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Casper-Emil T Pedersen, Kirk E Lohmueller, Niels Grarup, Peter Bjerregaard, Torben Hansen, Hans R Siegismund, Ida Moltke, Anders Albrechtsen
The genetic consequences of population bottlenecks on patterns of deleterious genetic variation in human populations are of tremendous interest. Based on exome sequencing of 18 Greenlandic Inuit here we show that the Inuit have undergone a severe ~20,000 year long bottleneck. This has led to a markedly more extreme distribution of allele frequencies than seen for any other human population, making the Inuit the perfect population for investigating the effect of a bottleneck on patterns of deleterious variation...
November 30, 2016: Genetics
Yulong Wei, Xuhua Xia
Termination efficiency of stop codons depends on the first 3' flanking (+4) base in bacteria and eukaryotes. In both Escherichia coli and Saccharomyces cerevisiae, termination read-through is reduced in the presence of +4U; however, the molecular mechanism underlying +4U function is poorly understood. Here, we perform comparative genomics analysis on 25 bacterial species (covering Actinobacteria, Bacteriodetes, Cyanobacteria, Deinococcus-Thermus, Firmicutes, Proteobacteria and Spirochaetae) with bioinformatics approaches to examine the influence of +4U in bacterial translation termination by contrasting between highly and lowly expressed genes (HEGs and LEGs)...
November 30, 2016: Genetics
Xinzhu Wei, Jianzhi Zhang
Gene-environment interaction (G×E) refers to the phenomenon that the same mutation has different phenotypic effects in different environments. Although quantitative trait loci (QTLs) exhibiting G×E have been reported, little is known about the general properties of G×E and those of its underlying QTLs. Here we use the genotypes of 1005 segregants from a cross between two Saccharomyces cerevisiae strains and the growth rates of these segregants in 47 environments to identify growth rate QTLs (gQTLs) in each environment and QTLs that have different growth effects in each pair of environments (g×eQTLs)...
November 30, 2016: Genetics
Son C Nguyen, Stephanie Yu, Elaine Oberlick, Chao-Ting Wu
Polycomb group (PcG) proteins are major chromatin-bound factors that can read and modify chromatin states to maintain gene silencing throughout development. Here we focus on a close homolog of the PcG protein Posterior sex combs in order to better understand how these proteins affect regulation. This homolog, called Suppressor 2 of zeste, or Su(z)2 is comprised of two regions: the N-terminal "homology region" (HR), which serves as a hub for protein interactions, and the C-terminal region (CTR), which is believed to harbor the core activity of compacting chromatin...
November 23, 2016: Genetics
Jorge Pérez Heredia, Barbora Trubenová, Dirk Sudholt, Tiago Paixão
Adaptation depends critically on the effects of new mutations and their dependency on the genetic background they occur in. These two factors can be summarized by the fitness landscape. However, it would require testing all mutations in all backgrounds, making the definition and analysis of fitness landscapes mostly inaccessible. Instead of postulating a particular fitness landscape, we address this problem by considering general classes of landscapes and calculating an upper limit for the time it takes for a population to reach a fitness peak, circumventing the need to have full knowledge about the fitness landscape...
November 23, 2016: Genetics
Noah Zaitlen, Scott Huntsman, Donglei Hu, Melissa Spear, Celeste Eng, Sam S Oh, Marquitta J White, Angel Mak, Adam Davis, Kelly Meade, Emerita Brigino-Buenaventura, Michael A LeNoir, Kirsten Bibbins-Domingo, Esteban G Burchard, Eran Halperin
Statistical models in medical and population genetics typically assume that individuals assort randomly in a population. While this simplifies model complexity, it contradicts an increasing body of evidence of non-random mating in human populations. Specifically, it has been shown that assortative mating is significantly affected by genomic ancestry. In this work we examine the effects of ancestry-assortative mating on the linkage disequilibrium between local ancestry tracks of individuals in an admixed population...
November 22, 2016: Genetics
Felix Grassmann, Iris M Heid, Bernhard H F Weber
Age-related macular degeneration (AMD) is the leading cause of blindness in ageing societies and is caused by both environmental and genetic factors. The strongest genetic signal for AMD with odds ratios of up to 2.8 per adverse allele was found previously to center over two genes, ARMS2 and HTRA1 on 10q26, although with little knowledge as to the true functionally relevant gene or genetic variation. Due to extensive linkage disequilibrium (LD) at this locus, it was long assumed that the broad association signal cannot be dissected by statistical means...
November 22, 2016: Genetics
Ritika Gurung, Yosuke Ono, Sarah Baxendale, Samantha Lin Chiou Lee, Steven Moore, Meredith Calvert, Philip W Ingham
MYOSIN 18B is an unconventional myosin that has been implicated in tumour progression in humans. In addition, loss-of-function mutations of the MYO18B gene have recently been identified in several patients exhibiting symptoms of nemaline myopathy. In mouse, mutation of Myo18B results in early developmental arrest associated with cardiomyopathy, precluding analysis of its effects on skeletal muscle development. The zebrafish, frozen (fro) mutant was identified as one of a group of immotile mutants in the 1996 Tübingen genetic screen...
November 22, 2016: Genetics
Adam H Porter, Norman A Johnson, Alexander Y Tulchinsky
We report a new mechanism for allelic dominance in regulatory genetic interactions that we call binding dominance. We investigated a biophysical model of gene regulation, where the fractional occupancy of a transcription factor (TF) on the cis-regulated promoter site it binds to is determined by binding energy (-ΔG) and TF dosage. Transcription and gene expression proceed when the TF is bound to the promoter. In diploids, individuals may be heterozygous at the cis-site, at the TF's coding region, or at the TF's own promoter, which determines allele-specific dosage...
November 18, 2016: Genetics
Kazuhiro Bessho, Sarah P Otto
Classical population genetic theory generally assumes either a fully haploid or fully diploid life cycle. However, many organisms exhibit more complex life cycles, with both free-living haploid and diploid stages. Here we ask what the probability of fixation is for selected alleles in organisms with haploid-diploid life cycles. We develop a genetic model that considers the population dynamics using both the Moran model and Wright-Fisher model. Applying a branching process approximation, we obtain an accurate fixation probability assuming that the population is large and the net effect of the mutation is beneficial...
November 18, 2016: Genetics
Dong-Hoon Yang, Kwang-Woo Jung, Soohyun Bang, Jang-Won Lee, Min-Hee Song, Anna Floyd-Averette, Richard A Festa, Giuseppe Ianiri, Alexander Idnurm, Dennis J Thiele, Joseph Heitman, Yong-Sun Bahn
Thermotolerance is a crucial virulence attribute for human pathogens, including the fungus Cryptococcus neoformans that causes fatal meningitis in humans. Loss of the protein kinase Sch9 increases C. neoformans thermotolerance, but its regulatory mechanism has remained unknown. Here, we studied the Sch9-dependent and Sch9-independent signaling networks modulating C. neoformans thermotolerance by using genome-wide transcriptome analysis and reverse genetic approaches. During temperature upshift, genes encoding for molecular chaperones and heat shock proteins were upregulated, whereas those for translation, transcription, and sterol biosynthesis were highly suppressed...
November 18, 2016: Genetics
Maximilian Oliver Press, Christine Queitsch
Short tandem repeats are hypervariable genetic elements that occur frequently in coding regions. Their high mutation rate readily generates genetic variation contributing to adaptive evolution and human diseases. We previously reported that natural ELF3 polyglutamine variants cause reciprocal genetic incompatibilities in two divergent Arabidopsis thaliana backgrounds. Here, we dissect the genetic architecture of this incompatibility, revealing as many as four loci putatively interacting with ELF3 We were able to specifically identify one such ELF3-interacting gene, LSH9 We further used a yeast two-hybrid strategy to identify proteins whose physical interactions with ELF3 were affected by polyglutamine tract length...
November 18, 2016: Genetics
Baptiste Roelens, Marie Clémot, Mathieu Leroux-Coyau, Benjamin Klapholz, Nathalie Dostatni
In eukaryotic cells, the organization of genomic DNA into chromatin regulates many biological processes, from the control of gene expression to the regulation of chromosome segregation. The proper maintenance of this structure upon cell division is therefore of prime importance during development for the maintenance of cell identity and genome stability. The Chromatin Assembly Factor 1 (CAF-1) is involved in the assembly of H3-H4 histone dimers on newly synthesized DNA and in the maintenance of a higher order structure, the heterochromatin, through an interaction of its large subunit with the heterochromatin protein HP1a...
November 11, 2016: Genetics
Kun Xiong, Jay P McEntee, David Porfirio, Joanna Masel
Gene expression is imperfect, sometimes leading to toxic products. Solutions take two forms: globally reducing error rates, or ensuring that the consequences of erroneous expression are relatively harmless. The latter is optimal, but because it must evolve independently at so many loci, it is subject to a stringent "drift barrier" - a limit to how weak the effects of a deleterious mutation s can be, while still being effectively purged by selection, expressed in terms of the population size N of an idealized population such that purging requires s < -1/N In previous work, only large populations evolved the optimal local solution, small populations instead evolved globally low error rates, and intermediate populations were bistable, with either solution possible...
November 11, 2016: Genetics
Beth L Dumont
The segregation of homologous chromosomes at the first meiotic division is dependent on the presence of at least one well-positioned crossover per chromosome. In some mammalian species, however, the genomic distribution of crossovers is consistent with a more stringent baseline requirement of one crossover per chromosome arm. Given that the meiotic requirement for crossing over defines the minimum frequency of recombination necessary for the production of viable gametes, determining the chromosomal-scale of this constraint is essential for defining crossover profiles predisposed to aneuploidy and understanding the parameters that shape patterns of recombination rate evolution across species...
November 11, 2016: Genetics
Francesco Montinaro, George B J Busby, Miguel Gonzalez-Santos, Ockie Oosthuitzen, Erika Oosthutizen, Paolo Anagnostou, Giovanni Destro-Bisol, Vincenzo L Pascali, Cristian Capelli
The characterization of the structure of southern Africa populations has been the subject of numerous genetic, medical, linguistic, archaeological and anthropological investigations. Current diversity in the subcontinent is the result of complex events of genetic admixture and cultural contact between early inhabitants and migrants that arrived in the region over the last 2,000 years. Here we analyze 1,856 individuals from 91 populations, comprising novel and published genotype data, to characterize the genetic ancestry profiles of 631 individuals from 51 southern African populations...
November 11, 2016: Genetics
Brandon S Cooper, Paul S Ginsberg, Michael Turelli, Daniel R Matute
Three hybridizing species-the clade ((Drosophila yakuba, D. santomea), D. teissieri) -comprise the yakuba complex in the D. melanogaster subgroup. Their ranges overlap on Bioko and São Tomé, islands off west Africa. All three species are infected with Wolbachia, maternally inherited, endosymbiotic bacteria, best known for manipulating host reproduction to favor infected females. Previous analyses reported no cytoplasmic incompatibility (CI) in these species. However, we discovered that Wolbachia from each species cause intra- and interspecific CI...
November 7, 2016: Genetics
Athanasios Kousathanas, Christoph Leuenberger, Vivian Link, Christian Sell, Joachim Burger, Daniel Wegmann
While genetic diversity can be quantified accurately from high coverage sequencing data, it is often desirable to obtain such estimates from data with low coverage, either to save costs or because of low DNA quality, as is observed for ancient samples. Here we introduce a method to accurately infer heterozygosity probabilistically from sequences with average coverage < 1 X of a single individual. The method relaxes the infinite sites assumption of previous methods, does not require a reference sequence except for the initial alignment of the sequencing data, and takes into account both variable sequencing errors and potential post-mortem damage...
November 7, 2016: Genetics
Nanna Torpe, Steffen Nørgaard, Anette M Høye, Roger Pocock
Nogo-A is a membrane-bound protein that functions to inhibit neuronal migration, adhesion and neurite outgrowth during development. In the mature nervous system, Nogo-A stabilizes neuronal wiring to inhibit neuronal plasticity and regeneration after injury. Here, we show that RET-1, the sole Nogo-A homolog in Caenorhabditis elegans, is required to control developmental wiring of a specific subset of neurons. In ret-1 deletion mutant animals, specific ventral nerve cord axons are misguided where they fail to respect the ventral midline boundary...
November 7, 2016: Genetics
Jennifer Tsialikas, Mitchell A Romens, Allison Abbott, Eric G Moss
In normal development, the order and synchrony of diverse developmental events must be explicitly controlled. In the nematode Caenorhabditis elegans, the timing of larval events is regulated by hierarchy of proteins and microRNAs known as the heterochronic pathway. These regulators are organized in feedforward and feedback interactions to form a robust mechanism for specifying the timing and execution of cell fates at successive stages. One member of this pathway is the RNA binding protein LIN-28, which promotes pluripotency and cell fate decisions in successive stages...
November 4, 2016: Genetics
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