Linked genetic variation and not genome structure causes widespread differential expression associated with chromosomal inversions

Abstract

Chromosomal inversions are widely thought to be favored by natural selection because they suppress recombination between alleles that have higher fitness on the same genetic background or in similar environments. Nonetheless, few selected alleles have been characterized at the molecular level. Gene expression profiling provides a powerful way to identify functionally important variation associated with inversions and suggests candidate phenotypes. However, altered genome structure itself might also impact gene expression by influencing expression profiles of the genes proximal to inversion breakpoint regions or by modifying expression patterns genome-wide due to rearranging large regulatory domains. In natural inversions, genetic differentiation and genome structure are inextricably linked. Here, we characterize differential expression patterns associated with two chromosomal inversions found in natural Drosophila melanogaster populations. To isolate the impacts of genome structure, we engineered synthetic chromosomal inversions on controlled genetic backgrounds with breakpoints that closely match each natural inversion. We find that synthetic inversions have negligible effects on gene expression. Nonetheless, natural inversions have broad-reaching regulatory impacts in cis and trans Furthermore, we find that differentially expressed genes associated with both natural inversions are enriched for loci associated with immune response to bacterial pathogens. Our results support the idea that inversions in D. melanogaster experience natural selection to maintain associations between functionally related alleles to produce complex phenotypic outcomes.

Keywords: chromosomal inversions; differential expression; genome structure.

Fig. 1.

Relative expression impacts of chromosomal inversions. Log fold-change in inversion heterozygotes and homozygotes relative to standard arrangement homozygotes for In(2L)t (Left) and In(3R)K (Right) with natural inversions (Top) and synthetic inversions (Bottom). Expression differences that are significant at the q < 0.2 level are shown as red (additive), blue (overdominant), and green (underdominant).

Fig. 2.

The genomic distributions of DE genes. (A) Differentially expressed genes with additive (red), overdominant (blue), and underdominant (green) expression patterns for each natural and synthetic inversion across the five major chromosome arms of D. melanogaster. In order from Left to Right, chromosome arms displayed in each panel are 2L, 2R, 3L, 3R, and ×. From Top to Bottom, inversions shown are In(3R)sK, In(3R)K, In(2L)st, and In(2L)t. Positions of inversion breakpoints are shown for each as dashed vertical lines. Each point was jittered vertically to improve visualization. (B) The number of additive (red) and nonadditive (blue) genes on chromosome arm 2L and off for In(2L)t. (C) The number of additive (red) and nonadditive (blue) genes on chromosome arm 3R and in the rest of the genome for In(3R)K.

Fig. 3.

Genetic differentiation is correlated with DE genes on inverted chromosome arms. F_ST, a measure of genetic differentiation, between standard arrangement homozygotes versus inverted arrangement homozygotes for In(2L)t (Top) and In(3R)K (Bottom). DE genes are marked along each panel as red (on the inverted chromosome) and gold (on collinear chromosomes); each panel corresponds to one of the major chromosome arms of this species: 2L, 2R, 3L, 3R, and X from Left to Right. Inversion breakpoint positions are marked with dashed vertical lines. On the right, histograms show the distributions of F_ST for windows containing DE genes on collinear chromosome arms (gold) and DE genes on inverted chromosome arms (red).