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Yeast epigenetics

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https://www.readbyqxmd.com/read/28202544/cdc15-phosphorylates-carboxy-terminal-domain-of-rna-polymerase-ii-for-transcription-during-mitosis
#1
Amit Kumar Singh, Shivangi Rastogi, Harish Shukla, Mohd Asalam, Srikanta Kumar Rath, Md Sohail Akhtar
In eukaryotes, the basal transcription in interphase is orchestrated through the regulation by kinases (Kin28, Bur1 and Ctk1) and phosphatases (Ssu72, Rtr1 and Fcp1) which act through the post-translational modification of CTD (carboxy terminal domain of the largest subunit of RNA Polymerase II). The CTD comprises of repeated Tyr1Ser2Pro3Thr4Ser5Pro6Ser7 motif with potential epigenetic modification sites. Despite the observation of transcription and periodic expression of genes during mitosis with entailing CTD phosphorylation and dephosphorylation, the associated CTD specific kinase/s and its role in transcription remains unknown...
February 15, 2017: Journal of Biological Chemistry
https://www.readbyqxmd.com/read/28191457/the-copper-transport-associated-protein-ctr4-can-form-prion-like-epigenetic-determinants-in-schizosaccharomyces-pombe
#2
Theodora Sideri, Yoko Yashiroda, David A Ellis, María Rodríguez-López, Minoru Yoshida, Mick F Tuite, Jürg Bähler
Prions are protein-based infectious entities associated with fatal brain diseases in animals, but also modify a range of host-cell phenotypes in the budding yeast, Saccharomyces cerevisiae. Many questions remain about the evolution and biology of prions. Although several functionally distinct prion-forming proteins exist in S. cerevisiae, [HET-s] of Podospora anserina is the only other known fungal prion. Here we investigated prion-like, protein-based epigenetic transmission in the fission yeast Schizosaccharomyces pombe...
January 2017: Microbial Cell
https://www.readbyqxmd.com/read/28125021/a-molecular-view-of-kinetochore-assembly-and-function
#3
REVIEW
Andrea Musacchio, Arshad Desai
Kinetochores are large protein assemblies that connect chromosomes to microtubules of the mitotic and meiotic spindles in order to distribute the replicated genome from a mother cell to its daughters. Kinetochores also control feedback mechanisms responsible for the correction of incorrect microtubule attachments, and for the coordination of chromosome attachment with cell cycle progression. Finally, kinetochores contribute to their own preservation, across generations, at the specific chromosomal loci devoted to host them, the centromeres...
January 24, 2017: Biology
https://www.readbyqxmd.com/read/28078514/the-molecular-basis-of-the-organization-of-repetitive-dna-containing-constitutive-heterochromatin-in-mammals
#4
REVIEW
Gohei Nishibuchi, Jérôme Déjardin
Constitutive heterochromatin is composed mainly of repetitive elements and represents the typical inert chromatin structure in eukaryotic cells. Approximately half of the mammalian genome is made of repeat sequences, such as satellite DNA, telomeric DNA, and transposable elements. As essential genes are not present in these regions, most of these repeat sequences were considered as junk DNA in the past. However, it is now clear that these regions are essential for chromosome stability and the silencing of neighboring genes...
January 11, 2017: Chromosome Research
https://www.readbyqxmd.com/read/28027291/interaction-of-prions-causes-heritable-traits-in-saccharomyces-cerevisiae
#5
Anton A Nizhnikov, Tatyana A Ryzhova, Kirill V Volkov, Sergey P Zadorsky, Julia V Sopova, Sergey G Inge-Vechtomov, Alexey P Galkin
The concept of "protein-based inheritance" defines prions as epigenetic determinants that cause several heritable traits in eukaryotic microorganisms, such as Saccharomyces cerevisiae and Podospora anserina. Previously, we discovered a non-chromosomal factor, [NSI+], which possesses the main features of yeast prions, including cytoplasmic infectivity, reversible curability, dominance, and non-Mendelian inheritance in meiosis. This factor causes omnipotent suppression of nonsense mutations in strains of S. cerevisiae bearing a deleted or modified Sup35 N-terminal domain...
December 2016: PLoS Genetics
https://www.readbyqxmd.com/read/28025271/no-evidence-that-protein-noise-induced-epigenetic-epistasis-constrains-gene-expression-evolution
#6
Gábor Boross, Balázs Papp
Changes in gene expression can affect phenotypes and therefore both its level and stochastic variability are frequently under selection. It has recently been proposed that epistatic interactions influence gene expression evolution: gene pairs where simultaneous knockout is more deleterious than expected should evolve reduced expression noise to avoid concurrent low expression of both proteins. In apparent support, yeast genes with many epistatic partners have low expression variation both among isogenic individuals and between species...
November 8, 2016: Molecular Biology and Evolution
https://www.readbyqxmd.com/read/27979908/disentangling-genetic-and-epigenetic-determinants-of-ultrafast-adaptation
#7
Arne B Gjuvsland, Enikö Zörgö, Jeevan Ka Samy, Simon Stenberg, Ibrahim H Demirsoy, Francisco Roque, Ewa Maciaszczyk-Dziubinska, Magdalena Migocka, Elisa Alonso-Perez, Martin Zackrisson, Robert Wysocki, Markus J Tamás, Inge Jonassen, Stig W Omholt, Jonas Warringer
A major rationale for the advocacy of epigenetically mediated adaptive responses is that they facilitate faster adaptation to environmental challenges. This motivated us to develop a theoretical-experimental framework for disclosing the presence of such adaptation-speeding mechanisms in an experimental evolution setting circumventing the need for pursuing costly mutation-accumulation experiments. To this end, we exposed clonal populations of budding yeast to a whole range of stressors. By growth phenotyping, we found that almost complete adaptation to arsenic emerged after a few mitotic cell divisions without involving any phenotypic plasticity...
December 15, 2016: Molecular Systems Biology
https://www.readbyqxmd.com/read/27932495/modulations-of-sir-nucleosome-interactions-of-reconstructed-yeast-silent-pre-heterochromatin-by-o-acetyl-adp-ribose-and-magnesium
#8
Shu-Yun Tung, Sue-Hong Wang, Sue-Ping Lee, Shu-Ping Tsai, Hsiao-Hsuian Shen, Feng-Jung Chen, Yu-Yi Wu, Sheng-Pin Hsiao, Gunn-Guang Liou
To study epigenetic inheritance, yeast silent heterochromatin provides an excellent model. Previously, we developed an in vitro assembly system to demonstrate the formation of filament structures with requirements that mirror yeast epigenetic gene silencing in vivo However, the properties of these filaments have not been investigated in detail. Here, we show that the assembly system requires Sir2, Sir3, Sir4, nucleosomes and O-acetyl-ADP-ribose. We also demonstrate that all Sir proteins and nucleosomes are components of these filaments to prove they are SIR-nucleosome filaments...
December 8, 2016: Molecular Biology of the Cell
https://www.readbyqxmd.com/read/27924023/methsmrt-an-integrative-database-for-dna-n6-methyladenine-and-n4-methylcytosine-generated-by-single-molecular-real-time-sequencing
#9
Pohao Ye, Yizhao Luan, Kaining Chen, Yizhi Liu, Chuanle Xiao, Zhi Xie
DNA methylation is an important type of epigenetic modifications, where 5- methylcytosine (5mC), 6-methyadenine (6mA) and 4-methylcytosine (4mC) are the most common types. Previous efforts have been largely focused on 5mC, providing invaluable insights into epigenetic regulation through DNA methylation. Recently developed single-molecule real-time (SMRT) sequencing technology provides a unique opportunity to detect the less studied DNA 6mA and 4mC modifications at single-nucleotide resolution. With a rapidly increased amount of SMRT sequencing data generated, there is an emerging demand to systematically explore DNA 6mA and 4mC modifications from these data sets...
January 4, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/27922451/direct-screening-for-chromatin-status-on-dna-barcodes-in-yeast-delineates-the-regulome-of-h3k79-methylation-by-dot1
#10
Hanneke Vlaming, Thom M Molenaar, Tibor van Welsem, Deepani W Poramba-Liyanage, Desiree E Smith, Arno Velds, Liesbeth Hoekman, Tessy Korthout, Sjoerd Hendriks, A F Maarten Altelaar, Fred van Leeuwen
Given the frequent misregulation of chromatin in cancer, it is important to understand the cellular mechanisms that regulate chromatin structure. However, systematic screening for epigenetic regulators is challenging and often relies on laborious assays or indirect reporter read-outs. Here we describe a strategy, Epi-ID, to directly assess chromatin status in thousands of mutants. In Epi-ID, chromatin status on DNA barcodes is interrogated by chromatin immunoprecipitation followed by deep sequencing, allowing for quantitative comparison of many mutants in parallel...
6, 2016: ELife
https://www.readbyqxmd.com/read/27906649/a-common-bacterial-metabolite-elicits-prion-based-bypass-of-glucose-repression
#11
David M Garcia, David Dietrich, Jon Clardy, Daniel F Jarosz
Robust preference for fermentative glucose metabolism has motivated domestication of the budding yeast Saccharomyces cerevisiae. This program can be circumvented by a protein-based genetic element, the [GAR(+)] prion, permitting simultaneous metabolism of glucose and other carbon sources. Diverse bacteria can elicit yeast cells to acquire [GAR(+)], although the molecular details of this interaction remain unknown. Here we identify the common bacterial metabolite lactic acid as a strong [GAR(+)] inducer. Transient exposure to lactic acid caused yeast cells to heritably circumvent glucose repression...
November 29, 2016: ELife
https://www.readbyqxmd.com/read/27890612/in%C3%A2-vitro-reconstitution-and-biochemical-analyses-of-the-schizosaccharomyces-pombe-nucleosome
#12
Masako Koyama, Wataru Nagakura, Hiroki Tanaka, Tomoya Kujirai, Yuji Chikashige, Tokuko Haraguchi, Yasushi Hiraoka, Hitoshi Kurumizaka
Schizosaccharomyces pombe, which has a small genome but shares many physiological functions with higher eukaryotes, is a useful single-cell, model eukaryotic organism. In particular, many features concerning chromatin structure and dynamics, including heterochromatin, centromeres, telomeres, and DNA replication origins, are well conserved between S. pombe and higher eukaryotes. However, the S. pombe nucleosome, the fundamental structural unit of chromatin, has not been reconstituted in vitro. In the present study, we established the method to purify S...
January 22, 2017: Biochemical and Biophysical Research Communications
https://www.readbyqxmd.com/read/27877178/an-s-adenosyl-methionine-synthetase-sams-gene-from-andropogon-virginicus-l-confers-aluminum-stress-tolerance-and-facilitates-epigenetic-gene-regulation-in-arabidopsis-thaliana
#13
Bunichi Ezaki, Aiko Higashi, Norie Nanba, Takumi Nishiuchi
Candidate clones which conferred Al tolerance to yeast transformants (TFs) were obtained from a cDNA library derived from a highly Al-tolerant poaceae, Andropogon virginicus L. One such clone, AL3A-4, encoded an S-adenosyl methionine synthetase (SAMS) gene. A full-length cDNA was obtained by 5'-RACE, designated AvSAMS1, and introduced into Arabidopsis thaliana to investigate its biological functions under Al stress. Two TF plant lines both showed higher tolerance than the Col-0 ecotype (non-TF) not only for Al stress, but also for Cu, Pb, Zn and diamide stresses, suggesting the AvSAMS1 was a multiple tolerance gene...
2016: Frontiers in Plant Science
https://www.readbyqxmd.com/read/27825925/molecular-mechanism-of-dna-topoisomerase-i-dependent-rdna-silencing-sir2p-recruitment-at-ribosomal-genes
#14
Anna D'Alfonso, Francesca Di Felice, Valentina Carlini, Christine M Wright, Marla I Hertz, Mary-Ann Bjornsti, Giorgio Camilloni
Saccharomyces cerevisiae sir2Δ or top1Δ mutants exhibit similar phenotypes involving ribosomal DNA, including (i) loss of transcriptional silencing, resulting in non-coding RNA hyperproduction from cryptic RNA polymerase II promoters; (ii) alterations in recombination; and (iii) a general increase in histone acetylation. Given the distinct enzymatic activities of Sir2 and Top1 proteins, a histone deacetylase and a DNA topoisomerase, respectively, we investigated whether genetic and/or physical interactions between the two proteins could explain the shared ribosomal RNA genes (rDNA) phenotypes...
December 4, 2016: Journal of Molecular Biology
https://www.readbyqxmd.com/read/27821526/split-hand-foot-malformation-genetics-supports-the-chromosome-7-copy-segregation-mechanism-for-human-limb-development
#15
REVIEW
Amar J S Klar
Genetic aberrations of several unlinked loci cause human congenital split hand/foot malformation (SHFM) development. Mutations of the DLX5 (distal-less) transcription factor-encoding gene in chromosome 7 cause SHFM through haploinsufficiency, but the vast majority of cases result from heterozygous chromosomal aberrations of the region without mutating the DLX5 gene. To resolve this paradox, we invoke a chromosomal epigenetic mechanism for limb development. It is composed of a monochromatid gene expression phenomenon that we discovered in two fission yeasts with the selective chromosome copy segregation phenomenon that we discovered in mouse cells...
December 19, 2016: Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences
https://www.readbyqxmd.com/read/27807647/epigenetic-transcriptional-memory
#16
REVIEW
Agustina D'Urso, Jason H Brickner
Organisms alter gene expression to adapt to changes in environmental conditions such as temperature, nutrients, inflammatory signals, and stress (Gialitakis et al. in Mol Cell Biol 30:2046-2056, 2010; Conrath in Trends Plant Sci 16:524-531, 2011; Avramova in Plant J 83:149-159, 2015; Solé et al. in Curr Genet 61:299-308, 2015; Ho and Gasch in Curr Genet 61:503-511, 2015; Bevington et al. in EMBO J 35:515-535, 2016; Hilker et al. in Biol Rev Camb Philos Soc 91:1118-1133, 2016). In some cases, organisms can "remember" a previous environmental condition and adapt to that condition more rapidly in the future (Gems and Partridge 2008)...
November 2, 2016: Current Genetics
https://www.readbyqxmd.com/read/27807261/clonal-yeast-biofilms-can-reap-competitive-advantages-through-cell-differentiation-without-being-obligatorily-multicellular
#17
Birgitte Regenberg, Kristian Ebbesen Hanghøj, Kaj Scherz Andersen, Jacobus J Boomsma
How differentiation between cell types evolved is a fundamental question in biology, but few studies have explored single-gene phenotypes that mediate first steps towards division of labour with selective advantage for groups of cells. Here, we show that differential expression of the FLO11 gene produces stable fractions of Flo11(+) and Flo11(-) cells in clonal Saccharomyces cerevisiae biofilm colonies on medium with intermediate viscosity. Differentiated Flo11(+/-) colonies, consisting of adhesive and non-adhesive cells, obtain a fourfold growth advantage over undifferentiated colonies by overgrowing glucose resources before depleting them, rather than depleting them while they grow as undifferentiated Flo11(-) colonies do...
November 16, 2016: Proceedings. Biological Sciences
https://www.readbyqxmd.com/read/27794026/histone-h4-facilitates-the-proteolysis-of-the-budding-yeast-cenp-acse4-centromeric-histone-variant
#18
Gary M R Deyter, Erica M Hildebrand, Adrienne D Barber, Sue Biggins
The incorporation of histone variants into nucleosomes can alter chromatin-based processes. CENP-A is the histone H3 variant found exclusively at centromeres that serves as an epigenetic mark for centromere identity and is required for kinetochore assembly. CENP-A mislocalization to ectopic sites appears to contribute to genomic instability, transcriptional misregulation, and tumorigenesis, so mechanisms exist to ensure its exclusive localization to centromeres. One conserved process is proteolysis, which is mediated by the Psh1 E3 ubiquitin ligase in Saccharomyces cerevisiae (budding yeast)...
January 2017: Genetics
https://www.readbyqxmd.com/read/27716500/remembering-the-past-a-new-form-of-protein-based-inheritance
#19
REVIEW
Mick F Tuite
A comprehensive analysis uncovered a set of yeast proteins promoting protein-based inheritance that shares many of the non-Mendelian properties of prions. Lacking any sequence or structural signatures of known prions, these proteins represent a new class of non-amyloid, protein-based epigenetic determinants that can control phenotype without impacting genotype.
October 6, 2016: Cell
https://www.readbyqxmd.com/read/27716056/histone-modifications-facilitate-the-coexpression-of-bidirectional-promoters-in-rice
#20
Yuan Fang, Lei Wang, Ximeng Wang, Qi You, Xiucai Pan, Jin Xiao, Xiu-E Wang, Yufeng Wu, Zhen Su, Wenli Zhang
BACKGROUND: Bidirectional gene pairs are highly abundant and mostly co-regulated in eukaryotic genomes. The structural features of bidirectional promoters (BDPs) have been well studied in yeast, humans and plants. However, the underlying mechanisms responsible for the coexpression of BDPs remain understudied, especially in plants. RESULTS: Here, we characterized chromatin features associated with rice BDPs. Several unique chromatin features were present in rice BDPs but were missing from unidirectional promoters (UDPs), including overrepresented active histone marks, canonical nucleosomes and underrepresented H3K27me3...
September 30, 2016: BMC Genomics
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