SummaryThe mammalian radiation has corresponded with rapid changes in noncoding regions of the genome, but we lack a comprehensive understanding of regulatory evolution in mammals. Here, we track the evolution of promoters and enhancers active in liver across 20 mammalian species from six diverse orders by profiling genomic enrichment of H3K27 acetylation and H3K4 trimethylation. We report that rapid evolution of enhancers is a universal feature of mammalian genomes. Most of the recently evolved enhancers arise from ancestral DNA exaptation, rather than lineage-specific expansions of repeat elements. In contrast, almost all liver promoters are partially or fully conserved across these species. Our data further reveal that recently evolved enhancers can be associated with genes under positive selection, demonstrating the power of this approach for annotating regulatory adaptations in genomic sequences. These results provide important insight into the functional genetics underpinning mammalian regulatory evolution.

Pathogenesis studies of SIV infection have not been performed to date in wild monkeys due to difficulty in collecting and storing samples on site and the lack of analytical reagents covering the extensive SIV diversity. We performed a large scale study of molecular epidemiology and natural history of SIVagm infection in 225 free-ranging AGMs from multiple locations in South Africa. SIV prevalence (established by sequencing pol, env, and gag) varied dramatically between infant/juvenile (7%) and adult animals (68%) (p<0.0001), and between adult females (78%) and males (57%). Phylogenetic analyses revealed an extensive genetic diversity, including frequent recombination events. Some AGMs harbored epidemiologically linked viruses. Viruses infecting AGMs in the Free State, which are separated from those on the coastal side by the Drakensberg Mountains, formed a separate cluster in the phylogenetic trees; this observation supports a long standing presence of SIV in AGMs, at least from the time of their speciation to their Plio-Pleistocene migration. Specific primers/probes were synthesized based on the pol sequence data and viral loads (VLs) were quantified. VLs were of 104–106 RNA copies/ml, in the range of those observed in experimentally-infected monkeys, validating the experimental approaches in natural hosts. VLs were significantly higher (107–108 RNA copies/ml) in 10 AGMs diagnosed as acutely infected based on SIV seronegativity (Fiebig II), which suggests a very active transmission of SIVagm in the wild. Neither cytokine levels (as biomarkers of immune activation) nor sCD14 levels (a biomarker of microbial translocation) were different between SIV-infected and SIV-uninfected monkeys. This complex algorithm combining sequencing and phylogeny, VL quantification, serology, and testing of surrogate markers of microbial translocation and immune activation permits a systematic investigation of the epidemiology, viral diversity and natural history of SIV infection in wild African natural hosts.

We have established the structures of 10 human microRNA (miRNA) precursors using biochemical methods. Eight of these structures turned out to be different from those that were computer-predicted. The differences localized in the terminal loop region and at the opposite side of the precursor hairpin stem. We have analyzed the features of these structures from the perspectives of miRNA biogenesis and active strand selection. We demonstrated the different thermodynamic stability profiles for pre-miRNA hairpins harboring miRNAs at their 5-and 3-sides and discussed their functional implications. Our results showed that miRNA prediction based on predicted precursor structures may give ambiguous results, and the success rate is significantly higher for the experimentally determined structures. On the other hand, the differences between the predicted and experimentally determined structures did not affect the stability of termini produced through "conceptual dicing." This result confirms the value of thermodynamic analysis based on mfold as a predictor of strand section by RNAi-induced silencing complex (RISC). MicroRNAs (miRNAs)1 are a large family of short 20 -25-nt single-stranded noncoding RNAs recently identified in many eukaryotes from nematode to human (1-4). The best known founding members of this family are lin-4 (5) and let-7 (6) of Caenorhabditis elegans that trigger the translational inhibition of their target mRNAs by partial base-pairing within the 3Ј-untranslated region. According to the results of recent surveys performed using the experimental (3, 7) and bioinformatic approaches (8, 9), the miRNA genes may contribute ϳ1% to the total gene content of the investigated organisms making this regulatory mechanism more common than previously thought.Primary transcripts of the miRNA genes, pri-microRNAs, are processed in the nucleus to pre-microRNAs by the ribonuclease Drosha (10) and exported from the nucleus by Exportin-5 (11). The 60 -90-nt miRNA precursors form the stem and loop structures, and the cytoplasmic ribonuclease class III enzyme Dicer (12-14) excises miRNAs from the pre-miRNA hairpin stem. Dicer, either alone or with the help of Drosha, cleaves both strands of the precursor to form a double-stranded microRNA/microRNA* duplex (10, 15, 16) but only this strand accumulates which enters the RNAi-induced silencing complex (RISC) (17, 18). Based on the mechanism of the precursor hairpin processing and the similarities between the miRNA and RNAi pathways, active siRNA duplexes could be predicted with a high success rate (17, 18). It appears that designing siRNAs so that their properties resemble those of putative double-stranded miRNA intermediates, produces highly effective siRNAs. The strand whose 5Ј-end is less tightly paired to its complement is selected to enter into the RNAi-induced silencing complex, whereas the opposite strand is degraded. Thus, the structure of miRNA precursors and their short lived processing intermediates turned out to be the key for successful siRNA design (17,18). In this ...

Vervet monkeys are amongst the most widely distributed nonhuman primates, show considerable phenotypic diversity, and have long been an important biomedical model for a variety of human diseases and in vaccine research. Using whole genome sequencing data from 163 vervets sampled from across Africa and the Caribbean, we find high diversity, within and between taxa, and clear evidence that taxonomic divergence was reticulate rather than following a simple branching pattern. A scan for diversifying selection across taxa reveals strong and highly polygenic selection signals affecting viral processes. Furthermore, selection scores are elevated in genes whose human orthologs interact with HIV, and in genes that show a response to experimental SIV infection in vervet monkeys but not in rhesus macaques, suggesting that part of the signal reflects taxon-specific adaptation to SIV.