Random genetic drift sets an upper limit on mRNA splicing accuracy in metazoans

Abstract

Most eukaryotic genes undergo alternative splicing (AS), but the overall functional significance of this process remains a controversial issue. It has been noticed that the complexity of organisms correlates positively with their genome-wide AS rate. This has been interpreted as evidence that AS plays an important role in adaptive evolution by increasing the functional repertoires of genomes. However, this observation also fits with a totally opposite interpretation: given that "complex" organisms tend to have small effective population sizes (Ne), they are expected to be more affected by genetic drift, and hence more prone to accumulate deleterious mutations that decrease splicing accuracy. Thus, according to this "drift barrier" theory, the elevated AS rate in complex organisms might simply result from a higher splicing error rate. To test this hypothesis, we performed a meta-analysis of 3,496 transcriptome sequencing samples to quantify AS in 53 metazoan species spanning a wide range of Ne values. Our results show a negative correlation between Ne proxies and the genome-wide AS rates among species, consistent with the drift barrier hypothesis. This pattern is dominated by low abundance isoforms, which represent the vast majority of the splice variant repertoire. We show that these low abundance isoforms are depleted in functional AS events, and most likely correspond to errors. Conversely, the AS rate of abundant isoforms, which are relatively enriched in functional AS events, tends to be lower in more complex species. All these observations are consistent with the hypothesis that variation in AS rates across metazoans reflects the limits set by drift on the capacity of selection to prevent gene expression errors.

GTDrift: A resource for exploring the interplay between genetic drift, genomic and transcriptomic characteristics in eukaryotes

“…Additionally, we have enriched the database with annotations for orthologous single-copy genes (BUSCO genes) and proxies of effective population size, including the molecular evolutionary rate dN /dS and life history traits such as longevity, body mass, body length. We used similar types of data in our recent publication exploring the relationship between random genetic drift and alternative splicing patterns (Bénitière et al, 2023). However, here we provide considerably more data, for 1,507 species compared to 53 in this publication.…”

“…Conversely, if AS predominantly involves deleterious processes, its rate should decline with increasing N e . We applied this reasoning in our previous work (Bénitière et al, 2023), which led us to deduce that AS is predominantly non-functional. This methodology for exploring the impact of N e on biological processes holds potential for broader applications.…”

“…We recently examined the variations in transcriptome complexity across animal species in light of the "drift barrier" hypothesis (Bénitière et al, 2023). In multicellular eukaryotes, the vast majority of genes give rise to multiple isoforms through alternative splicing (Chen et al, 2014).…”

Global impact of aberrant splicing on human gene expression levels

“…To this end, we analyzed exons whose length is divisible by three ("symmetric exons"), and thus are frame-preserving whether the exon is skipped or included. Previous studies using steady-state RNA-seq data found that highly-included and conserved alternatively spliced exons ("cassette exons") are biased towards being symmetric [1][2][3][4]47 , suggesting that there is selective pressure to maintain coding frame for highly-included cassette exons. Indeed, ~55% of highly-included cassette exons are symmetric compared to only ~35% of rarely-used cassette exons (Percent spliced-in, PSI < 1%).…”

“…This finding is often interpreted as supporting the role of AS in diversifying the proteome; however, most alternatively spliced isoforms are lowly expressed and lack cross-species conservation 1–6 . To explain these observations, multiple studies have suggested that the vast majority of mRNA isoforms are nonfunctional transcripts that result from mis-splicing rather than regulated AS 4–10 .…”