ALBERT

Description: When considering the evolution of a gene’s expression profile, we commonly assume that this is unaffected by its genomic neighborhood. This is, however, in contrast to what we know about the lack of autonomy between neighboring genes in gene expression profiles in extant taxa. Indeed, in all eukaryotic genomes genes of similar expression-profile tend to cluster, reflecting chromatin level dynamics. Does it follow that if a gene increases expression in a particular lineage then the genomic neighbors will also increase in their expression or is gene expression evolution autonomous? To address this here we consider evolution of human gene expression since the human-chimp common ancestor, allowing for both variation in estimation of current expression level and error in Bayesian estimation of the ancestral state. We find that in all tissues and both sexes, the change in gene expression of a focal gene on average predicts the change in gene expression of neighbors. The effect is highly pronounced in the immediate vicinity (〈100 kb) but extends much further. Sex-specific expression change is also genomically clustered. As genes increasing their expression in humans tend to avoid nuclear lamina domains and be enriched for the gene activator 5-hydroxymethylcytosine, we conclude that, most probably owing to chromatin level control of gene expression, a change in gene expression of one gene likely affects the expression evolution of neighbors, what we term expression piggybacking, an analog of hitchhiking.

Description: The nearly neutral theory predicts that small effective population size provides the conditions for weakened selection. This is postulated to explain why our genome is more "bloated" than that of, for example, yeast, ours having large introns and large intergene spacer. If a bloated genome is also an error prone genome might it, however, be the case that selection for error-mitigating properties is stronger in our genome? We examine this notion using splicing as an exemplar, not least because large introns can predispose to noisy splicing. We thus ask whether, owing to genomic decay, selection for splice error-control mechanisms is stronger, not weaker, in species with large introns and small populations. In humans much information defining splice sites is in cis- exonic motifs, most notably exonic splice enhancers (ESEs). These act as splice-error control elements. Here then we ask whether within and between-species intron size is a predictor of the commonality of exonic cis- splicing motifs. We show that, as predicted, the proportion of synonymous sites that are ESE-associated and under selection in humans is weakly positively correlated with the size of the flanking intron. In a phylogenetically controlled framework, we observe, also as expected, that mean intron size is both predicted by N e .μ and is a good predictor of cis- motif usage across species, this usage coevolving with splice site definition. Unexpectedly, however, across taxa intron density is a better predictor of cis -motif usage than intron size. We propose that selection for splice-related motifs is driven by a need to avoid decoy splice sites that will be more common in genes with many and large introns. That intron number and density predict ESE usage within human genes is consistent with this, as is the finding of intragenic heterogeneity in ESE density. As intronic content and splice site usage across species is also well predicted by N e .μ , the result also suggests an unusual circumstance in which selection (for cis- modifiers of splicing) might be stronger when population sizes are smaller, as here splicing is noisier, resulting in a greater need to control error-prone splicing.

Description: Shallow, subtidal waters of coastal embayments are the primary nursery habitats of juvenile Pacific cod through much of their range. However, the importance of these habitats to the Bering Sea population is poorly understood as the Bering Sea offers relatively little of this habitat. In this study, we examined the use of demersal and pelagic habitats in the southeast Bering Sea by age-0 Pacific cod. In 4 years of demersal beam trawling on the shelf at depths of 20–146 m, fish were most abundant along the Alaska Peninsula (AKP) at depths to 50 m. In addition, 1 year of spatially intensive beam trawl sampling was conducted at depths of 5–30 m in a nearshore focal area along the central AKP. In this survey, age-0 cod were more abundant along the open coastline than they were in two coastal embayments, counter to patterns observed in the Gulf of Alaska. Demersal sampling in 2012 was conducted synoptically with surveys of surface and subsurface waters over the continental shelf. Age-0 cod were captured in pelagic waters over the middle and outer shelf, with maximum catches occurring over depths of 60–80 m. The similar size distributions of fish in coastal-demersal and shelf-surface habitats and the proximity of concentrations in the two habitat types suggests that habitat use in the Bering Sea occurs along a gradient from coastal to pelagic. While capture efficiencies may differ among trawl types, trawl-based estimates of age-0 cod density in demersal waters along the AKP was 10 times that observed in the highest density pelagic-shelf habitats, demonstrating the importance of coastal nursery habitats in this population. Despite representing a much smaller habitat area, the coastal waters along the AKP appear an important nursery area and support a significant fraction of the age-0 Pacific cod in the Bering Sea.

Description: Although both genotypes with elevated mutation rate (mutators) and mobilization of insertion sequence (IS) elements have substantial impact on genome diversification, their potential interactions are unknown. Moreover, the evolutionary forces driving gradual accumulation of these elements are unclear: Do these elements spread in an initially transposon-free bacterial genome as they enable rapid adaptive evolution? To address these issues, we inserted an active IS 1 element into a reduced Escherichia coli genome devoid of all other mobile DNA. Evolutionary laboratory experiments revealed that IS elements increase mutational supply and occasionally generate variants with especially large phenotypic effects. However, their impact on adaptive evolution is small compared with mismatch repair mutator alleles, and hence, the latter impede the spread of IS-carrying strains. Given their ubiquity in natural populations, such mutator alleles could limit early phase of IS element evolution in a new bacterial host. More generally, our work demonstrates the existence of an evolutionary conflict between mutation-promoting mechanisms.

Description: The Bering Sea and Gulf of Alaska support a number of commercially important flatfish fisheries. These high latitude ecosystems are predicted to be most immediately impacted by ongoing ocean acidification, but the range of responses by commercial fishery species has yet to be fully explored. In this study, we examined the growth responses of northern rock sole ( Lepidopsetta polyxystra ) eggs and larvae across a range of CO 2 levels (ambient to 1500 µatm) to evaluate the potential sensitivity to ocean acidification. Laboratory-spawned eggs and larvae were reared at 8°C in a flow-through culture system in which CO 2 levels were maintained via computer-controlled injection of CO 2 into a seawater conditioning tank. Overall, we observed only minor effects of elevated CO 2 level on sizes of northern rock sole larvae. Size at hatch differed among offspring from four different females, but there was no significant effect of CO 2 level on egg survival or size at hatch. In three separate larval growth trials, there was little effect of CO 2 level on growth rates through the first 28 d post-hatch (DPH). However, in the one trial extended to 60 DPH, fish reared at the highest CO 2 level had lower condition factors after 28 DPH, suggesting that larvae undergoing metamorphosis may be more sensitive to environmental hypercapnia than earlier pre-flexion stages. These results suggest that while early life stages of northern rock sole are less sensitive to ocean acidification than previously examined flatfish, they may be more sensitive to elevated CO 2 levels than a previously studied gadid with a similar geographic range.

Description: Where in genes do pathogenic mutations tend to occur and does this provide clues as to the possible underlying mechanisms by which single nucleotide polymorphisms (SNPs) cause disease? As splice-disrupting mutations tend to occur predominantly at exon ends, known also to be hot spots of cis -exonic splice control elements, we examine the relationship between the relative density of such exonic cis -motifs and pathogenic SNPs. In particular, we focus on the intragene distribution of exonic splicing enhancers (ESE) and the covariance between them and disease-associated SNPs. In addition to showing that disease-causing genes tend to be genes with a high intron density, consistent with missplicing, five factors established as trends in ESE usage, are considered: relative position in exons, relative position in genes, flanking intron size, splice sites usage, and phase. We find that more than 76% of pathogenic SNPs are within 3–69 bp of exon ends where ESEs generally reside, this being 13% more than expected. Overall from enrichment of pathogenic SNPs at exon ends, we estimate that approximately 20–45% of SNPs affect splicing. Importantly, we find that within genes pathogenic SNPs tend to occur in splicing-relevant regions with low ESE density: they are found to occur preferentially in the terminal half of genes, in exons flanked by short introns and at the ends of phase (0,0) exons with 3' non-"AGgt" splice site. We suggest the concept of the "fragile" exon, one home to pathogenic SNPs owing to its vulnerability to splice disruption owing to low ESE density.

Description: Inactivating mutations of STAG2 have been reported at low frequency in several cancers. In glioblastoma, the function of STAG2 has been related to maintenance of euploidy via its role in the cohesin complex. In a screen of a large series of bladder tumours and cell lines, we found inactivating mutations (nonsense, frameshift and splicing) in 67 of 307 tumours (21.8%) and 6 of 47 cell lines. Thirteen missense mutations of unknown significance were also identified. Inactivating mutation was associated with low tumour stage ( P = 0.001) and low grade ( P = 0.0002). There was also a relationship with female patient gender ( P = 0.042). Examination of copy number profiles revealed an inverse relationship of mutation with both fraction of genome altered and whole chromosome copy number changes. Immunohistochemistry showed that in the majority of cases with inactivating mutations, STAG2 protein expression was absent. Strikingly, we identified a relatively large subset of tumours (12%) with areas of both positive and negative immunoreactivity, in only four of which a potentially function-altering mutation was detected. Regions of differential expression were contiguous and showed similar morphological phenotype in all cases. Microdissected positive and negative areas from one tumour showed an inactivating mutation to be present only in the negative area, suggesting intra-tumoral sub-clonal genomic evolution. Our findings indicate that loss of STAG2 function plays a more important role in non-invasive than that in muscle-invasive bladder cancer and suggest that cohesin complex-independent functions are likely to be important in these cases.

Description: Hurst, T. P., Moss, J. H., and Miller, J. A. 2012. Distributional patterns of 0-group Pacific cod ( Gadus macrocephalus ) in the eastern Bering Sea under variable recruitment and thermal conditions. – ICES Journal of Marine Science, 69: 163–174. Despite the importance of Pacific cod in Bering Sea fisheries and foodwebs, little is known about the habitat use and the distribution of early life stages. We analysed 6 years of catch data for 0-group Pacific cod in fishery-independent surveys of the Bering Sea shelf. Juvenile cod were most commonly captured on the middle shelf over depths of 50–80 m and were rarely captured north of 58°N. Consistently high catches were observed east of the Pribilof Islands and north of Port Moller along the Alaska Peninsula. There was evidence of density-dependent habitat selection at the local scale as the frequency of occurrence increased with regional catch per unit effort. At the basin scale, the southerly distribution of the weak 2009 cohort suggested the possibility of a range contraction for small cohorts. There was no consistent shift in the distribution of juvenile Pacific cod in response to interannual climate variability. These results for Pacific cod contrast with those observed for walleye pollock, which appears to exhibit greater variance in distribution, but are similar to patterns observed for juvenile Atlantic cod. Future work should focus on distribution in nearshore habitats and examine the patterns of dispersal and the connectivity of the Bering Sea and Gulf of Alaska populations.

Description: There are two strong and equally important predictors of rates of human protein evolution: The amount the gene is expressed and the proportion of exonic sequence devoted to control splicing, mediated largely by selection on exonic splice enhancer (ESE) motifs. Is the same true for noncoding RNAs, known to be under very weak purifying selection? Prior evidence suggests that selection at splice sites in long intergenic noncoding RNAs (lincRNAs) is important. We now report multiple lines of evidence indicating that the great majority of purifying selection operating on lincRNAs in humans is splice related. Splice-related parameters explain much of the between-gene variation in evolutionary rate in humans. Expression rate is not a relevant predictor, although expression breadth is weakly so. In contrast to protein-coding RNAs, we observe no relationship between evolutionary rate and lincRNA stability. As in protein-coding genes, ESEs are especially abundant near splice junctions and evolve slower than non-ESE sequence equidistant from boundaries. Nearly all constraint in lincRNAs is at exon ends (N.B. the same is not witnessed in Drosophila ). Although we cannot definitely answer the question as to why splice-related selection is so important, we find no evidence that splicing might enable the nonsense-mediated decay pathway to capture transcripts incorrectly processed by ribosomes. We find evidence consistent with the notion that splicing modifies the underlying chromatin through recruitment of splice-coupled chromatin modifiers, such as CHD1, which in turn might modulate neighbor gene activity. We conclude that most selection on human lincRNAs is splice mediated and suggest that the possibility of splice–chromatin coupling is worthy of further scrutiny.

Description: Genome-wide association studies (GWAS) of urinary bladder cancer (UBC) have yielded common variants at 12 loci that associate with risk of the disease. We report here the results of a GWAS of UBC including 1670 UBC cases and 90 180 controls, followed by replication analysis in additional 5266 UBC cases and 10 456 controls. We tested a dataset containing 34.2 million variants, generated by imputation based on whole-genome sequencing of 2230 Icelanders. Several correlated variants at 20p12, represented by rs62185668, show genome-wide significant association with UBC after combining discovery and replication results (OR = 1.19, P = 1.5 x 10 –11 for rs62185668-A, minor allele frequency = 23.6%). The variants are located in a non-coding region approximately 300 kb upstream from the JAG1 gene, an important component of the Notch signaling pathways that may be oncogenic or tumor suppressive in several forms of cancer. Our results add to the growing number of UBC risk variants discovered through GWAS.