Effects of cis and trans Genetic Ancestry on Gene Expression in African Americans

Variation in gene expression is a fundamental aspect of human phenotypic variation. Several recent studies have analyzed gene expression levels in populations of different continental ancestry and reported population differences at a large number of genes. However, these differences could largely be due to non-genetic (e.g., environmental) effects. Here, we analyze gene expression levels in African American cell lines, which differ from previously analyzed cell lines in that individuals from this population inherit variable proportions of two continental ancestries. We first relate gene expression levels in individual African Americans to their genome-wide proportion of European ancestry. The results provide strong evidence of a genetic contribution to expression differences between European and African populations, validating previous findings. Second, we infer local ancestry (0, 1, or 2 European chromosomes) at each location in the genome and investigate the effects of ancestry proximal to the expressed gene (cis) versus ancestry elsewhere in the genome (trans). Both effects are highly significant, and we estimate that 12±3% of all heritable variation in human gene expression is due to cis variants

Hominid-specific SVA elements: Genomic impact and insights into L1-mediated retrotransposition

Mammalian genomes have expanded through the duplication of large blocks of DNA and retrotransposition of different cellular RNAs. Roughly 35% of the human genome can be attributed to retrotransposed sequences. In humans, three retrotransposon families are still active: the autonomous LINE-1 (L1), and the non-autonomous Alu, and SINE-VNTR-Alu (SVA) elements. However, most copies of L1, Alu, and SVA are no longer active, with new genomic insertions being derived from a small subset of elements. L1 encodes a reverse transcriptase activity in its second ORF (ORF2) required for its own mobilization in cis and the mobilization of Alu and SVA RNAs in trans. These elements may impact host genomes as insertional mutagens or through other mechanisms not dependent upon them actively retrotransposing, such as altering the local epigenetic environment or alternative splicing. Here we carried out molecular and computational experiments and found a number of functional 3’ splice sites within many different transcribed SVAs across the human and chimpanzee genomes. Using a mini-gene splicing construct containing an SVA, we observed splicing in cell culture, up to 20% of wild-type levels, along with SVA exonization events that introduced premature termination codons (PTC). These data imply that an SVA residing within an intron in the same orientation as the gene may alter normal gene transcription either by gene-trapping or by introducing PTCs through exonization, possibly creating differences within and across species. Cell culture retrotransposition assays have provided great insight into the genomic impact of retrotransposons, in particular, LINE-1(L1) and Alu elements; however, no such assay exists for SVA elements. Here we report the development of an SVA cell culture retrotransposition assay and demonstrate L1 mobilization of SVA elements in trans. Engineered SVAs retrotranspose at 1-54 times the frequency of a marked non-L1 pseudogene in HeLa HA cells. Our cell culture data suggest a variable L1 ORF1p dependency for SVA elements in retrotransposition. Previously intractable questions regarding SVA biology can now be addressed

Exon-trapping mediated by the human retrotransposon SVA

Although most human retrotransposons are inactive, both inactive and active retrotransposons drive genome evolution and may influence transcription through various mechanisms. In humans, three retrotransposon families are still active, but one of these, SVA, remains mysterious. Here we report the identification of a new subfamily of SVA, which apparently formed after an alternative splicing event where the first exon of the MAST2 gene spliced into an intronic SVA and subsequently retrotransposed. Additional examples of SVA retrotransposing upstream exons due to splicing into SVA were also identified in other primate genomes. After molecular and computational experiments, we found a number of functional 3′ splice sites within many different transcribed SVAs across the human and chimpanzee genomes. Using a minigene splicing construct containing an SVA, we observed splicing in cell culture, along with SVA exonization events that introduced premature termination codons (PTCs). These data imply that an SVA residing within an intron in the same orientation as the gene may alter normal gene transcription either by gene-trapping or by introducing PTCs through exonization, possibly creating differences within and across species

Pathogenic orphan transduction created by a nonreference LINE-1 retrotransposon

Long INterspersed Element-1 (LINE-1) retrotransposons comprise 17% of the human genome, and move by a potentially mutagenic "copy and paste" mechanism via an RNA intermediate. Recently, the retrotransposition-mediated insertion of a new transcript was described as a novel cause of genetic disease, Duchenne muscular dystrophy, in a Japanese male. The inserted sequence was presumed to derive from a single-copy, noncoding RNA transcribed from chromosome 11q22.3 that retrotransposed into the dystrophin gene. Here, we demonstrate that a nonreference fulllength LINE-1 is situated in the proband and maternal genome at chromosome 11q22.3, directly upstream of the sequence, whose copy was inserted into the dystrophin gene. This LINE-1 is highly active in a cell culture assay. LINE-1 insertions are often associated with 3' transduction of adjacent genomic sequences. Thus, the likely explanation for the mutagenic insertion is a LINE-1-mediated 3' transduction with severe 5' truncation. This is the first example of LINE-1-induced human disease caused by an "orphan" 3' transduction

Proposed models for shared and distinct modes of adaptation for cGAS and OAS proteins in primates.

<p>An ancestral protein (red) with template independent polymerase activity was challenged by pathogens (green), which led to gene duplications and divergence resulting in ancestral cGAS (blue) and ancestral OAS (yellow). cGAS and OAS likely faced shared and distinct inhibitors encoded by pathogens (colored hexagons). Extensive positive selection of cGAS and OAS resulted in a variety of substitutions that evade inhibition by pathogens. For cGAS, sampling of amino acid substitutions on protein surfaces (gray stars) and the expression of spliceforms that may produce molecular mimics or cGAS variant proteins that evade antagonism could provide diverse mechanisms of escape from pathogen-encoded inhibitors. Some OAS genes also fix amino acid substitutions (gray stars) and may also evade pathogens via duplications and gene fusion events evident in OAS2 and OAS3.</p

Evolutionary histories vary across the OAS gene family in primates.

<p>Phylogenetic analyses of OAS1, OAS2, OAS3, and OASL were carried out using sequences from 11 matching primate species. <b>(A)</b> Gene structures of the OAS gene family members in primates. NTase (red) and OAS1-C (gray) domains are indicated. For OASL the ubiquitin-like domains (yellow) are also indicated. Amino acid sites with statistically significant ω values obtained from NSsites (PAML [<a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1005203#pgen.1005203.ref044" target="_blank">44</a>]), FUBAR, and MEME (HyPhy [<a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1005203#pgen.1005203.ref045" target="_blank">45</a>]) are indicated above the gene. <b>(B)</b> Primate species trees with ω values obtained from free-ratio analyses in PAML [<a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1005203#pgen.1005203.ref044" target="_blank">44</a>] for each lineage. dN/dS values and lineages with ω > 1 or at least 3 nonsynonymous:0 synonymous amino acid substitutions are highlighted in red.</p

Widespread signatures of positive selection for cGAS and OAS1 across the primate lineage.

<p>Phylogenetic analyses of cGAS <b>(A,B)</b> and OAS1 <b>(C,D)</b> were carried out using sequences from 22 matching primate species. <b>(A)</b> A species tree displaying sampled primate sequences for cGAS with dN/dS (ω) values obtained from free-ratio analyses (PAML[<a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1005203#pgen.1005203.ref045" target="_blank">45</a>], see <a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1005203#sec013" target="_blank">Methods</a>) indicated above each branch. ω values > 1 or at least 3 nonsynonymous: 0 synonymous amino acid changes are labeled in red with the corresponding branch (red branch). <b>(B)</b> cGAS gene structure with annotated domains and catalytic residues (below). Amino acid sites with statistically significant ω values obtained from NSsites (PAML [<a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1005203#pgen.1005203.ref044" target="_blank">44</a>]), FUBAR, and MEME (HyPhy [<a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1005203#pgen.1005203.ref046" target="_blank">46</a>]) are indicated above the gene. <b>(C)</b> ω values for OAS1 across primate evolution. The species tree is labeled as described for the cGAS tree. <b>(D)</b> OAS1 gene structure with amino acids displaying statistical significant ω values. Actual amino acid residue refers to human reference sequence. Catalytic amino acid residues for both cGAS and OAS1 are indicated within the gene diagram.</p

cGAS and OAS1 act in parallel innate defense signaling pathways.

<p><b>(A)</b> Model of cGAS signaling. Upon detection and binding of cytoplasmic DNA from viruses (green), cGAS (blue) dimerizes and generates cGAMP, which in turn activates STING signaling (TBK1-IRF3) to promote transcription of interferon beta. <b>(B)</b> Model of OAS signaling. Upon detection and binding of double-stranded RNA in the cytoplasm from viruses (green), OAS synthesizes 2–5 oligoadenylate, which activates RNase L and leads to the destruction of viral and cellular RNAs.</p