adhesion and repulsion. Our findings reveal that combinatorial synaptic organizing codes are surprisingly flexible and highlight a mechanism by which inducible transcription factors can influence neural circuit structure and function. The first goal of this study was to identify genes whose expression levels are altered in cortical Parvalbumin (PV)- or Somatostatin (Sst)-positive GABAergic interneurons (INs) during associative learning. This was achieved using RiboTag, a technique for immuno-isolation of translating mRNAs in complexes with ribosomes containing a genetically targeted HA epitope-tagged protein, Rpl22. We introduced RiboTag into each IN population by crossing the Cre recombinase-dependent Rpl22-HA mouse allele with well characterized PvalbCre and SstCre drivers, extracted cell-specific pools of mRNAs from the cortices and hippocampi of young adults at postnatal day (p) 60, and analyzed these mRNAs by deep sequencing (RNA-seq). We surveyed acute changes in IN transcriptomes that were elicited by contextual fear conditioning (CFC), a neurobehavioral paradigm for the acquisition of stable associative memory from an adverse environment where animals received series of foot shocks. In parallel experiments, PvalbCre/RiboTag and SstCre/RiboTag mice received single doses of the GABA receptor antagonist, pentylenetetrazol (PTZ), to identify genes whose mRNA levels were altered by artificial widespread network excitation as a frame of reference. We also used RiboTag to survey transcriptional profiles of Nr4a1-deficient PV and Sst cells in Nr4a1 conditional knockpoiut mice.