Coordination of two enhancers drives expression of olfactory trace amine-associated receptors

Olfactory sensory neurons (OSNs) are functionally defined by their expression of a unique odorant receptor (OR). Mechanisms underlying singular OR expression are well studied, and involve a massive cross-chromosomal enhancer interaction network. Trace amine-associated receptors (TAARs) form a distinct family of olfactory receptors, and here we find that mechanisms regulating Taar gene choice display many unique features. The epigenetic signature of Taar genes in TAAR OSNs is different from that in OR OSNs. We further identify that two TAAR enhancers conserved across placental mammals are absolutely required for expression of the entire Taar gene repertoire. Deletion of either enhancer dramatically decreases the expression probabilities of different Taar genes, while deletion of both enhancers completely eliminates the TAAR OSN populations.

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Fig: Enrichment of TAAR OSNs: a Schematic illustration of the design strategy for ires-Cre knockin mice. DNA sequences encoding the ires-Cre alleles were inserted after the endogenous stop codon of Taar5 or Taar6 genes, along with the gene encoding neomycin (neo) resistance. The neo cassette flanked by flippase recognition target (FRT) sites was further excised by crossing to mice that express germline Flp recombinase. Taar5-ires-Cre or Taar6-ires-Cre mice were then crossed with Cre-dependent reporter lines to allow for fluorescent labeling of TAAR OSNs. b FACS-sorted reporter-positive (Taar5+ or Taar6+) and reporter-negative (control) cells were collected for RNA-seq experiments. The values of transcripts per million (TPM) extracted for the total Taar and OR genes were plotted. c The TPM values of all the 15 Taar genes were plotted in reporter-positive (Taar5+ or Taar6+) and reporter-negative (control) cells, showing that reporter-positive cells were composed of mixed TAAR OSN populations. d The canonical olfactory signaling molecules were expressed at similar level in reporter-positive (Taar5+ or Taar6+) and reporter-negative (control) cells, including Gnal,Adcy3, Cnga2, and Ano2. e H3K9me3 ChIP-seq results showed that both theTaar cluster and the OR cluster were decorated by H3K9me3 in Taar5+ OSNs. In contrast, the Taar cluster was devoid of H3K9me3 decoration in control cells that are mainly OR OSNs. In bd, n = 10 for control cells, n = 7 for Taar5+ reporter-positive cells, n = 1 for Taar6+ reporter-positive cells. Data are presented as mean values ± SEM.

In addition, both of the enhancers are sufficient to drive transgene expression in the partially overlapped TAAR OSNs. We also show that the TAAR enhancers operate in cis to regulate Taar gene expression. Our findings reveal a coordinated control of Taar gene choice in OSNs by two remote enhancers, and provide an excellent model to study molecular mechanisms underlying formation of an olfactory subsystem.

Fei, A., Wu, W., Tan, L. et al. Coordination of two enhancers drives expression of olfactory trace amine-associated receptors. Nat Commun 12, 3798 (2021). https://doi.org/10.1038/s41467-021-23823-4

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