A Cre Transcription Fidelity Reporter Identifies GreA as a Major RNA Proofreading Factor in Escherichia coli [Gene Expression]
We made a coupled genetic reporter that detects rare transcription misincorporation errors to measure RNA polymerase transcription fidelity in Escherichia coli. Using this reporter, we demonstrated in vivo that the transcript cleavage factor GreA, but not GreB, is essential for proofreading of a transcription error where a riboA has been misincorporated instead of a riboG. A greA mutant strain had more than a 100-fold increase in transcription errors relative to wild-type or a greB mutant. However, overexpression of GreB in greA cells reduced the misincorporation errors to wild-type levels, demonstrating that GreB at high ...
Source: Genetics - May 5, 2017 Category: Genetics & Stem Cells Authors: Bubunenko, M. G., Court, C. B., Rattray, A. J., Gotte, D. R., Kireeva, M. L., Irizarry-Caro, J. A., Li, X., Jin, D. J., Court, D. L., Strathern, J. N., Kashlev, M. Tags: Gene Expression Source Type: research
Germ Granules Prevent Accumulation of Somatic Transcripts in the Adult Caenorhabditis elegans Germline [Gene Expression]
In this study, we performed transcriptome and single molecule RNA-FISH analyses of dissected P granule-depleted gonads at different developmental stages. Our results demonstrate that P granules are necessary for adult germ cells to downregulate spermatogenesis RNAs and to prevent the accumulation of numerous soma-specific RNAs. P granule-depleted gonads that express the unc-119::gfp transgene also express many other genes involved in neuronal development and concomitantly lose expression of germ cell fate markers. Finally, we show that removal of either of two critical P-granule components, PGL-1 or GLH-1, is sufficient to...
Source: Genetics - May 5, 2017 Category: Genetics & Stem Cells Authors: Knutson, A. K., Egelhofer, T., Rechtsteiner, A., Strome, S. Tags: Gene Expression Source Type: research
Adaptation of Candida albicans to Reactive Sulfur Species [Gene Expression]
Candida albicans is an opportunistic fungal pathogen that is highly resistant to different oxidative stresses. How reactive sulfur species (RSS) such as sulfite regulate gene expression and the role of the transcription factor Zcf2 and the sulfite exporter Ssu1 in such responses are not known. Here, we show that C. albicans specifically adapts to sulfite stress and that Zcf2 is required for that response as well as induction of genes predicted to remove sulfite from cells and to increase the intracellular amount of a subset of nitrogen metabolites. Analysis of mutants in the sulfate assimilation pathway show that sulfite c...
Source: Genetics - May 5, 2017 Category: Genetics & Stem Cells Authors: Chebaro, Y., Lorenz, M., Fa, A., Zheng, R., Gustin, M. Tags: Gene Expression Source Type: research
Structure and Origin of the White Cap Locus and Its Role in Evolution of Grain Color in Maize [Gene Expression]
Selection for yellow- and white-grain types has been central to postdomestication improvement of maize. While genetic control of carotenoid biosynthesis in endosperm is attributed primarily to the Yellow1 (Y1) phytoene synthase gene, less is known about the role of the dominant white endosperm factor White Cap (Wc). We show that the Wc locus contains multiple, tandem copies of a Carotenoid cleavage dioxygenase 1 (Ccd1) gene that encodes a carotenoid-degrading enzyme. A survey of 111 maize inbreds and landraces, together with 22 teosinte accessions, reveals that Wc is exclusive to maize, where it is prevalent in white-grain...
Source: Genetics - May 5, 2017 Category: Genetics & Stem Cells Authors: Tan, B.-C., Guan, J.-C., Ding, S., Wu, S., Saunders, J. W., Koch, K. E., McCarty, D. R. Tags: Gene Expression Source Type: research
Bivariate Analysis of Age-Related Macular Degeneration Progression Using Genetic Risk Scores [Statistical Genetics and Genomics]
Age-related macular degeneration (AMD) is a leading cause of blindness in the developed world. While many AMD susceptibility variants have been identified, their influence on AMD progression has not been elucidated. Using data from two large clinical trials, Age-Related Eye Disease Study (AREDS) and AREDS2, we evaluated the effects of 34 known risk variants on disease progression. In doing so, we calculated the eye-level time-to-late AMD and modeled them using a bivariate survival analysis approach, appropriately accounting for between-eye correlation. We then derived a genetic risk score (GRS) based on these 34 risk varia...
Source: Genetics - May 5, 2017 Category: Genetics & Stem Cells Authors: Ding, Y., Liu, Y., Yan, Q., Fritsche, L. G., Cook, R. J., Clemons, T., Ratnapriya, R., Klein, M. L., Abecasis, G. R., Swaroop, A., Chew, E. Y., Weeks, D. E., Chen, W. Tags: Statistical Genetics and Genomics Source Type: research
Estimating Seven Coefficients of Pairwise Relatedness Using Population-Genomic Data [Statistical Genetics and Genomics]
Population structure can be described by genotypic-correlation coefficients between groups of individuals, the most basic of which are the pairwise relatedness coefficients between any two individuals. There are nine pairwise relatedness coefficients in the most general model, and we show that these can be reduced to seven coefficients for biallelic loci. Although all nine coefficients can be estimated from pedigrees, six coefficients have been beyond empirical reach. We provide a numerical optimization procedure that estimates all seven reduced coefficients from population-genomic data. Simulations show that the procedure...
Source: Genetics - May 5, 2017 Category: Genetics & Stem Cells Authors: Ackerman, M. S., Johri, P., Spitze, K., Xu, S., Doak, T. G., Young, K., Lynch, M. Tags: Statistical Genetics and Genomics Source Type: research
GeneImp: Fast Imputation to Large Reference Panels Using Genotype Likelihoods from Ultralow Coverage Sequencing [Methods, Technology, and Resources]
We describe GeneImp, a program for genotype imputation that does not require prephasing and is computationally tractable for whole-genome imputation. GeneImp does not explicitly model recombination, instead it capitalizes on the existence of large reference panels—comprising thousands of reference haplotypes—and assumes that the reference haplotypes can adequately represent the target haplotypes over short regions unaltered. We validate GeneImp based on data from ultralow coverage sequencing (0.5x), and compare its performance to the most recent version of BEAGLE that can perform this task. We show that GeneImp...
Source: Genetics - May 5, 2017 Category: Genetics & Stem Cells Authors: Spiliopoulou, A., Colombo, M., Orchard, P., Agakov, F., McKeigue, P. Tags: Methods, Technology, and Resources Source Type: research
Maize Transposon Storm Kicks up a White Cap [Commentary]
(Source: Genetics)
Source: Genetics - May 5, 2017 Category: Genetics & Stem Cells Authors: Peterson, T. Tags: Commentary Source Type: research
The Natural Biotic Environment of Caenorhabditis elegans [Evolution and Ecology]
Organisms evolve in response to their natural environment. Consideration of natural ecological parameters are thus of key importance for our understanding of an organism’s biology. Curiously, the natural ecology of the model species Caenorhabditis elegans has long been neglected, even though this nematode has become one of the most intensively studied models in biological research. This lack of interest changed ~10 yr ago. Since then, an increasing number of studies have focused on the nematode’s natural ecology. Yet many unknowns still remain. Here, we provide an overview of the currently available information...
Source: Genetics - May 5, 2017 Category: Genetics & Stem Cells Authors: Schulenburg, H., Felix, M.-A. Tags: Evolution and Ecology Source Type: research
The Centrioles, Centrosomes, Basal Bodies, and Cilia of Drosophila melanogaster [Repair, Recombination, and Cell Division]
Centrioles play a key role in the development of the fly. They are needed for the correct formation of centrosomes, the organelles at the poles of the spindle that can persist as microtubule organizing centers (MTOCs) into interphase. The ability to nucleate cytoplasmic microtubules (MTs) is a property of the surrounding pericentriolar material (PCM). The centriole has a dual life, existing not only as the core of the centrosome but also as the basal body, the structure that templates the formation of cilia and flagellae. Thus the structure and functions of the centriole, the centrosome, and the basal body have an impact u...
Source: Genetics - May 5, 2017 Category: Genetics & Stem Cells Authors: Lattao, R., Kovacs, L., Glover, D. M. Tags: Repair, Recombination, and Cell Division Source Type: research
An Evolutionary Perspective on Yeast Mating-Type Switching [Review]
Cell differentiation in yeast species is controlled by a reversible, programmed DNA-rearrangement process called mating-type switching. Switching is achieved by two functionally similar but structurally distinct processes in the budding yeast Saccharomyces cerevisiae and the fission yeast Schizosaccharomyces pombe. In both species, haploid cells possess one active and two silent copies of the mating-type locus (a three-cassette structure), the active locus is cleaved, and synthesis-dependent strand annealing is used to replace it with a copy of a silent locus encoding the opposite mating-type information. Each species has ...
Source: Genetics - May 5, 2017 Category: Genetics & Stem Cells Authors: Hanson, S. J., Wolfe, K. H. Tags: Reviews Source Type: research
William Friedman, Geneticist Turned Cryptographer [Perspectives]
William Friedman (1891–1969), trained as a plant geneticist at Cornell University, was employed at Riverbank Laboratories by the eccentric millionaire George Fabyan to work on wheat breeding. Friedman, however, soon became intrigued by and started working on a pet project of Fabyan’s involving the conjecture that Francis Bacon, a polymath known for the study of ciphers, was the real author of Shakespeare’s plays. Thus, beginning in ~1916, Friedman turned his attention to the so called "Baconian cipher," and developed decryption techniques that bore similarity to approaches for solving problems in populati...
Source: Genetics - May 5, 2017 Category: Genetics & Stem Cells Authors: Goldman, I. L. Tags: Perspectives Source Type: research
ISSUE HIGHLIGHTS [Issue Highlights]
(Source: Genetics)
Source: Genetics - May 5, 2017 Category: Genetics & Stem Cells Tags: Issue Highlights Source Type: research
Corrigendum [Corrigendum]
(Source: Genetics)
Source: Genetics - March 30, 2017 Category: Genetics & Stem Cells Tags: Corrigendum Source Type: research
Elevated Rate of Genome Rearrangements in Radiation-Resistant Bacteria [Genome and Systems Biology]
In conclusion, the opposing effects of environmental DNA damage and DNA repair result in elevated rates of genome rearrangements in radiation-resistant bacteria. (Source: Genetics)
Source: Genetics - March 30, 2017 Category: Genetics & Stem Cells Authors: Repar, J., Supek, F., Klanjscek, T., Warnecke, T., Zahradka, K., Zahradka, D. Tags: Genome and Systems Biology Source Type: research
