Genetics

doi: 10.1093/genetics/195.1.nppmid: N/A

Correlation between mutation rate and genome size in riboviruses: mutation rate of bacteriophage Qβ, pp. 243–251 Katie Bradwell, Marine Combe, Pilar Domingo-Calap, and Rafael Sanjuán Mutation rates have been shown to depend on genome size in many viruses and eukaryotes. RNA viruses mutate quickly, but their mutation rates vary considerably. These investigators found that mutation rates of RNA viruses correlate negatively with genome size. This explains why RNA viruses with small genomes tend to have faster rates of molecular evolution, and has implications for antiviral therapy. A DNA damage checkpoint pathway coordinates the division of dikaryotic cells in the ink cap mushroom Coprinopsis cinerea, pp. 47–57 Carmen de Sena-Tomás, Mónica Navarro-González, Ursula Kües, and José Pérez-Martín Having two non-identical nuclei share the same cytoplasm presents a challenge to the dikaryotic cell: both nuclei must enter mitosis at the same time to ensure each daughter cell inherits both genomes. These authors identified the DNA damage checkpoint as a major contributor to maintenance of the dikaryotic state in the ink cap mushroom Coprinopsis cinerea. Robust identification of local adaptation from allele frequencies, pp. 205–220 Torsten Günther and Graham Coop This article describes a powerful tool to robustly identify loci involved in local adaptation. By comparing multiple populations from different environments, loci important for adaptation to local environments can be identified. But such comparisons should acknowledge the shared history of populations and uncertainties involved in allele frequency estimates due to sampling. The new tool accounts for these potential sources of spurious results, and its utility is shown through simulations and the analysis of empirical data from humans and Atlantic herring. Cloning and characterization of a critical regulator for pre-harvest sprouting in wheat, pp. 263–273 Shubing Liu, Sunish K. Sehgal, Jiarui Li, Meng Lin, Harold N. Trick, Jianming Yu, Bikram S. Gill, and Guihua Bai Consumers prefer white wheat, but it is prone to pre-harvest sprouting (PHS), which causes crop losses of $1 billion annually. Cultivars resistant to PHS exist, but the mechanism of resistance is unknown. This article reveals that a MOTHER OF FLOWERING TIME-like gene plays a role in PHS resistance. Two mutations in the coding region of the gene lead to mis-splicing and a truncated protein. A DNA marker in the gene will facilitate deployment of these mutations to protect grain yield and quality and extend the range of white wheat production. The FACT histone chaperone guides histone H4 into its nucleosomal conformation in Saccharomyces cerevisiae, pp. 101–113 Laura McCullough, Bryan Poe, Zaily Connell, Hua Xin, and Tim Formosa FACT is a histone chaperone that can destabilize nucleosomes and can also tether nucleosome components together to promote their efficient reassembly. This article describes a FACT mutation that can cause FACT:nucleosome complexes to become permanently stuck together. Histone mutations that prevent these dead ends from forming reveal hinges that allow the histones to adopt their nucleosomal conformations. Thus, FACT has the previously unknown function of guiding histones into the shapes they need for nucleosome assembly. Learning natural selection from the site frequency spectrum, pp. 181–193 Roy Ronen, Nitin Udpa, Eran Halperin, and Vineet Bafna This article presents a novel method for identifying signatures of selective sweeps. Using supervised learning, the authors trained models of the Site Frequency Spectrum that best separate genomic regions evolving neutrally from those affected by a wide range of selective sweeps. The resulting test can be used without knowledge of the sweep parameters, and can easily be applied to WGS data from large populations. The RNA-binding protein Whi3 is a key regulator of developmental signaling and ploidy in Saccharomyces cerevisiae, pp. 73–86 Sarah Schladebeck and Hans-Ulrich Mösch RNA-binding proteins are well known to govern cell growth and development, but the number and nature of their targets are mostly unknown. These authors show that budding yeast Whi3 protein, which carries an RNA-binding motif, is a post-transcriptional regulator of several key components of signaling pathways that control cell division and biofilm development. They also found that Whi3 regulates ploidy by controlling expression of genes involved in chromosome segregation. Maintenance of interphase chromosome compaction and homolog pairing in Drosophila is regulated by the condensin Cap-H2 and its partner Mrg15, pp. 127–146 Helen F. Smith, Meredith A. Roberts, Huy Q. Nguyen, Maureen Peterson, Tom A. Hartl, Xiao-Jun Wang, Joseph E. Klebba, Gregory C. Rogers, and Giovanni Bosco Condensins are structural components of chromosomes that modulate compaction and pairing of homologs. How do condensins find their way onto chromosomes? Smith and Bosco and colleagues identified the Mrg15 chromodomain protein as an adaptor for the Cap-H2 subunit of condensin. They demonstrate that Mrg15 cooperates with condensins to antagonize somatic homolog pairing and maintain proper interphase compaction levels. This new condensin adaptor points to histone modifications as possible chromatin landing pads for condensin on interphase chromosomes. This Month’s Perspectives Wilhelm Weinberg’s early contribution to segregation analysis Alan Stark and Eugene Seneta Most geneticists will recognize the name Weinberg if it is paired with Hardy, but few geneticists know Weinberg’s solo contributions to the field. This Perspectives article describes Weinberg’s signal contribution—the demonstration that Mendel’s laws apply to human heredity—and the controversy it stimulated. This Month in the American Journal of Human Genetics Whole genome sequencing uncovers the genetic basis of chronic mountain sickness in Andean highlanders, Am. J. Hum. Genet. 93(3) Dan Zhou, Nitin Udpa, Roy Ronen, Tsering Stobdan, Junbin Liang, Otto Appenzeller, Huiwen W. Zhao, Yi Yin, Yuanping Du, Lixia Guo, Rui Cao, Yu Wang, Xin Jin, Chen Huang, Wenlong Jia, Dandan Cao, Guangwu Guo, Jorge L. Gamboa, Francisco Villafuerte , David Callacondo, Jin Xue, Siqi Liu, Kelly A. Frazer, Yingrui Li, Vineet Bafna, and Gabriel G. Haddad Most high-altitude dwelling populations are well-adapted to hypoxic conditions, but some individuals suffer from chronic mountain sickness (CMS). Zhou et al. utilized whole-genome sequencing to identify the genetic basis of CMS in Andean highlanders. They found that the tumor suppressor ANP32D and the SUMO deconjugator SENP1 are involved in the cellular response to hypoxia. These findings could provide key insights into other pathological conditions, such as ischemia and cancer, in which hypoxia plays a contributing role. © Genetics 2013 This article is published and distributed under the terms of the Oxford University Press, Standard Journals Publication Model (https://academic.oup.com/journals/pages/open_access/funder_policies/chorus/standard_publication_model)

Stark, Alan; Seneta, Eugene

doi: 10.1534/genetics.113.152975pmid: 24018765

Wilhelm Weinberg (1862–1937) is a largely forgotten pioneer of human and medical genetics. His name is linked with that of the English mathematician G. H. Hardy in the Hardy–Weinberg law, pervasive in textbooks on population genetics since it expresses stability over generations of zygote frequencies AA, Aa, aa under random mating. One of Weinberg’s signal contributions, in an article whose centenary we celebrate, was to verify that Mendel’s segregation law still held in the setting of human heredity, contrary to the then-prevailing view of William Bateson (1861–1926), the leading Mendelian geneticist of the time. Specifically, Weinberg verified that the proportion of recessive offspring genotypes aa in human parental crossings Aa × Aa (that is, the segregation ratio for such a setting) was indeed p=14. We focus in a nontechnical way on his procedure, called the simple sib method, and on the heated controversy with Felix Bernstein (1878–1956) in the 1920s and 1930s over work stimulated by Weinberg’s article.

Kulathinal, Rob J

doi: 10.1534/genetics.113.156497pmid: 24018766

In this commentary, Rob Kulathinal describes two articles from the Perrimon lab, each describing a new online resource that can assist geneticists with the design of their RNA interference (RNAi) experiments. Hu et al.’s “UP-TORR: online tool for accurate and up-to-date annotation of RNAi reagents” and “FlyPrimerBank: An online database for Drosophila melanogaster gene expression analysis and knockdown evaluation of RNAi reagents” are published, respectively, in this month’s issues of GENETICS and G3.

Hughes, Timothy R; de Boer, Carl G

doi: 10.1534/genetics.113.153262pmid: 24018767

The term “transcriptional network” refers to the mechanism(s) that underlies coordinated expression of genes, typically involving transcription factors (TFs) binding to the promoters of multiple genes, and individual genes controlled by multiple TFs. A multitude of studies in the last two decades have aimed to map and characterize transcriptional networks in the yeast Saccharomyces cerevisiae. We review the methodologies and accomplishments of these studies, as well as challenges we now face. For most yeast TFs, data have been collected on their sequence preferences, in vivo promoter occupancy, and gene expression profiles in deletion mutants. These systematic studies have led to the identification of new regulators of numerous cellular functions and shed light on the overall organization of yeast gene regulation. However, many yeast TFs appear to be inactive under standard laboratory growth conditions, and many of the available data were collected using techniques that have since been improved. Perhaps as a consequence, comprehensive and accurate mapping among TF sequence preferences, promoter binding, and gene expression remains an open challenge. We propose that the time is ripe for renewed systematic efforts toward a complete mapping of yeast transcriptional regulatory mechanisms.

Hu, Yanhui; Roesel, Charles; Flockhart, Ian; Perkins, Lizabeth; Perrimon, Norbert; Mohr, Stephanie E

doi: 10.1534/genetics.113.151340pmid: 23792952

RNA interference (RNAi) is a widely adopted tool for loss-of-function studies but RNAi results only have biological relevance if the reagents are appropriately mapped to genes. Several groups have designed and generated RNAi reagent libraries for studies in cells or in vivo for Drosophila and other species. At first glance, matching RNAi reagents to genes appears to be a simple problem, as each reagent is typically designed to target a single gene. In practice, however, the reagent–gene relationship is complex. Although the sequences of oligonucleotides used to generate most types of RNAi reagents are static, the reference genome and gene annotations are regularly updated. Thus, at the time a researcher chooses an RNAi reagent or analyzes RNAi data, the most current interpretation of the RNAi reagent–gene relationship, as well as related information regarding specificity (e.g., predicted off-target effects), can be different from the original interpretation. Here, we describe a set of strategies and an accompanying online tool, UP-TORR (for Updated Targets of RNAi Reagents; www.flyrnai.org/up-torr), useful for accurate and up-to-date annotation of cell-based and in vivo RNAi reagents. Importantly, UP-TORR automatically synchronizes with gene annotations daily, retrieving the most current information available, and for Drosophila, also synchronizes with the major reagent collections. Thus, UP-TORR allows users to choose the most appropriate RNAi reagents at the onset of a study, as well as to perform the most appropriate analyses of results of RNAi-based studies.

de Sena-Tomás, Carmen; Navarro-González, Mónica; Kües, Ursula; Pérez-Martín, José

doi: 10.1534/genetics.113.152231pmid: 23792951

The fungal fruiting body or mushroom is a multicellular structure essential for sexual reproduction. It is composed of dikaryotic cells that contain one haploid nucleus from each mating partner sharing the same cytoplasm without undergoing nuclear fusion. In the mushroom, the pileus bears the hymenium, a layer of cells that includes the specialized basidia in which nuclear fusion, meiosis, and sporulation occur. Coprinopsis cinerea is a well-known model fungus used to study developmental processes associated with the formation of the fruiting body. Here we describe that knocking down the expression of Atr1 and Chk1, two kinases shown to be involved in the response to DNA damage in a number of eukaryotic organisms, dramatically impairs the ability to develop fruiting bodies in C. cinerea, as well as other developmental decisions such as sclerotia formation. These developmental defects correlated with the impairment in silenced strains to sustain an appropriated dikaryotic cell cycle. Dikaryotic cells in which chk1 or atr1 genes were silenced displayed a higher level of asynchronous mitosis and as a consequence aberrant cells carrying an unbalanced dose of nuclei. Since fruiting body initiation is dependent on the balanced mating-type regulator doses present in the dikaryon, we believe that the observed developmental defects were a consequence of the impaired cell cycle in the dikaryon. Our results suggest a connection between the DNA damage response cascade, cell cycle regulation, and developmental processes in this fungus.

Kern, Jeannine V; Zhang, Yao V; Kramer, Stella; Brenman, Jay E; Rasse, Tobias M

doi: 10.1534/genetics.113.151639pmid: 23770702

Kinesin-based transport is important for synaptogenesis, neuroplasticity, and maintaining synaptic function. In an anatomical screen of neurodevelopmental mutants, we identified the exchange of a conserved residue (R561H) in the forkhead-associated domain of the kinesin-3 family member Unc-104/KIF1A as the genetic cause for defects in synaptic terminal- and dendrite morphogenesis. Previous structure-based analysis suggested that the corresponding residue in KIF1A might be involved in stabilizing the activated state of kinesin-3 dimers. Herein we provide the first in vivo evidence for the functional importance of R561. The R561H allele (unc-104bris) is not embryonic lethal, which allowed us to investigate consequences of disturbed Unc-104 function on postembryonic synapse development and larval behavior. We demonstrate that Unc-104 regulates the reliable apposition of active zones and postsynaptic densities, possibly by controlling site-specific delivery of its cargo. Next, we identified a role for Unc-104 in restraining neuromuscular junction growth and coordinating dendrite branch morphogenesis, suggesting that Unc-104 is also involved in dendritic transport. Mutations in KIF1A/unc-104 have been associated with hereditary spastic paraplegia and hereditary sensory and autonomic neuropathy type 2. However, we did not observe synapse retraction or dystonic posterior paralysis. Overall, our study demonstrates the specificity of defects caused by selective impairments of distinct molecular motors and highlights the critical importance of Unc-104 for the maturation of neuronal structures during embryonic development, larval synaptic terminal outgrowth, and dendrite morphogenesis.

Schladebeck, Sarah; Mösch, Hans-Ulrich

doi: 10.1534/genetics.113.153775pmid: 23770701

In Saccharomyces cerevisiae, the RNA-binding protein Whi3 controls cell cycle progression, biofilm formation, and stress response by post-transcriptional regulation of the Cdc28-Cln3 cyclin-dependent protein kinase and the dual-specificity protein kinase Yak1. Previous work has indicated that Whi3 might govern these processes by additional, yet unknown mechanisms. In this study, we have identified additional effectors of Whi3 that include the G1 cyclins Cln1/Cln2 and two known regulators of biofilm formation, the catalytic PKA subunit Tpk1 and the transcriptional activator Tec1. We also provide evidence that Whi3 regulates production of these factors by post-transcriptional control and might exert this function by affecting translational elongation. Unexpectedly, we also discovered that Whi3 is a key regulator of cellular ploidy, because haploid whi3Δ mutant strains exhibit a significant increase-in-ploidy phenotype that depends on environmental conditions. Our data further suggest that Whi3 might control stability of ploidy by affecting the expression of many key genes involved in sister chromatid cohesion and of NIP100 that encodes a component of the yeast dynactin complex for chromosome distribution. Finally, we show that absence of Whi3 induces a transcriptional stress response in haploid cells that is relieved by whole-genome duplication. In summary, our study suggests that the RNA-binding protein Whi3 acts as a central regulator of cell division and development by post-transcriptional control of key genes involved in chromosome distribution and cell signaling.

Wasserstrom, Lisa; Lengeler, Klaus B; Walther, Andrea; Wendland, Jürgen

doi: 10.1534/genetics.113.151019pmid: 23833180

Regulation of development and entry into sporulation is critical for fungi to ensure survival of unfavorable environmental conditions. Here we present an analysis of gene sets regulating sporulation in the homothallic ascomycete Ashbya gossypii. Deletion of components of the conserved pheromone/starvation MAP kinase cascades, e.g., STE11 and STE7, results in increased sporulation. In kar3 mutants sporulation is severely reduced, while deletion of KAR4 as well as of homologs of central Saccharomyces cerevisiae regulators of sporulation, IME1, IME2, IME4, and NDT80, abolishes sporulation in A. gossypii. Comparison of RNAseq transcript profiles of sporulation-deficient mutants identified a set of 67 down-regulated genes, most of which were up-regulated in the oversporulating ste12 mutant. One of these differentially expressed genes is an endoglucanase encoded by ENG2. We found that Eng2p promotes hyphal fragmentation as part of the developmental program of sporulation, which generates single-celled sporangia. Sporulation-deficient strains are arrested in their development but form sporangia. Supply of new nutrients enabled sporangia to return to hyphal growth, indicating that these cells are not locked in meiosis. Double-strand break (DSB) formation by Spo11 is apparently not required for sporulation; however, the absence of DMC1, which repairs DSBs in S. cerevisiae, results in very poor sporulation in A. gossypii. We present a comprehensive analysis of the gene repertoire governing sporulation in A. gossypii and suggest an altered regulation of IME1 expression compared to S. cerevisiae.

McCullough, Laura; Poe, Bryan; Connell, Zaily; Xin, Hua; Formosa, Tim

doi: 10.1534/genetics.113.153080pmid: 23833181

The pob3-Q308K mutation alters the small subunit of the Saccharomyces cerevisiae histone/nucleosome chaperone Facilitates Chromatin Transactions (FACT), causing defects in both transcription and DNA replication. We describe histone mutations that suppress some of these defects, providing new insight into the mechanism of FACT activity in vivo. FACT is primarily known for its ability to promote reorganization of nucleosomes into a more open form, but neither the pob3-Q308K mutation nor the compensating histone mutations affect this activity. Instead, purified mutant FACT complexes fail to release from nucleosomes efficiently, and the histone mutations correct this flaw. We confirm that pob3-T252E also suppresses pob3-Q308K and show that combining two suppressor mutations can be detrimental, further demonstrating the importance of balance between association and dissociation for efficient FACT:nucleosome interactions. To explain our results, we propose that histone H4 can adopt multiple conformations, most of which are incompatible with nucleosome assembly. FACT guides H4 to adopt appropriate conformations, and this activity can be enhanced or diminished by mutations in Pob3 or histones. FACT can therefore destabilize nucleosomes by favoring the reorganized state, but it can also promote assembly by tethering histones and DNA together and maintaining them in conformations that promote canonical nucleosome formation.