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Yeast epigenetics

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https://www.readbyqxmd.com/read/28619824/the-histone-3-lysine-4-methyltransferase-setd1b-is-a-maternal-effect-gene-required-for-the-oogenic-gene-expression-program
#1
David Brici, Qinyu Zhang, Susanne Reinhardt, Andreas Dahl, Hella Hartmann, Kerstin Schmidt, Neha Goveas, Jiahao Huang, Lenka Gahurova, Gavin Kelsey, Konstantinos Anastassiadis, A Francis Stewart, Andrea Kranz
Germ cell development involves major reprogramming of the epigenome to prime the zygote for totipotency. Histone 3 lysine 4 (H3K4) methylations are universal epigenetic marks mediated in mammals by six H3K4 methyltransferases related to fly Trithorax, including two yeast Set1 orthologs: Setd1a and Setd1b. Whereas Setd1a plays no role in oogenesis, we report that Setd1b deficiency causes female sterility. Oocyte specific Gdf9iCre conditional knockout (Setd1b(Gdf9) cKO) ovaries develop through all stages however follicular loss accumulated with age and unfertilized metaphase II (MII) oocytes exhibited irregularities of the zona pellucida and meiotic spindle...
June 15, 2017: Development
https://www.readbyqxmd.com/read/28607149/polycomb-repressive-complex-2-in-an-autoinhibited-state
#2
Matthew Bratkowski, Xin Yang, Xin Liu
Polycomb-group proteins control many fundamental biological processes, such as anatomical development in mammals and vernalization in plants. Polycomb repressive complex 2 (PRC2) is responsible for methylation of histone H3 lysine 27 (H3K27), and trimethylated H3K27 (H3K27me3) is implicated in epigenetic gene silencing. Recent genomic, biochemical, and structural data indicate that PRC2 is broadly conserved from yeast to human in many aspects. Here, we determined the crystal structure of an apo PRC2 from the fungus Chaetomium thermophilum captured in a bona fide autoinhibited state, which represents a novel conformation of PRC2 associated with enzyme regulation in light of the basal and stimulated states that we reported previously...
June 12, 2017: Journal of Biological Chemistry
https://www.readbyqxmd.com/read/28554479/rice-pcg-gene-osemf2b-controls-seed-dormancy-and-seedling-growth-by-regulating-the-expression-of-osvp1
#3
Min Chen, Shiyong Xie, Yidan Ouyang, Jialing Yao
The induction and release of seed dormancy are a precisely regulated process that influences seed germination. ABA promotes seed dormancy but suppresses seed germination and seedling growth. However, how chromatin and epigenetic mechanisms regulate the expression of ABA related genes during these processes remains unclear. Polycomb gene OsEMF2b was required for regulation of seed dormancy and seedling growth by dynamically activating and repressing ABA signal response genes. Downregulation of OsEMF2b led to vivipary and decreased expression level of OsVP1, which was involved in ABA signal pathway in seed dormancy...
July 2017: Plant Science: An International Journal of Experimental Plant Biology
https://www.readbyqxmd.com/read/28532323/quantitative-regulation-of-histone-variant-h2a-z-during-cell-cycle-by-ubiquitin-proteasome-system-and-sumo-targeted-ubiquitin-ligases
#4
Daisuke Takahashi, Yuki Orihara, Saho Kitagawa, Masayuki Kusakabe, Takahiro Shintani, Yukako Oma, Masahiko Harata
Quantitative control of histones and histone variants during cell cycle is relevant to their epigenetic functions. We found that the level of yeast histone variant H2A.Z in the G2/M-phase is actively kept low by the ubiquitin proteasome system and SUMO-targeted ubiquitin ligases. Overexpression of H2A.Z induced defects in mitotic progression, suggesting functional importance of this quantitative control.
May 22, 2017: Bioscience, Biotechnology, and Biochemistry
https://www.readbyqxmd.com/read/28520954/h2b-ubiquitylation-and-the-histone-chaperone-asf1-cooperatively-mediate-the-formation-and-maintenance-of-heterochromatin-silencing
#5
Meng-Ying Wu, Chia-Yeh Lin, Hsin-Yi Tseng, Fei-Man Hsu, Pao-Yang Chen, Cheng-Fu Kao
Heterochromatin is a heritable form of gene repression, with critical roles in development and cell identity. Understanding how chromatin factors results in such repression is a fundamental question. Chromatin is assembled and disassembled during transcription, replication and repair by anti-silencing function 1 (Asf1), a highly conserved histone chaperone. Transcription and DNA replication are also affected by histone modifications that modify nucleosome dynamics, such as H2B ubiquitylation (H2Bub). We report here that H2Bub and Asf1 cooperatively promote transcriptional silencing at yeast telomeres and mating loci...
May 17, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/28431147/detection-of-epigenetic-mutagens-including-anthracene-derived-compounds-using-yeast-flo1-promoter-gfp-reporter-gene-assay
#6
Kei-Ichi Sugiyama, Hiroko Furusawa, Petr Grúz, Masamitsu Honma
Recently, we have reported that the FLO1-mediated flocculation levels of yeast are affected by an epigenetic mutagen, alizarin. Alizarin promoted flocculation and reduced the bulk levels of histone H3 in yeast cells. Since alizarin has been known to possess carcinogenesis-promoting properties, it is important to estimate the effect of alizarin-related compounds on epigenome as measured by the flocculation of yeast. In this study, we examined the effects of two anthracene-derived compounds other than alizarin on the flocculation level of yeast...
April 20, 2017: Mutagenesis
https://www.readbyqxmd.com/read/28421568/prions-prionoid-complexes-and-amyloids-the-bad-the-good-and-something-in-between
#7
Iva Hafner Bratkovič
Prions are infectious agents causing transmissible spongiform encephalopathies in humans and animals. These protein-based particles template conformational changes in a host-encoded prion protein to an insoluble self-like conformation. Prions are also present in yeast, where they support protein-based epigenetic inheritance. There is emerging evidence that prion-like (prionoid) particles can support a variety of pathological and beneficial functions. The recent data on the prionoid spread of other pathological amyloids are discussed in light of differences between prions and prion-like aggregates...
April 19, 2017: Swiss Medical Weekly
https://www.readbyqxmd.com/read/28414025/alterations-of-the-translation-apparatus-during-aging-and-stress-response
#8
REVIEW
Yulia Gonskikh, Norbert Polacek
Aging is a biological process characterized by the irreversible and time-dependent deterioration of cell functions, tissues, and organs. Accumulating studies in a wide range of species from yeast to human revealed changes associated with the aging process to be conserved throughout evolution. The main characteristics of aging are (i) genomic instability, (ii) loss of telomere function, (iii) epigenetic changes,(iv) increased cellular senescence, (v) depletion of the stem cell pool, (vi) altered intercellular communication and (vii) loss of protein homeostasis...
April 13, 2017: Mechanisms of Ageing and Development
https://www.readbyqxmd.com/read/28394944/identification-of-a-rice-metal-tolerance-protein-osmtp11-as-a-manganese-transporter
#9
Mei Zhang, Baoxiu Liu
Metal tolerance proteins (MTPs) are a gene family of cation efflux transporters that occur widely in plants and might serve an essential role in metal homeostasis and tolerance. Our research describes the identification, characterization, and localization of OsMTP11, a member of the MTP family from rice. OsMTP11 was expressed constitutively and universally in different tissues in rice plant. Heterologous expression in yeast showed that OsMTP11 complemented the hypersensitivity of mutant strains to Mn, and also complemented yeast mutants to other metals, including Co and Ni...
2017: PloS One
https://www.readbyqxmd.com/read/28357364/evidence-for-the-hallmarks-of-human-aging-in-replicatively-aging-yeast
#10
REVIEW
Georges E Janssens, Liesbeth M Veenhoff
Recently, efforts have been made to characterize the hallmarks that accompany and contribute to the phenomenon of aging, as most relevant for humans 1. Remarkably, studying the finite lifespan of the single cell eukaryote budding yeast (recently reviewed in 2 and 3) has been paramount for our understanding of aging. Here, we compile observations from literature over the past decades of research on replicatively aging yeast to highlight how the hallmarks of aging in humans are present in yeast. We find strong evidence for the majority of these, and summarize how yeast aging is especially characterized by the hallmarks of genomic instability, epigenetic alterations, loss of proteostasis, deregulated nutrient sensing, and mitochondrial dysfunction...
June 20, 2016: Microbial Cell
https://www.readbyqxmd.com/read/28333343/centromere-destiny-in-dicentric-chromosomes-new-insights-from-the-evolution-of-human-chromosome-2-ancestral-centromeric-region
#11
Giorgia Chiatante, Giuliana Giannuzzi, Francesco Maria Calabrese, Evan E Eichler, Mario Ventura
Dicentric chromosomes are products of genomic rearrangements that place two centromeres on the same chromosome. Due to the presence of two primary constrictions, they are inherently unstable and overcome their instability by epigenetically inactivating and/or deleting one of the two centromeres, thus resulting in functionally monocentric chromosomes that segregate normally during cell division. Our understanding to date of dicentric chromosome formation, behavior and fate has been largely inferred from observational studies in plants and humans as well as artificially produced de novo dicentrics in yeast and in human cells...
July 1, 2017: Molecular Biology and Evolution
https://www.readbyqxmd.com/read/28318821/snf2-family-protein-fft3-suppresses-nucleosome-turnover-to-promote-epigenetic-inheritance-and-proper-replication
#12
Nitika Taneja, Martin Zofall, Vanivilasini Balachandran, Gobi Thillainadesan, Tomoyasu Sugiyama, David Wheeler, Ming Zhou, Shiv I S Grewal
Heterochromatin can be epigenetically inherited in cis, leading to stable gene silencing. However, the mechanisms underlying heterochromatin inheritance remain unclear. Here, we identify Fft3, a fission yeast homolog of the mammalian SMARCAD1 SNF2 chromatin remodeler, as a factor uniquely required for heterochromatin inheritance, rather than for de novo assembly. Importantly, we find that Fft3 suppresses turnover of histones at heterochromatic loci to facilitate epigenetic transmission of heterochromatin in cycling cells...
April 6, 2017: Molecular Cell
https://www.readbyqxmd.com/read/28302794/dna-sequence-dependent-epigenetic-inheritance-of-gene-silencing-and-histone-h3k9-methylation
#13
Xiaoyi Wang, Danesh Moazed
Epigenetic inheritance mechanisms play fundamental roles in maintaining cellular memory of gene expression states. In fission yeast, histone H3 lysine 9 (H3K9) is methylated (H3K9me) at heterochromatic domains. These domains can be epigenetically inherited when epe1(+) , encoding an enzyme that promotes H3K9 demethylation, is deleted. How native epigenetic states are stably maintained in epe1(+) cells remains unknown. Here, we developed a system to examine the role of DNA sequence and genomic context in propagation of a cis-heritable H3K9me-dependent silenced state...
April 7, 2017: Science
https://www.readbyqxmd.com/read/28277978/targeted-dna-demethylation-in-human-cells-by-fusion-of-a-plant-5-methylcytosine-dna-glycosylase-to-a-sequence-specific-dna-binding-domain
#14
Jara Teresa Parrilla-Doblas, Rafael R Ariza, Teresa Roldán-Arjona
DNA methylation is a crucial epigenetic mark associated to gene silencing, and its targeted removal is a major goal of epigenetic editing. In animal cells, DNA demethylation involves iterative 5mC oxidation by TET enzymes followed by replication-dependent dilution and/or replication-independent DNA repair of its oxidized derivatives. In contrast, plants use specific DNA glycosylases that directly excise 5mC and initiate its substitution for unmethylated C in a base excision repair process. In this work, we have fused the catalytic domain of Arabidopsis ROS1 5mC DNA glycosylase (ROS1_CD) to the DNA binding domain of yeast GAL4 (GBD)...
April 3, 2017: Epigenetics: Official Journal of the DNA Methylation Society
https://www.readbyqxmd.com/read/28202544/cdc15-phosphorylates-the-c-terminal-domain-of-rna-polymerase-ii-for-transcription-during-mitosis
#15
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 the C-terminal domain (CTD) of the largest subunit of RNA polymerase II. The CTD comprises the repeated Tyr-Ser-Pro-Thr-Ser-Pro-Ser 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...
March 31, 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
#16
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
#17
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
#18
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
#19
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
#20
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...
February 1, 2017: Molecular Biology and Evolution
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