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https://www.readbyqxmd.com/read/29330348/weak-epistasis-may-drive-adaptation-in-recombining-bacteria
#1
Brian J Arnold, Michael U Gutmann, Yonatan H Grad, Samuel K Sheppard, Jukka Corander, Marc Lipsitch, William P Hanage
The impact of epistasis on the evolution of multilocus traits depends on recombination. While sexually-reproducing eukaryotes recombine so frequently that epistasis between polymorphisms is not considered to play a large role in short-term adaptation, many bacteria also recombine, some to the degree that their populations are described as 'panmictic' or 'freely recombining'. However, whether this recombination is sufficient to limit the ability of selection to act on epistatic contributions to fitness is unknown...
January 12, 2018: Genetics
https://www.readbyqxmd.com/read/29321173/an-autophagy-independent-role-for-atg41-in-sulfur-metabolism-during-zinc-deficiency
#2
Michael D Bucci, Erin Weisenhorn, Spencer Haws, Zhiyuan Yao, Ginelle Zimmerman, Molly Gannon, Janet Taggart, Traci Lee, Daniel J Klionsky, Jason Russell, Joshua Coon, David J Eide
The Zap1 transcription factor of Saccharomyces cerevisiae is a key regulator in the genomic responses to zinc deficiency. Among the genes regulated by Zap1 during zinc deficiency is the autophagy-related gene ATG41 Here, we report that Atg41 is required for growth in zinc-deficient conditions but not when zinc is abundant or when other metals are limiting. Consistent with a role for Atg41 in macroautophagy, we show that nutritional zinc deficiency induces autophagy and that mutation of ATG41 diminishes that response...
January 10, 2018: Genetics
https://www.readbyqxmd.com/read/29311149/estimating-barriers-to-gene-flow-from-distorted-isolation-by-distance-patterns
#3
Harald Ringbauer, Alexander Kolesnikov, David L Field, Nicholas H Barton
In continuous populations with local migration, nearby pairs of individuals have on average more similar genotypes than geographically well separated pairs. A barrier to gene flow distorts this classical pattern of isolation by distance. Genetic similarity is decreased for sample pairs on different sides of the barrier and increased for pairs on the same side near the barrier. Here, we introduce an inference scheme that utilizes this signal to detect and estimate the strength of a linear barrier to gene flow in two-dimensions...
January 8, 2018: Genetics
https://www.readbyqxmd.com/read/29305387/simple-and-complex-centromeric-satellites-in-drosophila-sibling-species
#4
Paul Talbert, Sivakanthan Kasinathan, Steven Henikoff
Centromeres are the chromosomal sites of assembly for kinetochores, the protein complexes that attach to spindle fibers and mediate separation of chromosomes to daughter cells in mitosis and meiosis. In most multicellular organisms, centromeres comprise a single specific family of tandem repeats, often 100-400 bp in length, found on every chromosome, typically in one location within heterochromatin. Drosophila melanogaster is unusual in that the heterochromatin contains many families of mostly short (5-12 bp) tandem repeats, none of which appear to be present at all centromeres, and none of which are found only at centromeres...
January 5, 2018: Genetics
https://www.readbyqxmd.com/read/29305386/the-chromatin-remodeler-isw1-prevents-cag-repeat-expansions-during-transcription-in-saccharomyces-cerevisiae
#5
Melissa R Koch, Nealia C M House, Casey M Cosetta, Robyn M Jong, Christelle G Salomon, Cailin E Joyce, Elliot A Philips, Xiaofeng A Su, Catherine H Freudenreich
CAG/CTG trinucleotide repeats are unstable sequences that are difficult to replicate, repair, and transcribe due to their structure-forming nature. CAG repeats strongly position nucleosomes, however little is known about the chromatin remodeling needed to prevent repeat instability. In a Saccharomyces cerevisiae model system with CAG repeats carried on a yeast artificial chromosome, we discovered that the chromatin remodeler Isw1 is required to prevent CAG repeat expansions during transcription. CAG repeat expansions in the absence of Isw1 were dependent on both transcription-coupled repair (TCR) and base excision repair (BER)...
January 5, 2018: Genetics
https://www.readbyqxmd.com/read/29301907/selection-enhanced-mutagenesis-of-lac-genes-is-due-to-their-co-amplification-with-dinb-encoding-an-error-prone-dna-polymerase
#6
Itsugo Yamayoshi, Sophie Maisnier-Patin, John R Roth
To test whether growth limitation induces mutations, Cairns and Foster constructed an E. coli strain whose mutant lac allele provides 1-2% of normal ability to use lactose. This strain cannot grow on lactose, but produces about 50 Lac+ revertant colonies per 108 plated cells over 5 days. About 80% of revertants carry a stable lac+ mutation made by the error-prone DinB polymerase, which may be induced during growth limitation. Ten percent of Lac+ revertants are stable but form without DinB. The remaining 10% grow by amplifying their mutant lac allele and are unstably Lac+ Induced DinB mutagenesis has been explained in two ways: 1) Up-regulation of dinB expression in non-growing cells (stress-induced mutagenesis) or 2) Selected local over-replication of the lac and dinB+ genes on lactose medium (selected amplification) in cells that are not dividing...
January 4, 2018: Genetics
https://www.readbyqxmd.com/read/29301906/a-role-for-respiration-in-regulating-meiosis-initiation-in-saccharomyces-cerevisiae
#7
Haichao Zhao, Qian Wang, Chao Liu, Yongliang Shang, Fuping Wen, Fang Wang, Weixiao Liu, Wei Xiao, Wei Li
Meiosis is a specific type of cell division that is essential for sexual reproduction in most eukaryotes. Mitochondria are crucial cellular organelles that play important roles in reproduction, though the detailed mechanism by which the mitochondrial respiratory chain functions during meiosis remains elusive. Here, we show that components of the respiratory chain (Complexes I-V) play essential roles in meiosis initiation during the sporulation of budding yeast, Saccharomyces cerevisiae Any functional defects in the complex I component Ndi1p resulted in the abolishment of sporulation...
January 4, 2018: Genetics
https://www.readbyqxmd.com/read/29301905/maize-dek37-encodes-a-p-type-ppr-protein-that-affects-cis-splicing-of-mitochondrial-nad2-intron-1-and-seed-development
#8
Dawei Dai, Shengchao Luan, Xiuzu Chen, Qun Wang, Yang Feng, Chenguang Zhu, Weiwei Qi, Rentao Song
Mitochondrial group II introns require the participation of numerous nucleus-encoded general and specific factors to achieve efficient splicing in vivo Pentatricopeptide repeat (PPR) proteins have been implicated in assisting group II intron splicing. Here, we identified and characterized a new maize seed mutant, defective kernel 37 (dek37), which has significantly delayed endosperm and embryo development. Dek37 encodes a classic P-type PPR protein that targets mitochondria. The dek37 mutation causes no detectable DEK37 protein in mutant seeds...
January 4, 2018: Genetics
https://www.readbyqxmd.com/read/29301909/an-expanded-role-for-the-rfx-transcription-factor-daf-19-with-dual-functions-in-ciliated-and-non-ciliated-neurons
#9
Elizabeth A De Stasio, Katherine P Mueller, Rosemary J Bauer, Alexander J Hurlburt, Sophie A Bice, Sophie L Scholtz, Prasad Phirke, Debora Sugiaman-Trapman, Loraina A Stinson, Haili B Olson, Savannah L Vogel, Zabdiel Ek-Vazquez, Yagmur Esemen, Jessica Korzynski, Kelsey Wolfe, Bonnie N Arbuckle, He Zhang, Gaelen Lombard-Knapp, Brian P Piasecki, Peter Swoboda
Regulatory Factor X transcription factors (RFX TFs) are best known for activating genes required for ciliogenesis in both vertebrates and invertebrates. In humans, eight RFX TFs have a variety of tissue-specific functions, while in the worm Caenorhabditis elegans, the sole RFX gene, daf-19, encodes a set of nested isoforms. Null alleles of daf-19 confer pleiotropic effects including altered development with a dauer constitutive phenotype, complete absence of cilia and ciliary proteins, and defects in synaptic protein maintenance...
January 3, 2018: Genetics
https://www.readbyqxmd.com/read/29301908/deletion-of-a-long-range-dlx5-enhancer-disrupts-inner-ear-development-in-mice
#10
Kenneth R Johnson, Leona H Gagnon, Cong Tian, Chantal M Longo-Guess, Benjamin E Low, Michael V Wiles, Amy E Kiernan
Distal enhancers are thought to play important roles in the spatiotemporal regulation of gene expression during embryonic development, but few predicted enhancer elements have been shown to affect transcription of their endogenous genes or to alter phenotypes when disrupted. Here, we demonstrate that a 123.6 kb deletion within the mouse Slc25a13 gene is associated with reduced transcription of Dlx5, a gene located 660 kb away. Mice homozygous for the Slc25a13 deletion mutation (named hyperspin, hspn) have malformed inner ears and are deaf with balance defects, whereas previously reported Slc25a13 knockout mice showed no phenotypic abnormalities...
January 3, 2018: Genetics
https://www.readbyqxmd.com/read/29284660/the-modern-resource-genome-wide-binding-profiles-for-hundreds-of-drosophila-and-caenorhabditis-elegans-transcription-factors
#11
Michelle M Kudron, Alec Victorsen, Louis Gevirtzman, LaDeana W Hillier, William W Fisher, Dionne Vafeados, Matt Kirkey, Ann S Hammonds, Jeffery Gersch, Haneen Ammouri, Martha L Wall, Jennifer Moran, David Steffen, Matt Szynkarek, Samantha Seabrook-Sturgis, Nader Jameel, Madhura Kadaba, Jaeda Patton, Robert Terrell, Mitch Corson, Timothy J Durham, Soo Park, Swapna Samanta, Mei Han, Jinrui Xu, Koon-Kiu Yan, Susan E Celniker, Kevin P White, Lijia Ma, Mark Gerstein, Valerie Reinke, Robert Waterston
In order to develop a catalog of regulatory sites in two major model organisms, Drosophilia melanogaster and Caenorhabditis elegans, the modERN consortium has systematically assayed the binding sites of transcription factors (TFs). Combined with data produced by our predecessor, modENCODE, we now have data for 262 TFs identifying 1.23M sites in the fly genome and 217 TFs identifying 0.67M sites in the worm genome. Because sites from different TFs are often overlapping and tightly clustered, they fall into 91,011 and 59,150 regions in the fly and worm, respectively, and these binding sites span as little as 8...
December 28, 2017: Genetics
https://www.readbyqxmd.com/read/29279323/the-hidden-genomic-and-transcriptomic-plasticity-of-giant-marker-chromosomes-in-cancer
#12
Gemma Macchia, Marco Severgnini, Stefania Purgato, Doron Tolomeo, Hilen Casciaro, Ingrid Cifola, Alberto L'Abbate, Anna Loverro, Orazio Palumbo, Massimo Carella, Laurence Bianchini, Giovanni Perini, Gianluca De Bellis, Fredrik Mertens, Mariano Rocchi, Clelia T Storlazzi
Genome amplification in the form of rings or giant rod-shaped marker chromosomes is a common genetic alteration in soft tissue tumours. The mitotic stability of these structures is often rescued by perfectly functioning analphoid neocentromeres, which therefore significantly contribute to cancer progression. Here, we disentangled the genomic architecture of many neocentromeres stabilizing marker chromosomes in well-differentiated liposarcoma and lung sarcomatoid carcinoma samples. In cells carrying heavily rearranged RGMs, these structures were assembled as patchworks of multiple short amplified sequences, disclosing an extremely high level of complexity and definitely ruling out the existence of regions prone to the neocentromere seeding...
December 26, 2017: Genetics
https://www.readbyqxmd.com/read/29263029/fine-scale-recombination-maps-of-fungal-plant-pathogens-reveal-dynamic-recombination-landscapes-and-intragenic-hotspots
#13
Eva H Stukenbrock, Julien Y Dutheil
Meiotic recombination is an important driver of evolution. Variability in the intensity of recombination across chromosomes can affect sequence composition, nucleotide variation and rates of adaptation. In many organisms recombination events are concentrated within short segments termed recombination hotspots. The variation in recombination rate and positions of recombination hotspot can be studied using population genomics data and statistical methods. In this study, we conducted population genomics analyses to address the evolution of recombination in two closely related fungal plant pathogens: the prominent wheat pathogen Zymoseptoria tritici and a sister species infecting wild grasses Zymoseptoria ardabiliae We specifically addressed whether recombination landscapes, including hotspot positions, are conserved in the two recently diverged species and if recombination contributes to rapid evolution of pathogenicity traits...
December 20, 2017: Genetics
https://www.readbyqxmd.com/read/29263028/a-novel-sterol-signaling-pathway%C3%A2-governs-azole-antifungal-drug%C3%A2-resistance-and-hypoxic-gene-repression-in-saccharomyces-cerevisiae
#14
Nina D Serratore, Kortany M Baker, Lauren A Macadlo, Abigail R Gress, Brendan L Powers, Nadia Atallah, Kirsten M Westerhouse, Mark C Hall, Vikki M Weake, Scott D Briggs
During antifungal drug treatment and hypoxia, genetic and epigenetic changes occur to maintain sterol homeostasis and cellular function. In this study, we show that SET domain-containing epigenetic factors govern drug efficacy to the medically relevant azole class of antifungal drugs. Upon this discovery, we determined that Set4 is induced when Saccharomyces cerevisiae are treated with azole drugs or grown under hypoxic conditions, two conditions that deplete cellular ergosterol and increase sterol precursors...
December 20, 2017: Genetics
https://www.readbyqxmd.com/read/29263027/the-y-chromosome-modulates-splicing-and-sex-biased-intron-retention-rates-in%C3%A2-drosophila
#15
Meng Wang, Alan T Branco, Bernardo Lemos
The Drosophila Y chromosome is a 40MB segment of mostly repetitive DNA; it harbors a handful of protein coding genes and a disproportionate amount of satellite repeats, transposable elements, and multicopy DNA arrays. Intron retention (IR) is a type of alternative splicing (AS) event by which one or more introns remain within the mature transcript. IR recently emerged as a deliberate cellular mechanism to modulate gene expression levels and has been implicated in multiple biological processes. However, the extent of sex differences in IR and the contribution of the Y chromosome to the modulation of alternative splicing and intron retention rates has not been addressed...
December 20, 2017: Genetics
https://www.readbyqxmd.com/read/29259000/genes-important-for-schizosaccharomyces-pombe-meiosis-identified-through-a-functional-genomics-screen
#16
Julie Blyth, Vasso Makrantoni, Rachael E Barton, Christos Spanos, Juri Rappsilber, Adele L Marston
Meiosis is a specialized cell division that generates gametes, such as eggs and sperm. Errors in meiosis result in miscarriages and are the leading cause of birth defects, however the molecular origins of these defects remain unknown. Studies in model organisms are beginning to identify the genes and pathways important for meiosis, but the parts list is still poorly defined. Here we present a comprehensive catalog of genes important for meiosis in the fission yeast, Schizosaccharomyces pombe Our genome-wide functional screen surveyed all non-essential genes for roles in chromosome segregation and spore formation...
December 19, 2017: Genetics
https://www.readbyqxmd.com/read/29254995/compensatory-internalization-of-pma1-in-v-atpase-mutants-in-saccharomyces-cerevisiae-requires-calcium-and-glucose-sensitive-phosphatases
#17
Swetha Devi Velivela, Patricia M Kane
Loss of V-ATPase activity in organelles, whether through V-ATPase inhibition or V-ATPase ( vma) mutations, triggers a compensatory downregulation of the essential plasma membrane proton pump, Pma1 in S. cerevisiae We have previously determined that the a-arrestin Rim8 and ubiquitin ligase Rsp5 are essential for Pma1 ubiquination and endocytosis in response to loss of V-ATPase activity. Here, we show that Pma1 endocytosis in V-ATPase mutants does not require Rim101 pathway components upstream and downstream of Rim8, indicating that Rim8 is acting independently in Pma1 internalization...
December 18, 2017: Genetics
https://www.readbyqxmd.com/read/29254994/detection-of-epistasis-for-flowering-time-using-bayesian-multilocus-estimation-in-a-barley-magic-population
#18
Boby Mathew, Jens Léon, Wiebke Sannemann, Mikko J Sillanpää
Gene-by-gene interactions also known as epistasis, regulates many complex traits in different species. With the availability of low-cost genotyping it is now possible to  study epistasis on a genome-wide scale. However, identifying genome-wide epistasis is a high-dimensional multiple regression problem and needs application of dimensionality reduction techniques. Flowering Time (FT) in crops is a complex trait which is known to be influenced by many interacting genes and pathways in various crops. In this study, we successfully apply Sure Independence Screening (SIS) for dimensionality reduction to identify two-way and three-way epistasis for flowering time trait in a Multi-Parent Advanced Generation Inter-Cross (MAGIC) barley population using the Bayesian multilocus model...
December 18, 2017: Genetics
https://www.readbyqxmd.com/read/29247012/loss-of-drosophila-mei-41-atr-alters-meiotic-crossover-patterning
#19
Morgan M Brady, Susan McMahan, Jeff Sekelsky
Meiotic crossovers must be properly patterned to ensure accurate disjunction of homologous chromosomes during meiosis I. Disruption of the spatial distribution of crossovers can lead to nondisjunction, aneuploidy, gamete dysfunction, miscarriage, or birth defects. One of the earliest identified genes involved in proper crossover patterning is Drosophilamei-41, which encodes the ortholog of the checkpoint kinase ATR. Analysis of hypomorphic mutants suggested the existence of crossover patterning defects, but it was not possible to assess this in null mutants because of maternal-effect embryonic lethality...
December 15, 2017: Genetics
https://www.readbyqxmd.com/read/29247011/histone-demethylase-activity-of-utx-is-essential-for-viability-and-regulation-of%C3%A2-hox-gene-expression-in%C3%A2-drosophila
#20
Ömer Copur, Jürg Müller
The trimethylation of histone H3 at lysine 27 (H3K27me3) by Polycomb Repressive Complex 2 (PRC2) is essential for repression of Polycomb target genes. The role of enzymatic demethylation of H3K27me3 by the KDM6-family demethylases Utx, Uty and JmjD3 is however less clear. Studies in both mice and worms led to the proposal that KDM6 proteins but not their H3K27me3 demethylase activity is critical for normal development. Here, we investigated the requirement of the demethylase activity of the single KDM6 family member Utx in Drosophila We generated Drosophila expressing full-length but catalytic inactive Utx protein and found that these mutants show the same phenotypes like animals lacking Utx protein...
December 15, 2017: Genetics
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