Diverse Spatial, Temporal, and Sexual Expression of Recently Duplicated Androgen-Binding Protein Genes in \u3ci\u3eMus musculus\u3c/i\u3e

Background The genes for salivary androgen-binding protein (ABP) subunits have been evolving rapidly in ancestors of the house mouse Mus musculus, as evidenced both by recent and extensive gene duplication and by high ratios of nonsynonymous to synonymous nucleotide substitution rates. This makes ABP an appropriate model system with which to investigate how recent adaptive evolution of paralogous genes results in functional innovation (neofunctionalization). Results It was our goal to find evidence for the expression of as many of the Abp paralogues in the mouse genome as possible. We observed expression of six Abpa paralogues and five Abpbg paralogues in ten glands and other organs located predominantly in the head and neck (olfactory lobe of the brain, three salivary glands, lacrimal gland, Harderian gland, vomeronasal organ, and major olfactory epithelium). These Abp paralogues differed dramatically in their specific expression in these different glands and in their sexual dimorphism of expression. We also studied the appearance of expression in both late-stage embryos and postnatal animals prior to puberty and found significantly different timing of the onset of expression among the various paralogues. Conclusion The multiple changes in the spatial expression profile of these genes resulting in various combinations of expression in glands and other organs in the head and face of the mouse strongly suggest that neofunctionalization of these genes, driven by adaptive evolution, has occurred following duplication. The extensive diversification in expression of this family of proteins provides two lines of evidence for a pheromonal role for ABP: 1) different patterns of Abpa/Abpbg expression in different glands; and 2) sexual dimorphism in the expression of the paralogues in a subset of those glands. These expression patterns differ dramatically among various glands that are located almost exclusively in the head and neck, where the sensory organs are located. Since mice are nocturnal, it is expected that they will make extensive use of olfactory as opposed to visual cues. The glands expressing Abp paralogues produce secretions (lacrimal and salivary) or detect odors (MOE and VNO) and thus it appears highly likely that ABP proteins play a role in olfactory communication

Brain-expressed 3′UTR extensions strengthen miRNA cross-talk between ion channel/transporter encoding mRNAs

Why protein-coding genes express transcripts with longer 3'untranslated regions (3'UTRs) in the brain rather than in other tissues remains poorly understood. Given the established role of 3'UTRs in post-transcriptional regulation of transcript abundance and their recently highlighted contributions to miRNA-mediated cross-talk between mRNAs, we hypothesized that 3'UTR lengthening enhances coordinated expression between functionally-related genes in the brain. To test this hypothesis, we annotated 3'UTRs of human brain-expressed genes and found that transcripts encoding ion channels or transporters are specifically enriched among those genes expressing their longest 3'UTR extension in this tissue. These 3'UTR extensions have high density of response elements predicted for those miRNAs that are specifically expressed in the human frontal cortex (FC). Importantly, these miRNA response elements are more frequently shared among ion channel/transporter-encoding mRNAs than expected by chance. This indicates that miRNA-mediated cross-talk accounts, at least in part, for the observed coordinated expression of ion channel/transporter genes in the adult human brain. We conclude that extension of these genes' 3'UTRs enhances the miRNA-mediated cross-talk among their transcripts which post-transcriptionally regulates their mRNAs' relative levels

Rapid Bursts of \u3ci\u3eAndrogen-Binding Protein (Abp)\u3c/i\u3e Gene Duplication Occurred Independently in Diverse Mammals

Background The draft mouse (Mus musculus) genome sequence revealed an unexpected proliferation of gene duplicates encoding a family of secretoglobin proteins including the androgen-binding protein (ABP) α, β and γ subunits. Further investigation of 14 α-like (Abpa) and 13 β- or γ-like (Abpbg) undisrupted gene sequences revealed a rich diversity of developmental stage-, sex- and tissue-specific expression. Despite these studies, our understanding of the evolution of this gene family remains incomplete. Questions arise from imperfections in the initial mouse genome assembly and a dearth of information about the gene family structure in other rodents and mammals. Results Here, we interrogate the latest \u27finished\u27 mouse (Mus musculus) genome sequence assembly to show that the Abp gene repertoire is, in fact, twice as large as reported previously, with 30 Abpa and 34 Abpbg genes and pseudogenes. All of these have arisen since the last common ancestor with rat (Rattus norvegicus). We then demonstrate, by sequencing homologs from species within the Mus genus, that this burst of gene duplication occurred very recently, within the past seven million years. Finally, we survey Abp orthologs in genomes from across the mammalian clade and show that bursts of Abp gene duplications are not specific to the murid rodents; they also occurred recently in the lagomorph (rabbit, Oryctolagus cuniculus) and ruminant (cattle, Bos taurus) lineages, although not in other mammalian taxa. Conclusion We conclude that Abp genes have undergone repeated bursts of gene duplication and adaptive sequence diversification driven by these genes\u27 participation in chemosensation and/or sexual identification

Human Genetics Seen Through An Evolutionary Lens

Most DNA bases crucial for species perpetuation are marked by a dearth of sequence change among species related over long evolutionary time. Recently, Christmas et al.1 and Sullivan et al.2 cast light on human DNA and its variants through comparison with 239 other mammalian species' genomes

Signatures of adaptive evolution within human non-coding sequence

The human genome is often portrayed as consisting of three sequence types, each distinguished by their mode of evolution. Purifying selection is estimated to act on 2.5 - 5.0% of the genome, whereas virtually all remaining sequence is considered to have evolved neutrally and to be devoid of functionality. The third mode of evolution, positive selection of advantageous changes, is considered rare. Such instances have been inferred only for a handful of sites, and these lie almost exclusively within protein-coding genes. Nevertheless, the majority of positively selected sequence is expected to lie within the wealth of functional 'dark matter' present outside of the coding sequence. Here, we review the evolutionary evidence for the majority of human-conserved DNA lying outside of the protein-coding sequence. We argue that within this non-coding fraction lies at least 1 Mb of functional sequence that has accumulated many beneficial nucleotide replacements. Illuminating the functions of this adaptive dark matter will lead to a better understanding of the sequence changes that have shaped the innovative biology of our species

Defining a High-Quality Myalgic Encephalomyelitis/Chronic Fatigue Syndrome cohort in UK Biobank

BackgroundProgress in Myalgic Encephalomyelitis/Chronic Fatigue Syndrome (ME/CFS) research is being slowed by the relatively small-scale studies being performed whose results are often not replicated. Progress could be accelerated by analyses of large population-scale projects, such as UK Biobank (UKB), which provide extensive phenotype and genotype data linked to both ME/CFS cases and controls.MethodsHere, we analysed the overlap and discordance among four UKB-defined ME/CFS cohorts, and additional questionnaire data when available.ResultsA total of 5,354 UKB individuals were linked to at least one piece of evidence of MECFS, a higher proportion (1.1%) than most prevalence estimates. Only a third (36%; n=1,922) had 2 or more pieces of evidence for MECFS, in part due to data missingness. For the same UKB participant, ME/CFS status defined by ICD-10 (International Classification of Diseases, Tenth Revision) code G93.3 (Post-viral fatigue syndrome) was most likely to be supported by another data type (72%); ME/CFS status defined by Pain Questionnaire responses is least likely to be supported (43%), in part due to data missingness.ConclusionsWe conclude that ME/CFS status in UKB, and potentially other biobanks, is best supported by multiple, and not single, lines of evidence. Finally, we raise the estimated ME/CFS prevalence in the UK to 410,000 using the most consistent evidence for ME/CFS status, and accounting for those who had no opportunity to participate in UKB due to being bed- or house-bound