Fig. 5: Nonsense mutations in lemur immune genes and their transcriptional phenotypes.

a, Scheme for finding and transcriptional phenotyping of nonsense mutations in the profiled lemurs. b, NMD pathway showing the degradation of mRNA with a nonsense mutation (bottom) but not the corresponding WT mRNA (top). c–n, Identified heterozygous nonsense mutations and their transcriptional consequences for three lemur immune genes present in lemur and human genomes but missing in the mouse genome: CD58 (c–f), a ubiquitously expressed CD2-binding T cell activator; GBP1 (g–j), an interferon-inducible GTPase highly expressed in endothelial cells; and LOC105864482 (PYH1N1 homologue; k–n), an interferon-inducible protein abundant in T cells and NK cells. c,g,k, Diagram of mutations (arrowhead) with the affected exon (E) in red in the affected (heterozygous mutant) individual lemurs. ‘Stop’ indicates a change to a stop codon in the mutant allele. d,h,l, Bar plots of relative transcript read counts in the mutant allele normalized to counts from the WT allele (raw values above bars) for each affected individual (10x data). Dots, each tissue. Note that transcript reads analysed here are only those that covered the mutation position. P values, one-tailed binomial test (combining reads from all tissues). Sample size (unique read count) indicated above the bar. e,i,m, Dot plots of the relative expression levels of the gene in mutant (heterozygous) versus WT individuals, normalized to the mean expression level across all WT cells (dashed line). Dots, cell types separated by each individual, coloured by compartment (n = 46, 49 (e); 9, 3 (i); 44, 19 (m) for WT and mutant, respectively). P values, two-tailed student t-test. f,j,n, Models of the effects of the nonsense mutation on the expression of the mutant and WT alleles of the gene. f, Simple model showing how NMD degrades only the mutant and not the WT transcript. Around 90% depletion of CD58 mutant transcript (d) results in about 45% less transcripts in heterozygous mutants (e). j, NMD destroys both mutant and WT transcripts (or, there is attenuation of a positive-feedback loop). Thus heterozygous mutants have a reduction in total GBP1 transcripts (i) greater than expected (h) from the simple model. n, NMD destroys mutant transcripts, but the gene exhibits compensatory transcriptional upregulation. Despite almost complete (99%) elimination of mutant transcripts (l), heterozygotes show only about 30% less total gene transcripts than WT animals (m). See also Extended Data Fig. 11. LOF, loss of function.

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