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We sequenced the transcriptome of brainstem interneurons in the specialized respiratory rhythmogenic site dubbed preBötzinger Complex (preBötC) from newborn mice. To distinguish molecular characteristics of the core oscillator we compared preBötC neurons derived from Dbx1-expressing progenitors that are respiratory rhythmogenic to neighbouring non-Dbx1-derived neurons, which support other respiratory and non-respiratory functions. Results in three categories are particularly salient. First, Dbx1 preBötC neurons express κ-opioid receptors in addition to μ-opioid receptors that heretofore have been associated with opiate respiratory depression, which may have clinical applications. Second, Dbx1 preBötC neurons express the hypoxia-inducible transcription factor  Hif1a  at levels three-times higher than non-Dbx1 neurons, which links core rhythmogenic microcircuits to O 2 -related chemosensation for the first time. Third, we detected a suite of transcription factors including  Hoxa4  whose expression pattern may define the rostral preBötC border,  Pbx3  that may influence ipsilateral connectivity, and  Pax8  that may pertain to a ventrally-derived subset of Dbx1 preBötC neurons. These data establish the transcriptomic signature of the core respiratory oscillator at a perinatal stage of development.

Transcriptome of neonatal preBötzinger complex neurones in Dbx1 reporter mice