Using comparative genomics to reorder the human genome sequence into a virtual sheep genome

Background

Is it possible to construct an accurate and detailed subgene-level map of a genome using bacterial artificial chromosome (BAC) end sequences, a sparse marker map, and the sequences of other genomes?

Results

A sheep BAC library, CHORI-243, was constructed and the BAC end sequences were determined and mapped with high sensitivity and low specificity onto the frameworks of the human, dog, and cow genomes. To maximize genome coverage, the coordinates of all BAC end sequence hits to the cow and dog genomes were also converted to the equivalent human genome coordinates. The 84,624 sheep BACs (about 5.4-fold genome coverage) with paired ends in the correct orientation (tail-to-tail) and spacing, combined with information from sheep BAC comparative genome contigs (CGCs) built separately on the dog and cow genomes, were used to construct 1,172 sheep BAC-CGCs, covering 91.2% of the human genome. Clustered non-tail-to-tail and outsize BACs located close to the ends of many BAC-CGCs linked BAC-CGCs covering about 70% of the genome to at least one other BAC-CGC on the same chromosome. Using the BAC-CGCs, the intrachromosomal and interchromosomal BAC-CGC linkage information, human/cow and vertebrate synteny, and the sheep marker map, a virtual sheep genome was constructed. To identify BACs potentially located in gaps between BAC-CGCs, an additional set of 55,668 sheep BACs were positioned on the sheep genome with lower confidence. A coordinate conversion process allowed us to transfer human genes and other genome features to the virtual sheep genome to display on a sheep genome browser.

Conclusion

We demonstrate that limited sequencing of BACs combined with positioning on a well assembled genome and integrating locations from other less well assembled genomes can yield extensive, detailed subgene-level maps of mammalian genomes, for which genomic resources are currently limited.     

Use of Genome-wide Heterospecific Single-Nucleotide Polymorphisms to Estimate Linkage Disequilibrium in Rhesus and Cynomolgus Macaques

Rhesus and cynomolgus macaques are frequently used in biomedical research, and the availability of their reference genomes now provides for their use in genome-wide association studies. However, little is known about linkage disequilibrium (LD) in their genomes, which can affect the design and success of such studies. Here we studied LD by using 1781 conserved single-nucleotide polymorphisms (SNPs) in 183 rhesus macaques (Macaca mulatta), including 97 purebred Chinese and 86 purebred Indian animals, and 96 cynomolgus macaques (M. fascicularis fascicularis). Correlation between loci pairs decayed to 0.02 at 1146.83, 2197.92, and 3955.83 kb for Chinese rhesus, Indian rhesus, and cynomolgus macaques, respectively. Differences between the observed heterozygosity and minor allele frequency (MAF) of pairs of these 3 taxa were highly statistically significant. These 3 nonhuman primate taxa have significantly different genetic diversities (heterozygosity and MAF) and rates of LD decay. Our study confirms a much lower rate of LD decay in Indian than in Chinese rhesus macaques relative to that previously reported. In contrast, the especially low rate of LD decay in cynomolgus macaques suggests the particular usefulness of this species in genome-wide association studies. Although conserved markers, such as those used here, are required for valid LD comparisons among taxa, LD can be assessed with less bias by using species-specific markers, because conserved SNPs may be ancestral and therefore not informative for LD.Abbreviations: GWAS, genome-wide association study; LD, linkage disequilibrium; MAF, minor allele frequencyContributing to the widespread use of nonhuman primates in biomedical research, captive-breeding programs such as those of the National Primate Research Center system in the United States were established initially by using animals imported from Asia. The 2 most commonly used primates are rhesus macaques (Macaca mulatta) and long-tailed or cynomolgus macaques (M. fascicularis fascicularis).After humans, rhesus macaques are the most widely distributed primate species.^37,38 This species is found throughout mainland Asia, ranging from Afghanistan to India and eastward through Thailand and southern China to the Yellow Sea.^31,34 In addition to their significant morphological differences,⁹ rhesus macaques of Indian and Chinese origins have been demonstrated to exhibit significant phenotypic differences that are directly relevant to their use as biomedical models in experimental studies.^2,23,42 Cynomolgus macaques are found south of the subtropical and temperate geographic distributions of rhesus macaques, in the south and southeast Indo-Malayan regions.^8,10The 2 species share a common ancestor that lived 1 to 2 million years ago.^3,13,25 This ancestral population of rhesus macaques diverged from a fascicularis-like ancestor shared in common with both rhesus and cynomolgus macaques after cynomolgus macaques expanded from their homeland in Indonesia.³⁶ For this reason, genetic markers present in Indian rhesus macaques are either highly derived or are conserved as ancestral markers shared with Chinese rhesus macaques. The interspecific boundaries of rhesus and cynomolgus macaques are delineated by a narrow zone of parapatry in northern Indochina,^7,8,10 within which male-biased gene flow^37,39 and relatively high, but highly variable, levels of introgression of genes³² have occurred from rhesus to cynomolgus macaque groups.^37,39 Because cynomolgus macaques originated in Indonesia³⁶ and because rhesus macaques probably diverged from cynomolgus macaques in southwestern China,¹¹ genetic markers shared between Indonesian cynomolgus macaques and Chinese rhesus macaques comprise a unique set of markers that are conserved in both macaque species.The wide assortment of morphometric differences^8,9 and the broad geographic distribution of these 2 macaque species foster an expectation of high genetic diversity within and between them that could be exploited for mapping genes responsible for phenotypic differences between taxa. A better understanding of linkage disequilibrium (LD) in these nonhuman primate species can lead to a more informed selection of study subjects for, and more efficient conduct of, genome-wide association studies (GWAS) of particular diseases that macaques share in common with humans. LD is the nonrandom association of alleles at 2 or more adjacent loci that descend from single, ancestral chromosomes.²⁹ LD plays a critical role in gene mapping, both as a tool for fine mapping of complex disease genes and in GWAS-based approaches. GWAS facilitate the identification of genes associated with complex and common traits or diseases by examining LD estimates among large numbers of common genetic variants, typically single-nucleotide polymorphisms (SNPs), between pairs of different groups of subjects to determine whether any variant is associated with a trait or disease of interest. LD data make tightly linked variants strongly correlated to produce successful association studies. For instance, LD reduces the number of markers and sample size of study subjects required to map genes influencing phenotypes to the genome because markers in LD are linked and inherited together.¹³ In addition, differences in LD can be used to identify orthologs for detecting the signatures of selective sweeps,²¹ as defined by d_N/d_S ratios obtained through the McDonald–Kreitman neutrality test.²⁴ Furthermore, LD assessments can provide a more complete understanding of genome structure by defining the boundaries of haplotype blocks, within which recombination is rare or absent and which are separated by recombination ‘hotspots,’ in genomes.⁴³Evidence from a study based on 1476 SNPs identified in ENCODE regions of the Indian rhesus macaque genome¹³ indicated that the rate of LD decay is higher in Chinese than in Indian rhesus macaques due to an hypothesized genetic bottleneck experienced by Indian rhesus macaques after diverging from the eastern subspecies, and, therefore, that Indian rhesus macaques, having higher LD, may be more useful for GWAS than Chinese rhesus macaques. In that study,¹³ only 33% of the SNPs were shared in common between the 2 subspecies, with Chinese rhesus macaques contributing to more than 60% of the remaining rhesus SNPs. Conversely, another study⁴¹ reported a slower rate of decay of LD in 25 Chinese than in 25 Indian rhesus macaques on the basis of 4040 SNPs, only 2% of which fell in coding regions, but 68% of those SNPs were shared between the 2 subspecies, with Indian rhesus macaques contributing almost 60% of the remaining SNPs. The marked disparity between the 2 studies in the proportions of shared SNPs used, the subspecies with the most genetic diversity, the sample size of Chinese rhesus macaques, the proportions of SNPs located in or near coding regions that are subject to functional constraints, and the greater disparity in LD decay between the 2 subspecies of rhesus macaques might reflect biases in either or both studies. For example, the use of markers whose frequencies are uncharacteristically low in one subspecies relative to the other can underestimate the rate of LD decay because lower frequency alleles, on average, are younger and have experienced less time for recombination.²⁶ To avoid the influence of such ascertainment biases, comparisons of LD between 2 taxa should involve only SNPs conserved in both taxa. Moreover, because 2 points do not provide a phylogenetic or cladistic analysis to assign specific SNPs to origin on one phylogenetic line or another, comparing just the Indian and Chinese rhesus macaques without an additional primate taxon makes it is difficult to establish polarity and distinguish between derived and conserved SNPs. This limitation likely led to the contradictory conclusions of the 2 previously cited studies^13,41 regarding the rate of LD decay in Chinese and Indian rhesus macaques.Because rhesus and cynomolgus macaques share a common fascicularis-like ancestor, a comparison of heterospecific SNPs among cynomolgus, Indian rhesus, and Chinese rhesus macaques would likely be fundamental to inferences regarding genome-wide LD estimates. The objective of the present study was to evaluate the conclusions of previous studies^13,41 by using our panel of 1781 autosomal SNPs that are conserved in both rhesus and cynomolgus macaques to estimate the rates at which genome-wide LD decays in Indian and Chinese rhesus macaques and cynomolgus macaques, the species ancestral to rhesus macaques, and to evaluate the suitability of these populations for GWAS.     

Prostaglandin E2 affects T cell responses through modulation of CD46 expression

The ubiquitous protein CD46, a regulator of complement activity, promotes T cell activation and differentiation toward a regulatory Tr1-like phenotype. The CD46-mediated differentiation pathway is defective in several chronic inflammatory diseases, underlying the importance of CD46 in controlling T cell function and the need to understand its regulatory mechanisms. Using an RNA interference-based screening approach in primary T cells, we have identified that two members of the G protein-coupled receptor kinases were involved in regulating CD46 expression at the surface of activated cells. We have investigated the role of PGE(2), which binds to the E-prostanoid family of G protein-coupled receptors through four subtypes of receptors called EP 1-4, in the regulation of CD46 expression and function. Conflicting roles of PGE(2) in T cell functions have been reported, and the reasons for these apparent discrepancies are not well understood. We show that addition of PGE(2) strongly downregulates CD46 expression in activated T cells. Moreover, PGE(2) differentially affects T cell activation, cytokine production, and phenotype depending on the activation signals received by the T cells. This was correlated with a distinct pattern of the PGE(2) receptors expressed, with EP4 being preferentially induced by CD46 activation. Indeed, addition of an EP4 antagonist could reverse the effects observed on cytokine production after CD46 costimulation. These data demonstrate a novel role of the PGE(2)-EP4 axis in CD46 functions, which might at least partly explain the diverse roles of PGE(2) in T cell functions.     

Human anti-prion antibodies block prion peptide fibril formation and neurotoxicity

Prion diseases are a group of rare, fatal neurodegenerative disorders associated with a conformational transformation of the cellular prion protein (PrP(C)) into a self-replicating and proteinase K-resistant conformer, termed scrapie PrP (PrP(Sc)). Aggregates of PrP(Sc) deposited around neurons lead to neuropathological alterations. Currently, there is no effective treatment for these fatal illnesses; thus, the development of an effective therapy is a priority. PrP peptide-based ELISA assay methods were developed for detection and immunoaffinity chromatography capture was developed for purification of naturally occurring PrP peptide autoantibodies present in human CSF, individual donor serum, and commercial preparations of pooled intravenous immunoglobulin (IVIg). The ratio of anti-PrP autoantibodies (PrP-AA) to total IgG was ～1:1200. The binding epitope of purified PrP-AA was mapped to an N-terminal region comprising the PrP amino acid sequence KTNMK. Purified PrP-AA potently blocked fibril formation by a toxic 21-amino acid fragment of the PrP peptide containing the amino acid alanine to valine substitution corresponding to position 117 of the full-length peptide (A117V). Furthermore, PrP-AA attenuated the neurotoxicity of PrP(A117V) and wild-type peptides in rat cerebellar granule neuron (CGN) cultures. In contrast, IgG preparations depleted of PrP-AA had little effect on PrP fibril formation or PrP neurotoxicity. The specificity of PrP-AA was demonstrated by immunoprecipitating PrP protein in brain tissues of transgenic mice expressing the human PrP(A117V) epitope and Sc237 hamster. Based on these intriguing findings, it is suggested that human PrP-AA may be useful for interfering with the pathogenic effects of pathogenic prion proteins and, thereby has the potential to be an effective means for preventing or attenuating human prion disease progression.     

Contingency in the direction and mechanics of soil organic matter responses to increased rainfall

Background and Aims

Rainfall is expected to show greater and more variable changes in response to anticipated rising of earth surface temperatures than most other climatic variables, and will be a major driver of ecosystem change.

Methods

We studied the effects of predicted changes in California’s rainy season for storage and stabilization mechanisms of soil organic matter (SOM). In a controlled and replicated experiment, we amended rainfall over large plots of natural grassland in accordance with alternative scenarios of future climate change.

Results

We found that increases in annual rainfall have important consequences for soil carbon (C) storage, but that the strength and even direction of these effects depend critically on seasonal timing. Additional rainfall during the winter rainy season led to C loss from soil while additions after the typical rainy season increased soil C content. Analysis of MIneral-Organic Matter (OM) associations reveals a potentially powerful mechanism underlying this difference: increased winter rainfall greatly diminished the role of Fe and Al oxides in SOM stabilization. Dithionite extractable crystalline Fe oxides explained more than 35% of the variability in C storage under ambient control and extended spring rainfall conditions, compared to less than 0.01% under increased winter rainfall. Likewise, poorly crystalline Fe and Al oxides explained more than 25 and 40% of the variability in C storage in the control and extended spring rainfall treatments, respectively, but less than 5% in the increased winter rainfall treatment.

Conclusions

Increases in annual precipitation identical in amount but at three-month offsets produced opposite effects on soil C storage. Such clear differences in the amount and chemical composition of SOM, and in the vertical distribution of oxides in the soil profile in response to treatment timing carry important implications for the C sequestration trajectory of this ecosystem.     

Crystal structure of the Kar3-like kinesin motor domain from the filamentous fungus Ashbya gossypii

Kar3 kinesins are microtubule (MT) minus‐end‐directed motors with pleiotropic functions in mitotic spindle formation and nuclear movement in budding and fission yeasts. A Kar3‐like kinesin is also expressed by the filamentous fungus Ashbya gossypi, which exhibits different nuclear movement challenges from its yeast relatives. Presented here is a 2.35 Å crystal structure and enzymatic analysis of the AgKar3 motor domain (AgKar3MD). Compared to the previously published Saccharomyces cerevisiae Kar3MD structure (ScKar3MD), AgKar3MD displays differences in the conformation of some of its nucleotide‐binding motifs and peripheral elements. Unlike ScKar3MD, the salt bridge between Switch I and Switch II in AgKar3MD is broken. Most of the Switch I, and the adjoining region of helix α3, are also disordered instead of bending into the active site cleft as is observed in ScKar3MD. These aspects of AgKar3MD are highly reminiscent of the ScKar3 R598A mutant that disrupts the Switch I–Switch II salt bridge and impairs MT‐stimulated ATPase activity of the motor. Subtle differences in the disposition of secondary structure elements in the small lobe (β1a, β1b, and β1c) at the edge of the MD are also apparent even though it contains approximately the same number of residues as ScKar3. These differences may reflect the unique enzymatic properties we measured for this motor, which include a lower MT‐stimulated ATPase rate relative to ScKar3, or they could relate to its interactions with different regulatory companion proteins than its budding yeast counterpart. Proteins 2011;. © 2011 Wiley Periodicals, Inc.     

Homologous recombination is required for genome stability in the absence of DOG-1 in Caenorhabditis elegans

In C. elegans, DOG-1 prevents deletions that initiate in polyG/polyC tracts (G/C tracts), most likely by unwinding secondary structures that can form in G/C tracts during lagging-strand DNA synthesis. We have used the dog-1 mutant to assay the in vivo contribution of various repair genes to the maintenance of G/C tracts. Here we show that DOG-1 and the BLM ortholog, HIM-6, act synergistically during replication; simultaneous loss of function of both genes results in replicative stress and an increase in the formation of small deletions that initiate in G/C tracts. Similarly, we demonstrate that the C. elegans orthologs of the homologous recombination repair genes BARD1, RAD51, and XPF and the trans-lesion synthesis polymerases poleta and polkappa contribute to the prevention of deletions in dog-1 mutants. Finally, we provide evidence that the small deletions generated in the dog-1 background are not formed through homologous recombination, nucleotide excision repair, or nonhomologous end-joining mechanisms, but appear to result from a mutagenic repair mechanism acting at G/C tracts. Our data support the hypothesis that absence of DOG-1 leads to replication fork stalling that can be repaired by deletion-free or deletion-prone mechanisms.     

Labile sex differences in long calling in cotton-top tamarins

Sex differences in behavior are quite common among nonhuman primates. In sexually monomorphic species, sex differences might be expected to be less evident than in polygynous and highly dimorphic species. Callitrichid primates (marmosets and tamarins) are cooperative breeders that exhibit little sexual size dimorphism. However, several sex differences in the structure and usage of vocalizations have been reported. In one such study, McConnell and Snowdon [Behaviour 97:273-296, 1986] reported that female cotton-top tamarins (Saguinus oedipus) emitted significantly more normal long calls than males during simulated intergroup encounters. In the course of collecting a library of normal long calls, we replicated a portion of that study 20 years later with the same colony and similar methods. To our surprise we found a reversal of sex differences. In the same experimental situation, males gave significantly more normal long calls than females. In a further replication 2 years later, males still called more but the effect was less pronounced. The dramatic change in sex differences within the same species and colony over a 22-year period suggests that behavioral sex differences in callitrichids may be quite labile, and that repeated sampling over several years may be necessary to establish true sex differences.     

A study of the regional effects of alpha-synuclein on the organization and stability of phospholipid bilayers

Associations between the protein alpha-synuclein (alpha-syn) and presynaptic vesicles have been implicated in synaptic plasticity and neurotransmitter release and may also affect how the protein aggregates into fibrils found in Lewy bodies, the cellular inclusions associated with neurodegenerative diseases. This work investigated how alpha-syn interacts with model phospholipid membranes and examined what effect protein binding has upon the physical properties of lipid bilayers. Wide line 2H and 31P NMR spectra of phospholipid vesicles revealed that alpha-syn associates with membranes containing lipids with anionic headgroups and can disrupt the integrity of the lipid bilayer, but the protein has little effect on membranes of zwitterionic phosphatidylcholine. A peptide, alpha-syn(10-48), which corresponds to the lysine-rich N-terminal region of alpha-syn, was found to associate with lipid headgroups with a preference for a negative membrane surface charge. Another peptide, alpha-syn(120-140), which corresponds to the glutamate-rich C-terminal region, also associates weakly with lipid headgroups but with a slightly higher affinity for membranes with no net surface charge than for negatively charged membrane surfaces. Binding of alpha-syn(10-48) and alpha-syn(120-140) to the lipid vesicles did not disrupt the lamellar structure of the membranes, but both peptides appeared to induce the lateral segregation of the lipids into clusters of acidic lipid-enriched and acidic lipid-deficient domains. From these findings, it is speculated that the N-terminal and C-terminal domains of full-length alpha-syn might act in concert to organize the membrane components during normal protein function and perhaps play a role in presynaptic vesicle synthesis, maintenance, and fusion.