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Yeast epigenetics

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https://www.readbyqxmd.com/read/27924023/methsmrt-an-integrative-database-for-dna-n6-methyladenine-and-n4-methylcytosine-generated-by-single-molecular-real-time-sequencing
#1
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...
October 18, 2016: 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
#2
Hanneke Vlaming, Thom M Molenaar, Tibor van Welsem, Deepani W Poramba-Liyanage, Desiree E Smith, Arno Velds, Liesbeth Hoekman, Tessy Korthout, Sjoerd Hendriks, Af 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...
December 6, 2016: ELife
https://www.readbyqxmd.com/read/27906649/a-common-bacterial-metabolite-elicits-prion-based-bypass-of-glucose-repression
#3
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
#4
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...
November 24, 2016: 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
#5
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
#6
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...
November 5, 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
#7
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
#8
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
#9
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
#10
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)...
October 28, 2016: Genetics
https://www.readbyqxmd.com/read/27716500/remembering-the-past-a-new-form-of-protein-based-inheritance
#11
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
#12
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
https://www.readbyqxmd.com/read/27694830/noise-reduction-facilitated-by-dosage-compensation-in-gene-networks
#13
Weilin Peng, Ruijie Song, Murat Acar
Genetic noise together with genome duplication and volume changes during cell cycle are significant contributors to cell-to-cell heterogeneity. How can cells buffer the effects of these unavoidable epigenetic and genetic variations on phenotypes that are sensitive to such variations? Here we show that a simple network motif that is essential for network-dosage compensation can reduce the effects of extrinsic noise on the network output. Using natural and synthetic gene networks with and without the network motif, we measure gene network activity in single yeast cells and find that the activity of the compensated network is significantly lower in noise compared with the non-compensated network...
October 3, 2016: Nature Communications
https://www.readbyqxmd.com/read/27616479/de-novo-mutations-in-chd4-an-atp-dependent-chromatin-remodeler-gene-cause-an-intellectual-disability-syndrome-with-distinctive-dysmorphisms
#14
Karin Weiss, Paulien A Terhal, Lior Cohen, Michael Bruccoleri, Melita Irving, Ariel F Martinez, Jill A Rosenfeld, Keren Machol, Yaping Yang, Pengfei Liu, Magdalena Walkiewicz, Joke Beuten, Natalia Gomez-Ospina, Katrina Haude, Chin-To Fong, Gregory M Enns, Jonathan A Bernstein, Judith Fan, Garrett Gotway, Mohammad Ghorbani, Koen van Gassen, Glen R Monroe, Gijs van Haaften, Lina Basel-Vanagaite, Xiang-Jiao Yang, Philippe M Campeau, Maximilian Muenke
Chromodomain helicase DNA-binding protein 4 (CHD4) is an ATP-dependent chromatin remodeler involved in epigenetic regulation of gene transcription, DNA repair, and cell cycle progression. Also known as Mi2β, CHD4 is an integral subunit of a well-characterized histone deacetylase complex. Here we report five individuals with de novo missense substitutions in CHD4 identified through whole-exome sequencing and web-based gene matching. These individuals have overlapping phenotypes including developmental delay, intellectual disability, hearing loss, macrocephaly, distinct facial dysmorphisms, palatal abnormalities, ventriculomegaly, and hypogonadism as well as additional findings such as bone fusions...
October 6, 2016: American Journal of Human Genetics
https://www.readbyqxmd.com/read/27614332/genome-wide-identification-evolution-of-chromobox-family-genes-and-their-expression-in-nile-tilapia
#15
Xing-Yong Liu, Xian-Bo Zhang, Ming-Hui Li, Shu-Qing Zheng, Zhi-Long Liu, Yun-Ying Cheng, De-Shou Wang
Chromobox (Cbx) family proteins are transcriptional repressors that involved in epigenetic and developmental processes. In this study, comprehensive analyses of Cbxs were performed using available genome databases from representative animal species. The Cbx family were originated from one Polycomb (Pc) gene like the yeast Pc, which duplicated into two and gave rise to the Pc and the Heterochromatin protein 1 (Hp1) identified in invertebrates from protozoon to lancelet. Rapid expansion of Cbx family members was observed in vertebrates as ~8 (5 Pc and 3 Hp1) were identified in spotted gar, coelacanth and tetrapods...
September 7, 2016: Comparative Biochemistry and Physiology. Part B, Biochemistry & Molecular Biology
https://www.readbyqxmd.com/read/27573382/understanding-how-mismatch-repair-proteins-participate-in-the-repair-anti-recombination-decision
#16
Ujani Chakraborty, Eric Alani
Mismatch repair (MMR) systems correct DNA mismatches that result from DNA polymerase misincorporation errors. Mismatches also appear in heteroduplex DNA intermediates formed during recombination between nearly identical sequences, and can be corrected by MMR or removed through an unwinding mechanism, known as anti-recombination or heteroduplex rejection. We review studies, primarily in baker's yeast, which support how specific factors can regulate the MMR/anti-recombination decision. Based on recent advances, we present models for how DNA structure, relative amounts of key repair proteins, the timely localization of repair proteins to DNA substrates and epigenetic marks can modulate this critical decision...
September 2016: FEMS Yeast Research
https://www.readbyqxmd.com/read/27549112/epigenetic-mutagen-as-histone-modulator-can-be-detected-by-yeast-flocculation
#17
Kei-Ichi Sugiyama, Hiroko Furusawa, Masatomi Shimizu, Petr Grúz, Masamitsu Honma
We have previously reported that flocculation of a yeast co-transformed with the human DNA methyltransferase 1 (DNMT1) and DNMT3B genes was inhibited by DNMT inhibitors. It is well known that epigenetic mutagens can disturb nucleosome positioning via DNA methylation and/or histone modification. In this study we first examined the effects of trichostatin A (TSA), a histone deacetylase inhibitor, on the flocculation level of yeast. TSA dose-dependently promoted the flocculation exhibited by the yeast transformed with the DNMT genes or empty vectors...
November 2016: Mutagenesis
https://www.readbyqxmd.com/read/27548429/the-oncogene-pdrg1-is-an-interaction-target-of-methionine-adenosyltransferases
#18
Claudia Pérez, Francisco J Pérez-Zúñiga, Francisco Garrido, Edel Reytor, Francisco Portillo, María A Pajares
Methionine adenosyltransferases MAT I and MAT III (encoded by Mat1a) catalyze S-adenosylmethionine synthesis in normal liver. Major hepatic diseases concur with reduced levels of this essential methyl donor, which are primarily due to an expression switch from Mat1a towards Mat2a. Additional changes in the association state and even in subcellular localization of these isoenzymes are also detected. All these alterations result in a reduced content of the moderate (MAT I) and high Vmax (MAT III) isoenzymes, whereas the low Vmax (MAT II) isoenzyme increases and nuclear accumulation of MAT I is observed...
2016: PloS One
https://www.readbyqxmd.com/read/27531901/the-pwwp-domain-of-the-human-oncogene-whsc1l1-nsd3-induces-a-metabolic-shift-toward-fermentation
#19
Germana B Rona, Diego S G Almeida, Anderson S Pinheiro, Elis C A Eleutherio
WHSC1L1/NSD3, one of the most aggressive human oncogenes, has two isoforms derived from alternative splicing. Overexpression of long or short NSD3 is capable of transforming a healthy into a cancer cell. NSD3s, the short isoform, contains only a PWWP domain, a histone methyl-lysine reader involved in epigenetic regulation of gene expression. With the aim of understanding the NSD3s PWWP domain role in tumorigenesis, we used Saccharomyces cerevisiae as an experimental model. We identified the yeast protein Pdp3 that contains a PWWP domain that closely resembles NSD3s PWWP...
August 12, 2016: Oncotarget
https://www.readbyqxmd.com/read/27531885/perspectives-on-the-interactions-between-metabolism-redox-and-epigenetics-in-plants
#20
Yuan Shen, Emmanuelle Issakidis-Bourguet, Dao-Xiu Zhou
Epigenetic modifications of chromatin usually involve consumption of key metabolites and redox-active molecules. Primary metabolic flux and cellular redox states control the activity of enzymes involved in chromatin modifications, such as DNA methylation, histone acetylation, and histone methylation, which in turn regulate gene expression and/or enzymatic activity of specific metabolic and redox pathways. Thus, coordination of metabolism and epigenetic regulation of gene expression is critical to control growth and development in response to the cellular environment...
October 2016: Journal of Experimental Botany
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