Abstract
Highly conserved noncoding elements (CNEs) constitute a significant proportion of the genomes of multicellular eukaryotes. The function of most CNEs remains elusive, but growing evidence indicates they are under some form of purifying selection. Noncoding regions in many species also harbor large numbers of transposable element (TE) insertions, which are typically lineage specific and depleted in exons because of their deleterious effects on gene function or expression. However, it is currently unknown whether the landscape of TE insertions in noncoding regions is random or influenced by purifying selection on CNEs. Here, we combine comparative and population genomic data in Drosophila melanogaster to show that the abundance of TE insertions in intronic and intergenic CNEs is reduced relative to random expectation, supporting the idea that selective constraints on CNEs eliminate a proportion of TE insertions in noncoding regions. However, we find no evidence for differences in the allele frequency spectra for polymorphic TE insertions in CNEs versus those in unconstrained spacer regions, suggesting that the distribution of fitness effects acting on observable TE insertions is similar across different functional compartments in noncoding DNA. Our results provide evidence that selective constraints on CNEs contribute to shaping the landscape of TE insertion in eukaryotic genomes, and provide further evidence that CNEs are indeed functionally constrained and not simply mutational cold spots.
Highlights
Transposable elements (TEs) are mobile DNA sequences that make up a significant fraction of the genomes of many multicellular organisms (Elliott and Gregory 2015), including the model insect species, Drosophila melanogaster (Bergman et al 2006; Sackton et al 2010)
We tested for depletion of nonreference TE insertions in genomic regions with putatively higher levels of functional constraint by comparing observed numbers of TEs in these regions to an empirical null distribution based of 10,000 random permutations of the observed TE insertion data sets
Our results are consistent either with 1) nonrandom transposition causing TEs to avoid functional compartments like exonic regions and conserved noncoding elements (CNEs), or 2) a mode of purifying selection that differentially eliminates TE insertions from functional regions but leaves behind polymorphic TEs insertions that have a similar distribution of fitness effects across genomic compartments
Summary
Transposable elements (TEs) are mobile DNA sequences that make up a significant fraction of the genomes of many multicellular organisms (Elliott and Gregory 2015), including the model insect species, Drosophila melanogaster (Bergman et al 2006; Sackton et al 2010). Restriction mapping studies on a limited number of loci revealed that large DNA insertions (assumed to be TEs) were rarely found in transcribed regions (Aquadro et al 1986, 1992; Langley and Aquadro 1987; Langley et al 1988; Schaeffer et al 1988). Subsequent analysis of the D. melanogaster reference genome showed that the paucity of TEs in transcribed regions is primarily driven by a strong depletion of the number of TE insertions in exons combined with a weaker reduction in introns (Kaminker et al 2002; Lipatov et al 2005). Analysis of population genomic data has confirmed that TE insertions are rare in D. melanogaster exonic regions (Kofler et al 2012; Cridland et al 2013; Zhuang et al 2014)
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