Variation in olfactory neuron repertoires is genetically controlled and environmentally modulated
- Wellcome Trust Sanger Institute, United Kingdom
- University of Campinas, Brazil
- Duke University Medical Center, United States
- Monell Chemical Senses Center, United States
- University of Pennsylvania, United States
Figures
Figure 1 with 1 supplement
RNAseq is highly sensitive for OR mRNA detection and provides a measurement of OSN diversity.
(A) Barplot of the mean normalized expression of 1249 OR genes from six biological replicates, accounting for gene length. Genes are ordered by decreasing abundance. The horizontal line is the …
Figure 1—figure supplement 1
RNAseq expression values are a proxy for OSN number.
(A) Scatter plot for the OR mRNA expression levels using Ensembl gene models (x-axis) or the extended gene models from Ibarra-Soria et al. (2014) (y-axis). The red line is the 1:1 diagonal. A …
Figure 2 with 1 supplement
OSN diversity varies between mouse strains.
(A) Mirrored barplot of the mean normalized RNAseq expression values for the OR genes in male (dark blue, top) and female (light blue, bottom) B6 animals (n = 3). (B) Scatter plot for the same data, …
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Figure 2—source data 1
OR expression data in three strains of mice.
Excel workbook containing the normalized expression data for all OR genes in B6, 129 and CAST, along with the results of the differential expression analysis.
- https://doi.org/10.7554/eLife.21476.006
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Figure 2—source data 2
Novel OR alleles in the CAST genome.
Text file with the fasta sequences of the novel alleles identified in the CAST genome.
- https://doi.org/10.7554/eLife.21476.007
Figure 2—figure supplement 1
Differences in genetic background result in great variance in OSN subtype diversity.
(A) The difference in mean expression values for OR gene mRNAs in 129 animals, as obtained by mapping to a pseudo-129 genome versus mapping to the B6 reference (n = 3). The genes are ordered by …
Figure 3 with 1 supplement
OSN diversity is determined by the genetic background and not by the olfactory environment.
(A) Experimental strategy to differentiate genetic from environmental influences on OSN diversity. B6 (blue) and 129 (yellow) embryos, depicted as circles, were transferred into F1 recipient mothers …
Figure 3—figure supplement 1
Genetic but not environmental factors regulate OSN subtype abundance.
MA plots of the transcriptome-wide differential expression analysis between aliens and cage-mates, testing for the effect of (A) a different genetic background and (B) a different olfactory …
Figure 4 with 1 supplement
OSN diversity is independent of OR activity and is controlled in cis.
(A) Mean normalized expression of the OR mRNA in the WOM of newborn B6 animals, arranged from most to least abundant (n = 3). (B) Mean normalized mRNA expression of 134 annotated OR pseudogenes in …
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Figure 4—source data 1
OR expression data in the Olfr2 > Olfr1507 mouse.
Excel workbook containing the normalized expression data for all OR genes in the Olfr2 > Olfr1507 mouse line and B6 controls, along with the results of the differential expression analysis.
- https://doi.org/10.7554/eLife.21476.012
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Figure 4—source data 2
Number and coordinates of OE and HD binding sites in OR gene promoters.
Excel workbook detailing the number of Olf1/Ebf1 (OE) and homeodomain (HD) transcription-factor-binding sites predicted by RegionMiner, for 1 kb upstream of the transcription start site (TSS) of OR genes (as reported in Ibarra-Soria et al., 2014) in all three strains. The genomic coordinates of each motif are also provided. Note that while the coordinates for the B6 data are from the reference mouse genome (GRCm38), those for 129 and CAST are based on the constructed pseudo-genomes and will not match the reference genome annotation.
- https://doi.org/10.7554/eLife.21476.013
Figure 4—figure supplement 1
Differentially represented ORs have more variation.
(A) The proportion of OR genes that have no SNPs (left) or at least one SNP (right), between the B6 and 129 (top) or B6 and CAST (bottom) genomes. Data are further subdivided by whether mRNA from …
Figure 5 with 1 supplement
Acute but not chronic exposure to odors alters OR mRNA abundance.
(A) Four different odorants were mixed together and used to stimulate B6 animals. In an acute paradigm, the odor mix was added to the drinking water supplied to the animals and WOM was collected at …
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Figure 5—source data 1
OR expression data in odor-exposed mice.
Excel workbook containing the normalized expression data for all OR genes in control and mice exposed to the mixture of (R)-carvone, heptanal, acetophenone and eugenol; along with the results of the differential expression analysis.
- https://doi.org/10.7554/eLife.21476.016
Figure 5—figure supplement 1
Specific OSN subtypes change in abundance upon olfactory stimulation.
Significantly DE OR genes (FDR < 5%) after 24 weeks exposure to a mixture of (R)-carvone, heptanal, acetophenone and eugenol. The boxplots represent expression values for six controls (grey) and six …
Figure 6 with 1 supplement
Odor-mediated changes in OR mRNA abundance are receptor specific.
(A) B6 animals were acutely exposed for 10 weeks to (R)-carvone, heptanal or both. (B) The fold-change of exposed compared to control animals based on RNAseq data (y-axis) is plotted against the OR …
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Figure 6—source data 1
OR expression data in odor-exposed mice.
Excel workbook containing the normalized expression data for all OR genes in control and mice exposed to (R)-carvone alone, heptanal alone or the combination of both; along with the results of the differential expression analysis.
- https://doi.org/10.7554/eLife.21476.019
Figure 6—figure supplement 1
Olfactory-induced changes in OSN abundance are odor-specific.
(A) qRT-PCR expression estimates for seven OR genes that were previously validated as DE in animals exposed to a mix of four odorants (Figure 5C), here in mice exposed singly to (R)-carvone (left), …
Additional files
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Supplementary file 1
Sample and gene accessions.
(1) Information on the sex, age and strain of the samples sequenced, along with the accession numbers for the raw data; and (2) information on the reconstructed OR alleles for the CAST strain.
- https://doi.org/10.7554/eLife.21476.021
