Sex-specific and lineage-specific alternative splicing in primates

Abstract

Comparative studies of gene regulation suggest an important role for natural selection in shaping gene expression patterns within and between species. Most of these studies, however, estimated gene expression levels using microarray probes designed to hybridize to only a small proportion of each gene. Here, we used recently developed RNA sequencing protocols, which sidestep this limitation, to assess intra- and interspecies variation in gene regulatory processes in considerably more detail than was previously possible. Specifically, we used RNA-seq to study transcript levels in humans, chimpanzees, and rhesus macaques, using liver RNA samples from three males and three females from each species. Our approach allowed us to identify a large number of genes whose expression levels likely evolve under natural selection in primates. These include a subset of genes with conserved sexually dimorphic expression patterns across the three species, which we found to be enriched for genes involved in lipid metabolism. Our data also suggest that while alternative splicing is tightly regulated within and between species, sex-specific and lineage-specific changes in the expression of different splice forms are also frequent. Intriguingly, among genes in which a change in exon usage occurred exclusively in the human lineage, we found an enrichment of genes involved in anatomical structure and morphogenesis, raising the possibility that differences in the regulation of alternative splicing have been an important force in human evolution.

Figure 1.

Examples of gene expression patterns that are consistent with the action of natural selection on gene regulation. Gene expression profiles from the three species are plotted for genes whose regulation has likely evolved under stabilizing (A) or directional selection (B) in the human lineage. In all panels, mean (±SEM) normalized expression levels (y-axis) of each species (x-axis) are plotted.

Figure 2.

Examples of conserved sexually dimorphic gene expression patterns. In all panels, mean (±SEM) normalized expression levels (y-axis) of each species (x-axis) are plotted separately for males (blue) and females (green).

Figure 3.

An example of human-specific change in exon usage. Mean (±SEM) relative exon expression levels (y-axis) are plotted separately for each species; (red) human; (blue) chimpanzee; (black) rhesus macaque. The gene structure appears above the x-axis, which denotes the genomic coordinates. Splice junctions identified for each species are shown as triangles connecting pairs of exons, solid lines between consecutive exons, and dotted lines between alternatively spliced exons. A typical difference in exon usage between humans and the non-human primates, which is also supported by junction reads, is circled.

Figure 4.

Examples of conserved exon usage and alternative splicing across the three species. Mean (±SEM) relative exon expression levels (y-axis) are plotted separately for each species; (red) human; (blue) chimpanzee; (black) rhesus macaque. The gene structure appears above the x-axis, which denotes the genomic coordinates. Splice junctions identified for each species are shown as triangles connecting pairs of exons, solid lines between consecutive exons, and dotted lines between alternatively spliced exons.