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2014 GENETICS Web Spotlight

2013 Web Spotlight


Since 1916, GENETICS has sought to publish significant advances in the field. To be accepted for publication, manuscripts must provide new insights into a biological process or demonstrate novel and creative approaches to an important biological problem or describe development of new resources, methods, technologies, or tools. And the study must be of interest to a wide range of genetics and genomics investigators. The editors of GENETICS seek to attract and publish articles that they believe will have a high impact on the field.


While it has a long and illustrious history, GENETICS has changed: it is not your mentor's journal. The editors make decisions quickly – in around 32 days – without sacrificing the excellence and scholarship for which the journal has long been known. GENETICS is constantly innovating; some of the new and expanded types of content include:

  • YeastBook – a comprehensive compendium of reviews that presents the current state of knowledge of the molecular biology, cellular biology, and genetics of the yeast Saccharomyces cerevisiae.

  • Educational Primers – tied to a current article in GENETICS, these educational resources lay out the necessary background (i.e., what was the question and why did that question matter?), explain the hypothesis or approach, describe the methodology, guide the reader through the results, and provide a precise summation of the discussion.

  • Genetic Toolbox Reviews – describes practical and intellectual resources available for the study of less commonly used experimental organisms.

  • Reviews

Thompson Reuters JCR Impact Factor (2014): 5.963
EigenFactor (2014): 0.06335
Cited Half-life (2014): >10 years


View the Editorial Board  |  Read GENETICS  Submit your manuscript  |  Contact us



 What's Inside the Current Issue of GENETICS


Wednesday, July 6 2016 08:32:43 AM

ISSUE HIGHLIGHTS [Issue Highlights]

Wednesday, July 6 2016 08:32:43 AM

Alfred Sturtevant and George Beadle Untangle Inversions [Classic]

Hawley, R. S., Ganetzky, B.

Wednesday, July 6 2016 08:32:43 AM

Na Li and Matthew Stephens on Modeling Linkage Disequilibrium [Classic]

Song, Y. S.

Wednesday, July 6 2016 08:32:43 AM

Back to the Future: Mutant Hunts Are Still the Way To Go [Commentary]

Winston, F., Koshland, D.

Innumerable breakthroughs in many fundamental areas of biology have come from unbiased screens and selections for mutations, either across the genome or within a gene. However, long-standing hurdles to key elements of mutant hunts (mutagenesis, phenotypic characterization, and linkage of phenotype to genotype) have limited the organisms in which mutant hunts could be used. These hurdles are now being eliminated by an explosion of new technologies. We believe that a renewed emphasis on unbiased mutant hunts, in both existing model systems and in those where genetics is just now becoming feasible, will lead to new seminal discoveries and surprises.

Wednesday, July 6 2016 08:32:43 AM

Weaving a Tapestry from Threads Spun by Geneticists: The Series Perspectives on Genetics, 1987-2008 [Perspectives]

Dove, W. F.

The Perspectives column was initiated in 1987 when Jan Drake, Editor-in-Chief of GENETICS, invited Jim Crow and William Dove to serve as coeditors of "Anecdotal, Historical, and Critical Commentaries." As the series evolved over 21 years, under the guidance of Crow and Dove, the input of stories told by geneticists from many countries created a panorama of 20th-century genetics. Three recurrent themes are visible: how geneticists have created the science (as solitary investigators, in pairs, or in cooperative groups); how geneticists work hard, but find ways to have fun; and how public and private institutions have sustained the science of genetics, particularly in the United States. This article ends by considering how the Perspectives series and other communication formats can carry forward the core science of genetics from the 20th into the 21st century.

Wednesday, July 6 2016 08:32:43 AM

Complex Traits and Simple Systems: An Interview with Leonid Kruglyak [The 2016 GSA Honors and Awards]

Kruglyak, L.

The Genetics Society of America’s Edward Novitski Prize recognizes an extraordinary level of creativity and intellectual ingenuity in the solution of significant problems in genetics research. The 2016 winner, Leonid Kruglyak, has made innovative contributions to the fields of linkage analysis, population genetics, and genomics, while drawing on a combination of mathematical, computational, and experimental approaches. Among other achievements, his work on statistical standards for genome-wide linkage studies has transformed their experimental design, and the linkage analysis program GENEHUNTER has been used to identify hundreds of human disease loci. Kruglyak’s group also pioneered expression quantitative trait locus studies, which enabled variation in global gene expression to shed light on the genetics of complex human diseases. In recent years, his laboratory has focused on using genomic technology to establish Saccharomyces cerevisiae and Caenorhabditis elegans as model organisms for studies of complex genetic variation.

Wednesday, July 6 2016 08:32:43 AM

Chromosome Duplication in Saccharomyces cerevisiae [Genome Organization and Integrity]

Bell, S. P., Labib, K.

The accurate and complete replication of genomic DNA is essential for all life. In eukaryotic cells, the assembly of the multi-enzyme replisomes that perform replication is divided into stages that occur at distinct phases of the cell cycle. Replicative DNA helicases are loaded around origins of DNA replication exclusively during G1 phase. The loaded helicases are then activated during S phase and associate with the replicative DNA polymerases and other accessory proteins. The function of the resulting replisomes is monitored by checkpoint proteins that protect arrested replisomes and inhibit new initiation when replication is inhibited. The replisome also coordinates nucleosome disassembly, assembly, and the establishment of sister chromatid cohesion. Finally, when two replisomes converge they are disassembled. Studies in Saccharomyces cerevisiae have led the way in our understanding of these processes. Here, we review our increasingly molecular understanding of these events and their regulation.

Wednesday, July 6 2016 08:32:43 AM

Learning to Fish with Genetics: A Primer on the Vertebrate Model Danio rerio [Primer]

Holtzman, N. G., Iovine, M. K., Liang, J. O., Morris, J.

In the last 30 years, the zebrafish has become a widely used model organism for research on vertebrate development and disease. Through a powerful combination of genetics and experimental embryology, significant inroads have been made into the regulation of embryonic axis formation, organogenesis, and the development of neural networks. Research with this model has also expanded into other areas, including the genetic regulation of aging, regeneration, and animal behavior. Zebrafish are a popular model because of the ease with which they can be maintained, their small size and low cost, the ability to obtain hundreds of embryos on a daily basis, and the accessibility, translucency, and rapidity of early developmental stages. This primer describes the swift progress of genetic approaches in zebrafish and highlights recent advances that have led to new insights into vertebrate biology.

Wednesday, July 6 2016 08:32:43 AM

Synaptonemal Complex Proteins of Budding Yeast Define Reciprocal Roles in MutS{gamma}-Mediated Crossover Formation [Communications]

Voelkel-Meiman, K., Cheng, S.-Y., Morehouse, S. J., MacQueen, A. J.

During meiosis, crossover recombination creates attachments between homologous chromosomes that are essential for a precise reduction in chromosome ploidy. Many of the events that ultimately process DNA repair intermediates into crossovers during meiosis occur within the context of homologous chromosomes that are tightly aligned via a conserved structure called the synaptonemal complex (SC), but the functional relationship between SC and crossover recombination remains obscure. There exists a widespread correlation across organisms between the presence of SC proteins and successful crossing over, indicating that the SC or its building block components are procrossover factors . For example, budding yeast mutants missing the SC transverse filament component, Zip1, and mutant cells missing the Zip4 protein, which is required for the elaboration of SC, fail to form MutS-mediated crossovers. Here we report the reciprocal phenotype—an increase in MutS-mediated crossovers during meiosis—in budding yeast mutants devoid of the SC central element components Ecm11 or Gmc2, and in mutants expressing a version of Zip1 missing most of its N terminus. This novel phenotypic class of SC-deficient mutants demonstrates unequivocally that the tripartite SC structure is dispensable for MutS-mediated crossover recombination in budding yeast. The excess crossovers observed in SC central element-deficient mutants are Msh4, Zip1, and Zip4 dependent, clearly indicating the existence of two classes of SC proteins—a class with procrossover function(s) that are also necessary for SC assembly and a class that is not required for crossover formation but essential for SC assembly. The latter class directly or indirectly limits MutS-mediated crossovers along meiotic chromosomes. Our findings illustrate how reciprocal roles in crossover recombination can be simultaneously linked to the SC structure.

Wednesday, July 6 2016 08:32:43 AM

Local Joint Testing Improves Power and Identifies Hidden Heritability in Association Studies [Statistical Genetics and Genomics]

Brown, B. C., Price, A. L., Patsopoulos, N. A., Zaitlen, N.

There is mounting evidence that complex human phenotypes are highly polygenic, with many loci harboring multiple causal variants, yet most genetic association studies examine each SNP in isolation. While this has led to the discovery of thousands of disease associations, discovered variants account for only a small fraction of disease heritability. Alternative multi-SNP methods have been proposed, but issues such as multiple-testing correction, sensitivity to genotyping error, and optimization for the underlying genetic architectures remain. Here we describe a local joint-testing procedure, complete with multiple-testing correction, that leverages a genetic phenomenon we call linkage masking wherein linkage disequilibrium between SNPs hides their signal under standard association methods. We show that local joint testing on the original Wellcome Trust Case Control Consortium (WTCCC) data set leads to the discovery of 22 associated loci, 5 more than the marginal approach. These loci were later found in follow-up studies containing thousands of additional individuals. We find that these loci significantly increase the heritability explained by genome-wide significant associations in the WTCCC data set. Furthermore, we show that local joint testing in a cis-expression QTL (eQTL) study of the gEUVADIS data set increases the number of genes containing significant eQTL by 10.7% over marginal analyses. Our multiple-hypothesis correction and joint-testing framework are available in a python software package called Jester, available at

Wednesday, July 6 2016 08:32:43 AM

A Parthenogenesis Gene Candidate and Evidence for Segmental Allopolyploidy in Apomictic Brachiaria decumbens [Genome Integrity and Transmission]

Worthington, M., Heffelfinger, C., Bernal, D., Quintero, C., Zapata, Y. P., Perez, J. G., De Vega, J., Miles, J., Dellaporta, S., Tohme, J.

Apomixis, asexual reproduction through seed, enables breeders to identify and faithfully propagate superior heterozygous genotypes by seed without the disadvantages of vegetative propagation or the expense and complexity of hybrid seed production. The availability of new tools such as genotyping by sequencing and bioinformatics pipelines for species lacking reference genomes now makes the construction of dense maps possible in apomictic species, despite complications including polyploidy, multisomic inheritance, self-incompatibility, and high levels of heterozygosity. In this study, we developed saturated linkage maps for the maternal and paternal genomes of an interspecific Brachiaria ruziziensis (R. Germ. and C. M. Evrard) x B. decumbens Stapf. F1 mapping population in order to identify markers linked to apomixis. High-resolution molecular karyotyping and comparative genomics with Setaria italica (L.) P. Beauv provided conclusive evidence for segmental allopolyploidy in B. decumbens, with strong preferential pairing of homologs across the genome and multisomic segregation relatively more common in chromosome 8. The apospory-specific genomic region (ASGR) was mapped to a region of reduced recombination on B. decumbens chromosome 5. The Pennisetum squamulatum (L.) R.Br. PsASGR-BABY BOOM-like (psASGR–BBML)-specific primer pair p779/p780 was in perfect linkage with the ASGR in the F1 mapping population and diagnostic for reproductive mode in a diversity panel of known sexual and apomict Brachiaria (Trin.) Griseb. and P. maximum Jacq. germplasm accessions and cultivars. These findings indicate that ASGR–BBML gene sequences are highly conserved across the Paniceae and add further support for the postulation of the ASGR–BBML as candidate genes for the apomictic function of parthenogenesis.

Wednesday, July 6 2016 08:32:43 AM

Genes and Small RNA Transcripts Exhibit Dosage-Dependent Expression Pattern in Maize Copy-Number Alterations [Gene Expression]

Zuo, T., Zhang, J., Lithio, A., Dash, S., Weber, D. F., Wise, R., Nettleton, D., Peterson, T.

Copy-number alterations are widespread in animal and plant genomes, but their immediate impact on gene expression is still unclear. In animals, copy-number alterations usually exhibit dosage effects, except for sex chromosomes which tend to be dosage compensated. In plants, genes within small duplications (<100 kb) often exhibit dosage-dependent expression, whereas large duplications (>50 Mb) are more often dosage compensated. However, little or nothing is known about expression in moderately-sized (1–50 Mb) segmental duplications, and about the response of small RNAs to dosage change. Here, we compared maize (Zea mays) plants with two, three, and four doses of a 14.6-Mb segment of chromosome 1 that contains ~300 genes. Plants containing the duplicated segment exhibit dosage-dependent effects on ear length and flowering time. Transcriptome analyses using GeneChip and RNA-sequencing methods indicate that most expressed genes and unique small RNAs within the duplicated segments exhibit dosage-dependent transcript levels. We conclude that dosage effect is the predominant regulatory response for both genes and unique small RNA transcripts in the segmental dosage series we tested. To our knowledge this is the first analysis of small RNA expression in plant gene dosage variants. Because segmental duplications comprise a significant proportion of eukaryotic genomes, these findings provide important new insight into the regulation of genes and small RNAs in response to dosage changes.

Wednesday, July 6 2016 08:32:43 AM

A Novel Strategy for Exploitation of Host RNase E Activity by a Marine Cyanophage [Gene Expression]

Stazic, D., Pekarski, I., Kopf, M., Lindell, D., Steglich, C.

Previous studies have shown that infection of Prochlorococcus MED4 by the cyanophage P-SSP7 leads to increased transcript levels of host endoribonuclease (RNase) E. However, it has remained enigmatic whether this is part of a host defense mechanism to degrade phage messenger RNA (mRNA) or whether this single-strand RNA-specific RNase is utilized by the phage. Here we describe a hitherto unknown means through which this cyanophage increases expression of RNase E during phage infection and concomitantly protects its own RNA from degradation. We identified two functionally different RNase E mRNA variants, one of which is significantly induced during phage infection. This transcript lacks the 5' UTR, is considerably more stable than the other transcript, and is likely responsible for increased RNase E protein levels during infection. Furthermore, selective enrichment and in vivo analysis of double-stranded RNA (dsRNA) during infection revealed that phage antisense RNAs (asRNAs) sequester complementary mRNAs to form dsRNAs, such that the phage protein-coding transcriptome is nearly completely covered by asRNAs. In contrast, the host protein-coding transcriptome is only partially covered by asRNAs. These data suggest that P-SSP7 orchestrates degradation of host RNA by increasing RNase E expression while masking its own transcriptome from RNase E degradation in dsRNA complexes. We propose that this combination of strategies contributes significantly to phage progeny production.

Wednesday, July 6 2016 08:32:43 AM

Phenotypic Consequences of a Spontaneous Loss of Heterozygosity in a Common Laboratory Strain of Candida albicans [Gene Expression]

Ciudad, T., Hickman, M., Bellido, A., Berman, J., Larriba, G.

By testing the susceptibility to DNA damaging agents of several Candida albicans mutant strains derived from the commonly used laboratory strain, CAI4, we uncovered sensitivity to methyl methanesulfonate (MMS) in CAI4 and its derivatives, but not in CAF2-1. This sensitivity is not a result of URA3 disruption because the phenotype was not restored after URA3 reintroduction. Rather, we found that homozygosis of a short region of chromosome 3R (Chr3R), which is naturally heterozygous in the MMS-resistant-related strains CAF4-2 and CAF2-1, confers MMS sensitivity and modulates growth polarization in response to MMS. Furthermore, induction of homozygosity in this region in CAF2-1 or CAF4-2 resulted in MMS sensitivity. We identified 11 genes by SNP/comparative genomic hybridization containing only the a alleles in all the MMS-sensitive strains. Four candidate genes, SNF5, POL1, orf19.5854.1, and MBP1, were analyzed by generating hemizygous configurations in CAF2-1 and CAF4-2 for each allele of all four genes. Only hemizygous MBP1a/mbp1b::SAT1-FLIP strains became MMS sensitive, indicating that MBP1a in the homo- or hemizygosis state was sufficient to account for the MMS-sensitive phenotype. In yeast, Mbp1 regulates G1/S genes involved in DNA repair. A second region of homozygosis on Chr2L increased MMS sensitivity in CAI4 (Chr3R homozygous) but not CAF4-2 (Chr3R heterozygous). This is the first example of sign epistasis in C. albicans.

Wednesday, July 6 2016 08:32:43 AM

Buffering of Genetic Regulatory Networks in Drosophila melanogaster [Gene Expression]

Fear, J. M., Leon-Novelo, L. G., Morse, A. M., Gerken, A. R., Van Lehmann, K., Tower, J., Nuzhdin, S. V., McIntyre, L. M.

Regulatory variation in gene expression can be described by cis- and trans-genetic components. Here we used RNA-seq data from a population panel of Drosophila melanogaster test crosses to compare allelic imbalance (AI) in female head tissue between mated and virgin flies, an environmental change known to affect transcription. Indeed, 3048 exons (1610 genes) are differentially expressed in this study. A Bayesian model for AI, with an intersection test, controls type I error. There are ~200 genes with AI exclusively in mated or virgin flies, indicating an environmental component of expression regulation. On average 34% of genes within a cross and 54% of all genes show evidence for genetic regulation of transcription. Nearly all differentially regulated genes are affected in cis, with an average of 63% of expression variation explained by the cis-effects. Trans-effects explain 8% of the variance in AI on average and the interaction between cis and trans explains an average of 11% of the total variance in AI. In both environments cis- and trans-effects are compensatory in their overall effect, with a negative association between cis- and trans-effects in 85% of the exons examined. We hypothesize that the gene expression level perturbed by cis-regulatory mutations is compensated through trans-regulatory mechanisms, e.g., trans and cis by trans-factors buffering cis-mutations. In addition, when AI is detected in both environments, cis-mated, cis-virgin, and trans-mated–trans-virgin estimates are highly concordant with 99% of all exons positively correlated with a median correlation of 0.83 for cis and 0.95 for trans. We conclude that the gene regulatory networks (GRNs) are robust and that trans-buffering explains robustness.

Wednesday, July 6 2016 08:32:43 AM

The Activity-Dependent Regulation of Protein Kinase Stability by the Localization to P-Bodies [Cellular Genetics]

Zhang, B., Shi, Q., Varia, S. N., Xing, S., Klett, B. M., Cook, L. A., Herman, P. K.

The eukaryotic cytoplasm contains a variety of ribonucleoprotein (RNP) granules in addition to the better-understood membrane-bound organelles. These granules form in response to specific stress conditions and contain a number of signaling molecules important for the control of cell growth and survival. However, relatively little is known about the mechanisms responsible for, and the ultimate consequences of, this protein localization. Here, we show that the Hrr25/CK1 protein kinase is recruited to cytoplasmic processing bodies (P-bodies) in an evolutionarily conserved manner. This recruitment requires Hrr25 kinase activity and the Dcp2 decapping enzyme, a core constituent of these RNP granules. Interestingly, the data indicate that this localization sequesters active Hrr25 away from the remainder of the cytoplasm and thereby shields this enzyme from the degradation machinery during these periods of stress. Altogether, this work illustrates how the presence within an RNP granule can alter the ultimate fate of the localized protein.

Wednesday, July 6 2016 08:32:43 AM

Timely Closure of the Prospore Membrane Requires SPS1 and SPO77 in Saccharomyces cerevisiae [Cellular Genetics]

Paulissen, S. M., Slubowski, C. J., Roesner, J. M., Huang, L. S.

During sporulation in Saccharomyces cerevisiae, a double lipid bilayer called the prospore membrane is formed de novo, growing around each meiotic nucleus and ultimately closing to create four new cells within the mother cell. Here we show that SPS1, which encodes a kinase belonging to the germinal center kinase III family, is involved in prospore membrane development and is required for prospore membrane closure. We find that SPS1 genetically interacts with SPO77 and see that loss of either gene disrupts prospore membrane closure in a similar fashion. Specifically, cells lacking SPS1 and SPO77 produce hyperelongated prospore membranes from which the leading edge protein complex is not removed from the prospore membrane in a timely fashion. The SPS1/SPO77 pathway is required for the proper phosphorylation and stability of Ssp1, a member of the leading edge protein complex that is removed and degraded when the prospore membrane closes. Genetic dissection of prospore membrane closure finds SPS1 and SPO77 act in parallel to a previously described pathway of prospore membrane closure that involves AMA1, an activator of the meiotic anaphase promoting complex.

Wednesday, July 6 2016 08:32:43 AM

Complex Haploinsufficiency-Based Genetic Analysis of the NDR/Lats Kinase Cbk1 Provides Insight into Its Multiple Functions in Candida albicans [Cellular Genetics]

Saputo, S., Norman, K. L., Murante, T., Horton, B. N., Diaz, J. D. L. C., DiDone, L., Colquhoun, J., Schroeder, J. W., Simmons, L. A., Kumar, A., Krysan, D. J.

Although the analysis of genetic interactions and networks is a powerful approach to understanding biology, it has not been applied widely to the pathogenic yeast Candida albicans. Here, we describe the use of both screening and directed genetic interaction studies based on complex haploinsufficiency to probe the function of the Regulation of Ace2 and Morphogenesis (RAM) pathway in C. albicans. A library of 5200 Tn7-mutagenized derivatives of a parental strain heterozygous at CBK1, the key kinase in the RAM pathway, was screened for alterations in serum-induced filamentation. Following confirmation of phenotypes and identification of insertion sites by sequencing, a set of 36 unique double heterozygous strains showing complex haploinsufficiency was obtained. In addition to a large set of genes regulated by the RAM transcription factor Ace2, genes related to cell wall biosynthesis, cell cycle, polarity, oxidative stress, and nitrogen utilization were identified. Follow-up analysis led to the first demonstration that the RAM pathway is required for oxidative stress tolerance in a manner related to the two-component-regulated kinase Chk1 and revealed a potential direct connection between the RAM pathway and the essential Mps1 spindle pole-related kinase. In addition, genetic interactions with CDC42-related genes MSB1, a putative scaffold protein, and RGD3, a putative Rho GTPase-activating protein (GAP) were identified. We also provide evidence that Rgd3 is a GAP for Cdc42 and show that its localization and phosphorylation are dependent on Cbk1.

Wednesday, July 6 2016 08:32:43 AM

Pioneer Axon Navigation Is Controlled by AEX-3, a Guanine Nucleotide Exchange Factor for RAB-3 in Caenorhabditis elegans [Developmental and Behavioral Genetics]

Bhat, J. M., Hutter, H.

Precise and accurate axon tract formation is an essential aspect of brain development. This is achieved by the migration of early outgrowing axons (pioneers) allowing later outgrowing axons (followers) to extend toward their targets in the embryo. In Caenorhabditis elegans the AVG neuron pioneers the right axon tract of the ventral nerve cord, the major longitudinal axon tract. AVG is essential for the guidance of follower axons and hence organization of the ventral nerve cord. In an enhancer screen for AVG axon guidance defects in a nid-1/Nidogen mutant background, we isolated an allele of aex-3. aex-3 mutant animals show highly penetrant AVG axon navigation defects. These defects are dependent on a mutation in nid-1/Nidogen, a basement membrane component. Our data suggest that AEX-3 activates RAB-3 in the context of AVG axon navigation. aex-3 genetically acts together with known players of vesicular exocytosis: unc-64/Syntaxin, unc-31/CAPS, and ida-1/IA-2. Furthermore our genetic interaction data suggest that AEX-3 and the UNC-6/Netrin receptor UNC-5 act in the same pathway, suggesting AEX-3 might regulate the trafficking and/or insertion of UNC-5 at the growth cone to mediate the proper guidance of the AVG axon.

Wednesday, July 6 2016 08:32:43 AM

Long-Term Memory in Drosophila Is Influenced by Histone Deacetylase HDAC4 Interacting with SUMO-Conjugating Enzyme Ubc9 [Developmental and Behavioral Genetics]

Schwartz, S., Truglio, M., Scott, M. J., Fitzsimons, H. L.

HDAC4 is a potent memory repressor with overexpression of wild type or a nuclear-restricted mutant resulting in memory deficits. Interestingly, reduction of HDAC4 also impairs memory via an as yet unknown mechanism. Although histone deacetylase family members are important mediators of epigenetic mechanisms in neurons, HDAC4 is predominantly cytoplasmic in the brain and there is increasing evidence for interactions with nonhistone proteins, suggesting HDAC4 has roles beyond transcriptional regulation. To that end, we performed a genetic interaction screen in Drosophila and identified 26 genes that interacted with HDAC4, including Ubc9, the sole SUMO E2-conjugating enzyme. RNA interference-induced reduction of Ubc9 in the adult brain impaired long-term memory in the courtship suppression assay, a Drosophila model of associative memory. We also demonstrate that HDAC4 and Ubc9 interact genetically during memory formation, opening new avenues for investigating the mechanisms through which HDAC4 regulates memory formation and other neurological processes.

Wednesday, July 6 2016 08:32:43 AM

Roles for the Histone Modifying and Exchange Complex NuA4 in Cell Cycle Progression in Drosophila melanogaster [Developmental and Behavioral Genetics]

Flegel, K., Grushko, O., Bolin, K., Griggs, E., Buttitta, L.

Robust and synchronous repression of E2F-dependent gene expression is critical to the proper timing of cell cycle exit when cells transition to a postmitotic state. Previously NuA4 was suggested to act as a barrier to proliferation in Drosophila by repressing E2F-dependent gene expression. Here we show that NuA4 activity is required for proper cell cycle exit and the repression of cell cycle genes during the transition to a postmitotic state in vivo. However, the delay of cell cycle exit caused by compromising NuA4 is not due to additional proliferation or effects on E2F activity. Instead NuA4 inhibition results in slowed cell cycle progression through late S and G2 phases due to aberrant activation of an intrinsic p53-independent DNA damage response. A reduction in NuA4 function ultimately produces a paradoxical cell cycle gene expression program, where certain cell cycle genes become derepressed in cells that are delayed during the G2 phase of the final cell cycle. Bypassing the G2 delay when NuA4 is inhibited leads to abnormal mitoses and results in severe tissue defects. NuA4 physically and genetically interacts with components of the E2F complex termed Drosophila, Rbf, E2F and Myb/Multi-vulva class B (DREAM/MMB), and modulates a DREAM/MMB-dependent ectopic neuron phenotype in the posterior wing margin. However, this effect is also likely due to the cell cycle delay, as simply reducing Cdk1 is sufficient to generate a similar phenotype. Our work reveals that the major requirement for NuA4 in the cell cycle in vivo is to suppress an endogenous DNA damage response, which is required to coordinate proper S and G2 cell cycle progression with differentiation and cell cycle gene expression.

Wednesday, July 6 2016 08:32:43 AM

Retinal Axon Guidance Requires Integration of Eya and the Jak/Stat Pathway into Phosphotyrosine-Based Signaling Circuitries in Drosophila [Developmental and Behavioral Genetics]

Hoi, C. S. L., Xiong, W., Rebay, I.

The transcriptional coactivator and phosphatase eyes absent (Eya) is dynamically compartmentalized between the nucleus and cytoplasm. Although the nuclear transcriptional circuits within which Eya operates have been extensively characterized, understanding of its cytoplasmic functions and interactions remains limited. Our previous work showed that phosphorylation of Drosophila Eya by the Abelson tyrosine kinase can recruit Eya to the cytoplasm and that eyaabelson interactions are required for photoreceptor axons to project to correct layers in the brain. Based on these observations, we postulated that photoreceptor axon targeting might provide a suitable context for identifying the cytoplasmic signaling cascades with which Eya interacts. Using a dose-sensitive eya misexpression background, we performed an RNA interference-based genetic screen to identify suppressors. Included among the top 10 hits were nonreceptor tyrosine kinases and multiple members of the Jak/Stat signaling network (hop, Stat92E, Socs36E, and Socs44A), a pathway not previously implicated in axon targeting. Individual loss-of-function phenotypes combined with analysis of axonal projections in Stat92E null clones confirmed the importance of photoreceptor autonomous Jak/Stat signaling. Experiments in cultured cells detected cytoplasmic complexes between Eya and Hop, Socs36E and Socs44A; the latter interaction required both the Src homology 2 motif in Socs44A and tyrosine phosphorylated Eya, suggesting direct binding and validating the premise of the screen. Taken together, our data provide new insight into the cytoplasmic phosphotyrosine signaling networks that operate during photoreceptor axon guidance and suggest specific points of interaction with Eya.

Wednesday, July 6 2016 08:32:43 AM

How Life History Can Sway the Fixation Probability of Mutants [Population and Evolutionary Genetics]

Li, X.-Y., Kurokawa, S., Giaimo, S., Traulsen, A.

In this work, we study the effects of demographic structure on evolutionary dynamics when selection acts on reproduction, survival, or both. In contrast to the previously discovered pattern that the fixation probability of a neutral mutant decreases while the population becomes younger, we show that a mutant with a constant selective advantage may have a maximum or a minimum of the fixation probability in populations with an intermediate fraction of young individuals. This highlights the importance of life history and demographic structure in studying evolutionary dynamics. We also illustrate the fundamental differences between selection on reproduction and selection on survival when age structure is present. In addition, we evaluate the relative importance of size and structure of the population in determining the fixation probability of the mutant. Our work lays the foundation for also studying density- and frequency-dependent effects in populations when demographic structures cannot be neglected.

Wednesday, July 6 2016 08:32:43 AM

Resolving the Conflict Between Associative Overdominance and Background Selection [Population and Evolutionary Genetics]

Zhao, L., Charlesworth, B.

In small populations, genetic linkage between a polymorphic neutral locus and loci subject to selection, either against partially recessive mutations or in favor of heterozygotes, may result in an apparent selective advantage to heterozygotes at the neutral locus (associative overdominance) and a retardation of the rate of loss of variability by genetic drift at this locus. In large populations, selection against deleterious mutations has previously been shown to reduce variability at linked neutral loci (background selection). We describe analytical, numerical, and simulation studies that shed light on the conditions under which retardation vs. acceleration of loss of variability occurs at a neutral locus linked to a locus under selection. We consider a finite, randomly mating population initiated from an infinite population in equilibrium at a locus under selection. With mutation and selection, retardation occurs only when S, the product of twice the effective population size and the selection coefficient, is of order 1. With S >> 1, background selection always causes an acceleration of loss of variability. Apparent heterozygote advantage at the neutral locus is, however, always observed when mutations are partially recessive, even if there is an accelerated rate of loss of variability. With heterozygote advantage at the selected locus, loss of variability is nearly always retarded. The results shed light on experiments on the loss of variability at marker loci in laboratory populations and on the results of computer simulations of the effects of multiple selected loci on neutral variability.

Wednesday, July 6 2016 08:32:43 AM

Epistasis and the Dynamics of Reversion in Molecular Evolution [Population and Evolutionary Genetics]

McCandlish, D. M., Shah, P., Plotkin, J. B.

Recent studies of protein evolution contend that the longer an amino acid substitution is present at a site, the less likely it is to revert to the amino acid previously occupying that site. Here we study this phenomenon of decreasing reversion rates rigorously and in a much more general context. We show that, under weak mutation and for arbitrary fitness landscapes, reversion rates decrease with time for any site that is involved in at least one epistatic interaction. Specifically, we prove that, at stationarity, the hazard function of the distribution of waiting times until reversion is strictly decreasing for any such site. Thus, in the presence of epistasis, the longer a particular character has been absent from a site, the less likely the site will revert to its prior state. We also explore several examples of this general result, which share a common pattern whereby the probability of having reverted increases rapidly at short times to some substantial value before becoming almost flat after a few substitutions at other sites. This pattern indicates a characteristic tendency for reversion to occur either almost immediately after the initial substitution or only after a very long time.

Wednesday, July 6 2016 08:32:43 AM

Genomic Conflicts that Cause Pollen Mortality and Raise Reproductive Barriers in Arabidopsis thaliana [Population and Evolutionary Genetics]

Simon, M., Durand, S., Pluta, N., Gobron, N., Botran, L., Ricou, A., Camilleri, C., Budar, F.

Species differentiation and the underlying genetics of reproductive isolation are central topics in evolutionary biology. Hybrid sterility is one kind of reproductive barrier that can lead to differentiation between species. Here, we analyze the complex genetic basis of the intraspecific hybrid male sterility that occurs in the offspring of two distant natural strains of Arabidopsis thaliana, Shahdara and Mr-0, with Shahdara as the female parent. Using both classical and quantitative genetic approaches as well as cytological observation of pollen viability, we demonstrate that this particular hybrid sterility results from two causes of pollen mortality. First, the Shahdara cytoplasm induces gametophytic cytoplasmic male sterility (CMS) controlled by several nuclear loci. Second, several segregation distorters leading to allele-specific pollen abortion (pollen killers) operate in hybrids with either cytoplasm. The complete sterility of the hybrid with the Shahdara cytoplasm results from the genetic linkage of the two causes of pollen mortality, i.e., CMS nuclear determinants and pollen killers. Furthermore, natural variation at these loci in A. thaliana is associated with different male-sterility phenotypes in intraspecific hybrids. Our results suggest that the genomic conflicts that underlie segregation distorters and CMS can concurrently lead to reproductive barriers between distant strains within a species. This study provides a new framework for identifying molecular mechanisms and the evolutionary history of loci that contribute to reproductive isolation, and possibly to speciation. It also suggests that two types of genomic conflicts, CMS and segregation distorters, may coevolve in natural populations.

Wednesday, July 6 2016 08:32:43 AM

Determinants of Genetic Diversity of Spontaneous Drug Resistance in Bacteria [Population and Evolutionary Genetics]

Couce, A., Rodriguez-Rojas, A., Blazquez, J.

Any pathogen population sufficiently large is expected to harbor spontaneous drug-resistant mutants, often responsible for disease relapse after antibiotic therapy. It is seldom appreciated, however, that while larger populations harbor more mutants, the abundance distribution of these mutants is expected to be markedly uneven. This is because a larger population size allows early mutants to expand for longer, exacerbating their predominance in the final mutant subpopulation. Here, we investigate the extent to which this reduction in evenness can constrain the genetic diversity of spontaneous drug resistance in bacteria. Combining theory and experiments, we show that even small variations in growth rate between resistant mutants and the wild type result in orders-of-magnitude differences in genetic diversity. Indeed, only a slight fitness advantage for the mutant is enough to keep diversity low and independent of population size. These results have important clinical implications. Genetic diversity at antibiotic resistance loci can determine a population’s capacity to cope with future challenges (i.e., second-line therapy). We thus revealed an unanticipated way in which the fitness effects of antibiotic resistance can affect the evolvability of pathogens surviving a drug-induced bottleneck. This insight will assist in the fight against multidrug-resistant microbes, as well as contribute to theories aimed at predicting cancer evolution.

Wednesday, July 6 2016 08:32:43 AM

Two-Locus Likelihoods Under Variable Population Size and Fine-Scale Recombination Rate Estimation [Population and Evolutionary Genetics]

Kamm, J. A., Spence, J. P., Chan, J., Song, Y. S.

Two-locus sampling probabilities have played a central role in devising an efficient composite-likelihood method for estimating fine-scale recombination rates. Due to mathematical and computational challenges, these sampling probabilities are typically computed under the unrealistic assumption of a constant population size, and simulation studies have shown that resulting recombination rate estimates can be severely biased in certain cases of historical population size changes. To alleviate this problem, we develop here new methods to compute the sampling probability for variable population size functions that are piecewise constant. Our main theoretical result, implemented in a new software package called LDpop, is a novel formula for the sampling probability that can be evaluated by numerically exponentiating a large but sparse matrix. This formula can handle moderate sample sizes ($$n\le 50$$) and demographic size histories with a large number of epochs ($$\mathcal{D}\ge 64$$). In addition, LDpop implements an approximate formula for the sampling probability that is reasonably accurate and scales to hundreds in sample size ($$n\ge 256$$). Finally, LDpop includes an importance sampler for the posterior distribution of two-locus genealogies, based on a new result for the optimal proposal distribution in the variable-size setting. Using our methods, we study how a sharp population bottleneck followed by rapid growth affects the correlation between partially linked sites. Then, through an extensive simulation study, we show that accounting for population size changes under such a demographic model leads to substantial improvements in fine-scale recombination rate estimation.

Wednesday, July 6 2016 08:32:43 AM

Heterozygote Advantage Is a Common Outcome of Adaptation in Saccharomyces cerevisiae [Population and Evolutionary Genetics]

Sellis, D., Kvitek, D. J., Dunn, B., Sherlock, G., Petrov, D. A.

Adaptation in diploids is predicted to proceed via mutations that are at least partially dominant in fitness. Recently, we argued that many adaptive mutations might also be commonly overdominant in fitness. Natural (directional) selection acting on overdominant mutations should drive them into the population but then, instead of bringing them to fixation, should maintain them as balanced polymorphisms via heterozygote advantage. If true, this would make adaptive evolution in sexual diploids differ drastically from that of haploids. The validity of this prediction has not yet been tested experimentally. Here, we performed four replicate evolutionary experiments with diploid yeast populations (Saccharomyces cerevisiae) growing in glucose-limited continuous cultures. We sequenced 24 evolved clones and identified initial adaptive mutations in all four chemostats. The first adaptive mutations in all four chemostats were three copy number variations, all of which proved to be overdominant in fitness. The fact that fitness overdominant mutations were always the first step in independent adaptive walks supports the prediction that heterozygote advantage can arise as a common outcome of directional selection in diploids and demonstrates that overdominance of de novo adaptive mutations in diploids is not rare.

Wednesday, July 6 2016 08:32:43 AM

Extra Microchromosomes Play Male Determination Role in Polyploid Gibel Carp [Genetics of Sex]

Li, X.-Y., Zhang, Q.-Y., Zhang, J., Zhou, L., Li, Z., Zhang, X.-J., Wang, D., Gui, J.-F.

Sex is generally determined by sex chromosomes in vertebrates, and sex chromosomes exhibit the most rapidly-evolving traits. Sex chromosome evolution has been revealed previously in numerous cases, but the association between sex chromosome origin and the reproduction mode transition from unisexual to sexual reproduction remains unclear. Here, we have isolated a male-specific sequence via analysis of amplified fragment length polymorphism from polyploid gibel carp (Carassius gibelio), a species that not only has the ability to reproduce unisexually but also contains males in wild populations. Subsequently, we have found through FISH analysis that males have several extra microchromosomes with repetitive sequences and transposable elements when compared to females. Moreover, we produced sex-reversed physiological females with a male-specific marker by using estradiol hormone treatment, and two gynogenetic families were established from them. In addition, the male incidence rates of two gynogenetic families were revealed to be closely associated with the extra microchromosome number of the sex-reversed physiological females. These results suggest that the extra microchromosomes in males might resemble a common feature of sex chromosomes and might play a significant role in male determination during the evolutionary trajectory of the reproduction mode transition from unisexual to sexual reproduction in the polyploid fish.

Wednesday, July 6 2016 08:32:43 AM

Increased Proportion of Variance Explained and Prediction Accuracy of Survival of Breast Cancer Patients with Use of Whole-Genome Multiomic Profiles [Genomic Selection]

Vazquez, A. I., Veturi, Y., Behring, M., Shrestha, S., Kirst, M., Resende, M. F. R., de los Campos, G.

Whole-genome multiomic profiles hold valuable information for the analysis and prediction of disease risk and progression. However, integrating high-dimensional multilayer omic data into risk-assessment models is statistically and computationally challenging. We describe a statistical framework, the Bayesian generalized additive model ((BGAM), and present software for integrating multilayer high-dimensional inputs into risk-assessment models. We used BGAM and data from The Cancer Genome Atlas for the analysis and prediction of survival after diagnosis of breast cancer. We developed a sequence of studies to (1) compare predictions based on single omics with those based on clinical covariates commonly used for the assessment of breast cancer patients (COV), (2) evaluate the benefits of combining COV and omics, (3) compare models based on (a) COV and gene expression profiles from oncogenes with (b) COV and whole-genome gene expression (WGGE) profiles, and (4) evaluate the impacts of combining multiple omics and their interactions. We report that (1) WGGE profiles and whole-genome methylation (METH) profiles offer more predictive power than any of the COV commonly used in clinical practice (e.g., subtype and stage), (2) adding WGGE or METH profiles to COV increases prediction accuracy, (3) the predictive power of WGGE profiles is considerably higher than that based on expression from large-effect oncogenes, and (4) the gain in prediction accuracy when combining multiple omics is consistent. Our results show the feasibility of omic integration and highlight the importance of WGGE and METH profiles in breast cancer, achieving gains of up to 7 points area under the curve (AUC) over the COV in some cases.

Wednesday, July 6 2016 08:32:43 AM

Hybrid Sterility in Rice (Oryza sativa L.) Involves the Tetratricopeptide Repeat Domain Containing Protein [Genetics of Complex Traits]

Yu, Y., Zhao, Z., Shi, Y., Tian, H., Liu, L., Bian, X., Xu, Y., Zheng, X., Gan, L., Shen, Y., Wang, C., Yu, X., Wang, C., Zhang, X., Guo, X., Wang, J., Ikehashi, H., Jiang, L., Wan, J.

Intersubspecific hybrid sterility is a common form of reproductive isolation in rice (Oryza sativa L.), which significantly hampers the utilization of heterosis between indica and japonica varieties. Here, we elucidated the mechanism of S7, which specially causes Aus-japonica/indica hybrid female sterility, through cytological and genetic analysis, map-based cloning, and transformation experiments. Abnormal positioning of polar nuclei and smaller embryo sac were observed in F1 compared with male and female parents. Female gametes carrying S7cp and S7i were aborted in S7ai/S7cp and S7ai/S7i, respectively, whereas they were normal in both N22 and Dular possessing a neutral allele, S7n. S7 was fine mapped to a 139-kb region in the centromere region on chromosome 7, where the recombination was remarkably suppressed due to aggregation of retrotransposons. Among 16 putative open reading frames (ORFs) localized in the mapping region, ORF3 encoding a tetratricopeptide repeat domain containing protein was highly expressed in the pistil. Transformation experiments demonstrated that ORF3 is the candidate gene: downregulated expression of ORF3 restored spikelet fertility and eliminated absolutely preferential transmission of S7ai in heterozygote S7ai/S7cp; sterility occurred in the transformants Cpslo17-S7ai. Our results may provide implications for overcoming hybrid embryo sac sterility in intersubspecific hybrid rice and utilization of hybrid heterosis for cultivated rice improvement.

Wednesday, July 6 2016 08:32:43 AM

Development and Genetic Characterization of an Advanced Backcross-Nested Association Mapping (AB-NAM) Population of Wild x Cultivated Barley [Multiparental Populations]

Nice, L. M., Steffenson, B. J., Brown-Guedira, G. L., Akhunov, E. D., Liu, C., Kono, T. J. Y., Morrell, P. L., Blake, T. K., Horsley, R. D., Smith, K. P., Muehlbauer, G. J.

The ability to access alleles from unadapted germplasm collections is a long-standing problem for geneticists and breeders. Here we developed, characterized, and demonstrated the utility of a wild barley advanced backcross-nested association mapping (AB-NAM) population. We developed this population by backcrossing 25 wild barley accessions to the six-rowed malting barley cultivar Rasmusson. The 25 wild barley parents were selected from the 318 accession Wild Barley Diversity Collection (WBDC) to maximize allelic diversity. The resulting 796 BC2F4:6 lines were genotyped with 384 SNP markers, and an additional 4022 SNPs and 263,531 sequence variants were imputed onto the population using 9K iSelect SNP genotypes and exome capture sequence of the parents, respectively. On average, 96% of each wild parent was introgressed into the Rasmusson background, and the population exhibited low population structure. While linkage disequilibrium (LD) decay (r2 = 0.2) was lowest in the WBDC (0.36 cM), the AB-NAM (9.2 cM) exhibited more rapid LD decay than comparable advanced backcross (28.6 cM) and recombinant inbred line (32.3 cM) populations. Three qualitative traits: glossy spike, glossy sheath, and black hull color were mapped with high resolution to loci corresponding to known barley mutants for these traits. Additionally, a total of 10 QTL were identified for grain protein content. The combination of low LD, negligible population structure, and high diversity in an adapted background make the AB-NAM an important tool for high-resolution gene mapping and discovery of novel allelic variation using wild barley germplasm.

Wednesday, July 6 2016 08:32:43 AM

Novel Intronic RNA Structures Contribute to Maintenance of Phenotype in Saccharomyces cerevisiae [Genome and System Biology]

Hooks, K. B., Naseeb, S., Parker, S., Griffiths-Jones, S., Delneri, D.

The Saccharomyces cerevisiae genome has undergone extensive intron loss during its evolutionary history. It has been suggested that the few remaining introns (in only 5% of protein-coding genes) are retained because of their impact on function under stress conditions. Here, we explore the possibility that novel noncoding RNA structures (ncRNAs) are embedded within intronic sequences and are contributing to phenotype and intron retention in yeast. We employed de novo RNA structure prediction tools to screen intronic sequences in S. cerevisiae and 36 other fungi. We identified and validated 19 new intronic RNAs via RNA sequencing (RNA-seq) and RT-PCR. Contrary to the common belief that excised introns are rapidly degraded, we found that, in six cases, the excised introns were maintained intact in the cells. In another two cases we showed that the ncRNAs were further processed from their introns. RNA-seq analysis confirmed that introns in ribosomal protein genes are more highly expressed when they contain predicted RNA structures. We deleted the novel intronic RNA structure within the GLC7 intron and showed that this region, rather than the intron itself, is responsible for the cell’s ability to respond to salt stress. We also showed a direct association between the in cis presence of the intronic RNA and GLC7 expression. Overall, these data support the notion that some introns may have been maintained in the genome because they harbor functional RNA structures.

Wednesday, July 6 2016 08:32:43 AM

Corrigendum [Corrigendum]