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Current Genetics

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https://www.readbyqxmd.com/read/30390097/epigenetic-fates-of-gene-silencing-established-by-heterochromatin-spreading-in-cell-identity-and-genome-stability
#1
REVIEW
R A Greenstein, Bassem Al-Sady
Heterochromatin spreading, the propagation of repressive chromatin along the chromosome, is a reaction critical to genome stability and defense, as well as maintenance of unique cell fates. Here, we discuss the intrinsic properties of the spreading reaction and circumstances under which its products, formed distal to DNA-encoded nucleation sites, can be epigenetically maintained. Finally, we speculate that the epigenetic properties of heterochromatin evolved together with the need to stabilize cellular identity...
November 2, 2018: Current Genetics
https://www.readbyqxmd.com/read/30382337/mating-type-switching-by-homology-directed-recombinational-repair-a-matter-of-choice
#2
REVIEW
Geneviève Thon, Takahisa Maki, James E Haber, Hiroshi Iwasaki
In eukaryotes, all DNA transactions happen in the context of chromatin that often takes part in regulatory mechanisms. In particular, chromatin structure can regulate exchanges of DNA occurring through homologous recombination. Few systems have provided as detailed a view on this phenomenon as mating-type switching in yeast. Mating-type switching entails the choice of a template for the gene conversions of the expressed mating-type locus. In the fission yeast Schizosaccharomyces pombe, correct template choice requires two competing small recombination enhancers, SRE2 and SRE3, that function in the context of heterochromatin...
October 31, 2018: Current Genetics
https://www.readbyqxmd.com/read/30377756/stressing-out-or-stressing-in-intracellular-pathways-for-sapk-activation
#3
REVIEW
Jongmin Lee, Li Liu, David E Levin
Stress-activated MAP kinases (SAPKs) respond to a wide variety of stressors. In most cases, the pathways through which specific stress signals are transmitted to the SAPKs are not known. Our recent findings have begun to address two important and related questions. First, do various stresses activate a SAPK through common pathways initiated at the cell surface, or through alternative, intracellular inputs? Second, how does an activated SAPK mount a specific response appropriate to the particular stress experienced? Our work has uncovered the mechanisms by which two stresses, arsenite treatment and DNA damage, stimulate the yeast SAPKs Hog1 and Mpk1, respectively...
October 30, 2018: Current Genetics
https://www.readbyqxmd.com/read/30367189/circadian-rhythms-metabolic-oscillators-and-the-target-of-rapamycin-tor-pathway-the-neurospora-connection
#4
REVIEW
Patricia Lakin-Thomas
Circadian (24-h) rhythmicity is a fundamental property of eukaryotic cells, and it is not surprising that it intersects with fundamental metabolic processes. Many links between these two processes have been documented, and speculation has been growing that there may be circadian "metabolic oscillators" that interact with and exist independently of the well-known circadian transcription/translation feedback loops (TTFLs) that have been extensively studied. This review takes a critical look at the evidence for the existence of metabolic oscillators at the cellular level, attempting to answer these questions: does metabolism affect circadian rhythmicity, and vice versa? Is metabolism rhythmic, and if so, is that rhythmicity cell autonomous? Systems displaying "non-canonical rhythmicity" in the absence of functional TTFLs provide opportunities for identifying metabolic oscillators, and this review emphasizes the fungus Neurospora crassa as a model system...
October 26, 2018: Current Genetics
https://www.readbyqxmd.com/read/30361853/condensin-action-and-compaction
#5
REVIEW
Matthew Robert Paul, Andreas Hochwagen, Sevinç Ercan
Condensin is a multi-subunit protein complex that belongs to the family of structural maintenance of chromosomes (SMC) complexes. Condensins regulate chromosome structure in a wide range of processes including chromosome segregation, gene regulation, DNA repair and recombination. Recent research defined the structural features and molecular activities of condensins, but it is unclear how these activities are connected to the multitude of phenotypes and functions attributed to condensins. In this review, we briefly discuss the different molecular mechanisms by which condensins may regulate global chromosome compaction, organization of topologically associated domains, clustering of specific loci such as tRNA genes, rDNA segregation, and gene regulation...
October 25, 2018: Current Genetics
https://www.readbyqxmd.com/read/30353359/ordering-up-gene-expression-by-slowing-down-transcription-factor-binding-kinetics
#6
REVIEW
Matthew J Culyba
Efficient regulation of a complex genetic response requires that the gene products, which catalyze the response, be synthesized in a temporally ordered manner to match the sequential nature of the reaction pathway they act upon. Transcription regulation networks coordinate this aspect of cellular control by modulating transcription factor (TF) concentrations through time. The effect a TF has on the timing of gene expression is often modeled assuming that the TF-promoter binding reaction is in thermodynamic equilibrium with changes in TF concentration over time; however, non-equilibrium dynamics resulting from relatively slow TF-binding kinetics can result in different network behavior...
October 23, 2018: Current Genetics
https://www.readbyqxmd.com/read/30349994/genetic-mechanisms-of-arsenic-detoxification-and-metabolism-in-bacteria
#7
REVIEW
Ge Yan, Xingxiang Chen, Shiming Du, Zixin Deng, Lianrong Wang, Shi Chen
Arsenic, distributed pervasively in the natural environment, is an extremely toxic substance which can severely impair the normal functions of living cells. Research on the genetic mechanisms of arsenic metabolism is of great importance for remediating arsenic-contaminated environments. Many organisms, including bacteria, have developed various strategies to tolerate arsenic, by either detoxifying this harmful element or utilizing it for energy generation. This review summarizes arsenic detoxification as well as arsenic respiratory metabolic pathways in bacteria and discusses novel arsenic resistance pathways in various bacterial strains...
October 22, 2018: Current Genetics
https://www.readbyqxmd.com/read/30328489/the-etiology-of-uracil-residues-in-the-saccharomyces-cerevisiae-genomic-dna
#8
REVIEW
Norah Owiti, Kasey Stokdyk, Nayun Kim
Non-canonical residue in DNA is a major and conserved source of genome instability. The appearance of uracil residues in DNA accompanies a significant mutagenic consequence and is regulated at multiple levels, from the concentration of available dUTP in the nucleotide pool to the excision repair for removal from DNA. Recently, an interesting phenomenon of transcription-associated elevation in uracil-derived mutations was described in Saccharomyces cerevisiae genome. While trying to understand the variability in mutagenesis, we uncovered that the frequency of uracil incorporation into DNA can vary depending on the transcription rate and that the non-replicative, repair-associated DNA synthesis underlies the higher uracil density of the actively transcribed genomic loci...
October 17, 2018: Current Genetics
https://www.readbyqxmd.com/read/30327879/correction-to-gene-overexpression-screen-for-chromosome-instability-in-yeast-primarily-identifies-cell-cycle-progression-genes
#9
Hanna Tutaj, Elzbieta Pogoda, Katarzyna Tomala, Ryszard Korona
In the original publication, 'Frumkin JP et al.' reference was missed to include in the reference list. The complete reference should read as below.
October 16, 2018: Current Genetics
https://www.readbyqxmd.com/read/30324432/yeast-two-hybrid-screening-reveals-a-dual-function-for-the-histone-acetyltransferase-gcne-by-controlling-glutamine-synthesis-and-development-in-aspergillus-fumigatus
#10
Marcel Nossmann, Jana M Boysen, Thomas Krüger, Claudia C König, Falk Hillmann, Thomas Munder, Axel A Brakhage
The acetyltransferase GcnE is part of the SAGA complex which regulates fungal gene expression through acetylation of chromatin. Target genes of the histone acetyltransferase GcnE include those involved in secondary metabolism and asexual development. Here, we show that the absence of GcnE not only abrogated conidiation, but also strongly impeded vegetative growth of hyphae in the human pathogenic fungus Aspergillus fumigatus. A yeast two-hybrid screen using a Saccharomyces cerevisiae strain whose tRNA molecules were specifically adapted to express A...
October 15, 2018: Current Genetics
https://www.readbyqxmd.com/read/30317392/the-nonsense-mediated-mrna-decay-nmd-pathway-differentially-regulates-cox17-cox19-and-cox23-mrnas
#11
Kaitlin Murtha, Munok Hwang, Megan C Peccarelli, Taylor D Scott, Bessie W Kebaara
The differential regulation of COX17, COX19 and COX23 mRNAs by the nonsense-mediated mRNA decay (NMD) pathway was investigated. The NMD pathway regulates mRNAs that aberrantly terminate translation. This includes mRNAs harboring premature translation termination codons and natural mRNAs. Most natural mRNAs regulated by NMD encode fully functional proteins involved in various cellular processes. However, the cause and targeting of most of these mRNAs by the pathway is not understood. Analysis of a set of mRNAs involved in copper homeostasis showed that a subset of these mRNAs function in mitochondrial copper homeostasis...
October 13, 2018: Current Genetics
https://www.readbyqxmd.com/read/30310994/proteomic-profiling-of-yeast-heterochromatin-connects-direct-physical-and-genetic-interactions
#12
Alexis Zukowski, Juliana Phillips, Soyeon Park, Ronghu Wu, Steven P Gygi, Aaron M Johnson
Heterochromatin domains are stably repressed chromatin structures composed of a core assembly of silencing proteins that condense adjacent nucleosomes. The minimal heterochromatin structure can serve as a platform for recruitment of complementary regulatory factors. We find that a reconstituted budding yeast heterochromatin domain can act as a platform to recruit multiple factors that play a role in regulating heterochromatin function. We uncover the direct interaction between the SIR heterochromatin complex and a chromosomal boundary protein that restricts the spread of heterochromatin...
October 12, 2018: Current Genetics
https://www.readbyqxmd.com/read/30310993/aggregation-and-degradation-scales-for-prion-like-domains-sequence-features-and-context-weigh-in
#13
REVIEW
Sean M Cascarina, Eric D Ross
Protein aggregation in vivo is generally combated by extensive proteostatic defenses. Many proteostasis factors specifically recognize aggregation-prone features and re-fold or degrade the targeted protein. However, protein aggregation is not uncommon, suggesting that some proteins employ evasive strategies to aggregate in spite of the proteostasis machinery. Therefore, in addition to understanding the inherent aggregation propensity of protein sequences, it is important to understand how these sequences affect proteostatic recognition and regulation in vivo...
October 11, 2018: Current Genetics
https://www.readbyqxmd.com/read/30259081/correction-to-pleiotropic-roles-of-o-mannosyltransferase-mopmt4-in-development-and-pathogenicity-of-magnaporthe-oryzae
#14
Yuemin Pan, Rui Pan, Leyong Tan, Zhengguang Zhang, Min Guo
In the original publication, Fig. 1 panel (b), the photo of MoPmt2-6 was incorrect. The correct Fig. 1 is shown below.
September 26, 2018: Current Genetics
https://www.readbyqxmd.com/read/30255296/yeast-genetic-interaction-screens-in-the-age-of-crispr-cas
#15
REVIEW
Neil R Adames, Jenna E Gallegos, Jean Peccoud
The ease of performing both forward and reverse genetics in Saccharomyces cerevisiae, along with its stable haploid state and short generation times, has made this budding yeast the consummate model eukaryote for genetics. The major advantage of using budding yeast for reverse genetics is this organism's highly efficient homology-directed repair, allowing for precise genome editing simply by introducing DNA with homology to the chromosomal target. Although plasmid- and PCR-based genome editing tools are quite efficient, they depend on rare spontaneous DNA breaks near the target sequence...
September 25, 2018: Current Genetics
https://www.readbyqxmd.com/read/30244281/intricate-regulation-on-epigenetic-stability-of-the-subtelomeric-heterochromatin-and-the-centromeric-chromatin-in-fission-yeast
#16
REVIEW
Min Lu, Xiangwei He
In eukaryotes, the integrity of chromatin structure and organization is crucial to diverse key cellular processes from development to disease avoidance. To maintain the cell identity through mitotic cell generations, the genome (the genomic DNA sequence) as well as the epigenome (pertaining various forms of epigenetic information carriers, such as histone modifications, nucleosome positioning and the chromatin organization) is inherited with high fidelity. In comparison to the wealth of knowledge on genetic stability, we know much less on what may control the accuracy of epigenetic inheritance...
September 22, 2018: Current Genetics
https://www.readbyqxmd.com/read/30244280/gene-overexpression-screen-for-chromosome-instability-in-yeast-primarily-identifies-cell-cycle-progression-genes
#17
Hanna Tutaj, Elzbieta Pogoda, Katarzyna Tomala, Ryszard Korona
Loss of heterozygosity (LOH) in a vegetatively growing diploid cell signals irregularity of mitosis. Therefore, assays of LOH serve to discover pathways critical for proper replication and segregation of chromosomes. We screened for enhanced LOH in a whole-genome collection of diploid yeast strains in which a single gene was strongly overexpressed. We found 39 overexpression strains with substantially increased LOH caused either by recombination or by chromosome instability. Most of them, 32 in total, belonged to the category of "cell division", a broadly defined biological process...
September 22, 2018: Current Genetics
https://www.readbyqxmd.com/read/30225534/protein-phosphatases-of-saccharomyces-cerevisiae
#18
REVIEW
Sarah R Offley, Martin C Schmidt
The phosphorylation status of a protein is highly regulated and is determined by the opposing activities of protein kinases and protein phosphatases within the cell. While much is known about the protein kinases found in Saccharomyces cerevisiae, the protein phosphatases are much less characterized. Of the 127 protein kinases in yeast, over 90% are in the same evolutionary lineage. In contrast, protein phosphatases are fewer in number (only 43 have been identified in yeast) and comprise multiple, distinct evolutionary lineages...
September 17, 2018: Current Genetics
https://www.readbyqxmd.com/read/30191307/diverse-roles-of-tup1p-and-cyc8p-transcription-regulators-in-the-development-of-distinct-types-of-yeast-populations
#19
REVIEW
Libuše Váchová, Zdena Palková
Yeasts create multicellular structures of varying complexity, such as more complex colonies and biofilms and less complex flocs, each of which develops via different mechanisms. Colony biofilms originate from one or more cells that, through growth and division, develop a complicated three-dimensional structure consisting of aerial parts, agar-embedded invasive parts and a central cavity, filled with extracellular matrix. In contrast, flocs arise relatively quickly by aggregation of planktonic cells growing in liquid cultures after they reach the appropriate growth phase and/or exhaust nutrients such as glucose...
September 6, 2018: Current Genetics
https://www.readbyqxmd.com/read/30167777/involvement-of-the-cysteine-protease-bcatg4-in-development-and-virulence-of-botrytis-cinerea
#20
Na Liu, Weichao Ren, Fengjie Li, Changjun Chen, Zhonghua Ma
Autophagy serves as a survival mechanism against starvation and has been reported to be important for cell growth and differentiation in eukaryotes. Here, we investigated the function of a cysteine protease BcAtg4 in the gray mold fungus Botrytis cinerea. Yeast complementation experiments revealed that Bcatg4 can functionally replace the counterpart of yeast. Subcellular localization exhibited that BcAtg4 diffused in cytoplasm at different developmental stages. Targeted gene deletion of Bcatg4 (ΔBcatg4) led to autophagy blocking and a significant retardation in growth and conidiation...
August 30, 2018: Current Genetics
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