Figure 1. Identification of UPF3B-regulated genes and NMD target genes in the olfactory system.

(A) The weight of Upf3b-null vs. WT (wild type) mice at the indicated time points. Upf3b-null mice gain weight slowly during postnatal development but then reach the weight of WT mice at the last time point (9 weeks), a pattern indicative of a partial olfactory defect. *, p<0.05. (B) qPCR analysis of olfactory marker genes in Upf3b-null and WT OE (n = 6). **, p<0.01; ****, p<0.0001. (C) Heatmap of genes differentially expressed in mOSNs from Upf3b-null (KO) vs. WT mice (four biological replicates from each are shown). Row names labeled as green are Olfr genes. Right, the most statistically significant GO terms associated with upregulated genes (top) and downregulated genes (bottom) after Upf3b loss. (D) A list of most statistically enriched GO terms associated with the 52 high-confidence UPF3B-dependent NMD target mRNAs we identified in mOSNs.

Figure 1—figure supplement 1. Upf3b-null mice behavior and purified mOSNs.

(A) Behavior analysis of Upf3b-null and control (wild type) mice in response to exposure to animal urine or food. (n = 10). (B) FACS plots of dissociated cells from Upf3b-null and control OEs used to purify Omp-eYPF+ cells for RNA-seq analysis. The y-axis measures YFP expression. For each sample, three male mice (8– to 9-weeks old) were pooled together for sorting. (n = 4).

Figure 1—figure supplement 2. UPF3B-regulated genes in mOSNs.

(A) Principal component analysis of RNAseq datasets from Upf3b-null (KO) and control (WT) mOSNs. (B) qPCR validation of genes shown by RNA-seq analysis to be upregulated (Adcy6, Fosl2, Gdpd3, and Ptch1) or downregulated (Cw22, Fut10, Olfr827, Olfr855, and Olfr1208) in Upf3b-null mOSNs relative to control mOSNs. The genes were chosen on the basis of having known functions, including in neural development. (n = 3). *p<0.05. (C) Immunofluorescence analysis of OE sections from Upf3b-null and wild-type (WT) samples stained with FUT10 and OMP antibodies. FUT10 was chosen on the basis of having known roles in neural development. Nuclei were labeled with DAPI. (n = 3). (D) Heatmap showing the expression of canonical OSN precursor/OSN markers in the indicated Upf3b-null (KO) and control (WT) mOSN-enriched samples, based on RNA-seq analysis. RNA expression levels are represented on a log10 scale of TPM values plus one (0, not expressed; 4, highly expressed). (E) Heatmap showing the expression of all annotated Olfr genes (in ascending order) in the indicated mOSN-enriched samples. RNA expression levels are represented on a log10 scale of TPM values plus one (0, not expressed; 3, highly expressed).