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https://www.readbyqxmd.com/read/29784772/a-heterochromatin-domain-forms-gradually-at-a-new-telomere-and-is-dynamic-at-stable-telomeres
#1
Jinyu Wang, Jessica R Eisenstatt, Julien Audry, Kristen Cornelius, Matthew Shaughnessy, Kathleen L Berkner, Kurt W Runge
Heterochromatin domains play important roles in chromosome biology, organismal development and aging, including centromere function, mammalian female X-chromosome inactivation and senescence-associated heterochromatin foci. In the fission yeast Schizosaccharomyces pombe and metazoans, heterochromatin contains histone H3 that is dimethylated at lysine 9. While factors required for heterochromatin have been identified, the dynamics of heterochromatin formation are poorly understood. Telomeres convert adjacent chromatin into heterochromatin...
May 21, 2018: Molecular and Cellular Biology
https://www.readbyqxmd.com/read/29761456/pombase-the-scientific-resource-for-fission-yeast
#2
Antonia Lock, Kim Rutherford, Midori A Harris, Valerie Wood
The fission yeast Schizosaccharomyces pombe has become well established as a model species for studying conserved cell-level biological processes, especially the mechanics and regulation of cell division. PomBase integrates the S. pombe genome sequence with traditional genetic, molecular, and cell biological experimental data as well as the growing body of large datasets generated by emerging high-throughput methods. This chapter provides insight into the curation philosophy and data organization at PomBase, and provides a guide to using PomBase for infrequent visitors and anyone considering exploring S...
2018: Methods in Molecular Biology
https://www.readbyqxmd.com/read/29727662/transcriptome-wide-interrogation-of-the-functional-intronome-by-spliceosome-profiling
#3
Weijun Chen, Jill Moore, Hakan Ozadam, Hennady P Shulha, Nicholas Rhind, Zhiping Weng, Melissa J Moore
Full understanding of eukaryotic transcriptomes and how they respond to different conditions requires deep knowledge of all sites of intron excision. Although RNA sequencing (RNA-seq) provides much of this information, the low abundance of many spliced transcripts (often due to their rapid cytoplasmic decay) limits the ability of RNA-seq alone to reveal the full repertoire of spliced species. Here, we present "spliceosome profiling," a strategy based on deep sequencing of RNAs co-purifying with late-stage spliceosomes...
May 3, 2018: Cell
https://www.readbyqxmd.com/read/29697047/rev7-and-53bp1-crb2-prevent-recq-helicase-dependent-hyper-resection-of-dna-double-strand-breaks
#4
Bryan A Leland, Angela C Chen, Amy Y Zhao, Robert C Wharton, Megan C King
Poly(ADP ribose) polymerase inhibitors (PARPi) target cancer cells deficient in homology-directed repair of DNA double-strand breaks (DSBs). In preclinical models, PARPi resistance is tied to altered nucleolytic processing (resection) at the 5' ends of a DSB. For example, loss of 53BP1 or Rev7/MAD2L2/FANCV derepresses resection to drive PARPi resistance, although the mechanisms are poorly understood. Long-range resection can be catalyzed by two machineries: the exonuclease Exo1, or the combination of a RecQ helicase and Dna2...
April 26, 2018: ELife
https://www.readbyqxmd.com/read/29622660/rnase-h-eliminates-r-loops-that-disrupt-dna-replication-but-is-nonessential-for-efficient-dsb-repair
#5
Hongchang Zhao, Min Zhu, Oliver Limbo, Paul Russell
In Saccharomyces cerevisiae , genome stability depends on RNases H1 and H2, which remove ribonucleotides from DNA and eliminate RNA-DNA hybrids (R-loops). In Schizosaccharomyces pombe , RNase H enzymes were reported to process RNA-DNA hybrids produced at a double-strand break (DSB) generated by I-PpoI meganuclease. However, it is unclear if RNase H is generally required for efficient DSB repair in fission yeast, or whether it has other genome protection roles. Here, we show that S. pombe rnh1∆ rnh201∆ cells, which lack the RNase H enzymes, accumulate R-loops and activate DNA damage checkpoints...
April 5, 2018: EMBO Reports
https://www.readbyqxmd.com/read/29599176/h3k4-methylation-dependent-and-independent-chromatin-regulation-by-jhd2-and-set1-in-budding-yeast
#6
Kwan Yin Lee, Ziyan Chen, River Jiang, Marc D Meneghini
Set1 and Jhd2 regulate the methylation state of histone H3 lysine-4 (H3K4me) through their opposing methyltransferase and demethylase activities in the budding yeast Saccharomyces cerevisiae H3K4me associates with actively transcribed genes and, like both SET1 and JHD2 themselves, is known to regulate gene expression diversely. It remains unclear, however, if Set1 and Jhd2 act solely through H3K4me. Relevantly, Set1 methylates lysine residues in the kinetochore protein Dam1 while genetic studies of the S. pombe SET1 ortholog suggest the existence of non-H3K4 Set1 targets relevant to gene regulation...
March 29, 2018: G3: Genes—Genomes—Genetics
https://www.readbyqxmd.com/read/29596413/lack-of-2-o-methylation-in-the-trna-anticodon-loop-of-two-phylogenetically-distant-yeast-species-activates-the-general-amino-acid-control-pathway
#7
Lu Han, Michael P Guy, Yoshiko Kon, Eric M Phizicky
Modification defects in the tRNA anticodon loop often impair yeast growth and cause human disease. In the budding yeast Saccharomyces cerevisiae and the phylogenetically distant fission yeast Schizosaccharomyces pombe, trm7Δ mutants grow poorly due to lack of 2'-O-methylation of C32 and G34 in the tRNAPhe anticodon loop, and lesions in the human TRM7 homolog FTSJ1 cause non-syndromic X-linked intellectual disability (NSXLID). However, it is unclear why trm7Δ mutants grow poorly. We show here that despite the fact that S...
March 29, 2018: PLoS Genetics
https://www.readbyqxmd.com/read/29550859/genetic-interactions-between-the-chromosome-axis-associated-protein-hop1-and-homologous-recombination-determinants-in-schizosaccharomyces-pombe
#8
Simon David Brown, Olga Dorota Jarosinska, Alexander Lorenz
Hop1 is a component of the meiosis-specific chromosome axis and belongs to the evolutionarily conserved family of HORMA domain proteins. Hop1 and its orthologs in higher eukaryotes are a major factor in promoting double-strand DNA break formation and inter-homolog recombination. In budding yeast and mammals, they are also involved in a meiotic checkpoint kinase cascade monitoring the completion of double-strand DNA break repair. We used the fission yeast, Schizosaccharomyces pombe, which lacks a canonical synaptonemal complex to test whether Hop1 has a role beyond supporting the generation of double-strand DNA breaks and facilitating inter-homolog recombination events...
March 17, 2018: Current Genetics
https://www.readbyqxmd.com/read/29549126/the-major-facilitator-transporter-str3-is-required-for-low-affinity-heme-acquisition-in-schizosaccharomyces-pombe
#9
Vincent Normant, Thierry Mourer, Simon Labbé
In the fission yeast Schizosaccharomyces pombe , acquisition of exogenous heme is largely mediated by the cell membrane-associated Shu1. Here, we report that Str3, a member of the major facilitator superfamily of transporters, promotes cellular heme import. Using a strain that cannot synthesize heme de novo ( hem1 Δ) and lacks Shu1, we found that the heme-dependent growth deficit of this strain is rescued by hemin supplementation in the presence of Str3. Microscopic analyses of a hem1 Δ shu1 Δ str3 Δ mutant strain in the presence of the heme analog zinc mesoporphyrin IX (ZnMP) revealed that ZnMP fails to accumulate within the mutant cells...
April 27, 2018: Journal of Biological Chemistry
https://www.readbyqxmd.com/read/29539401/characterization-of-cell-boundary-and-confocal-effects-improves-quantitative-frap-analysis
#10
James L Kingsley, Jeffrey P Bibeau, S Iman Mousavi, Cem Unsal, Zhilu Chen, Xinming Huang, Luis Vidali, Erkan Tüzel
Fluorescence recovery after photobleaching (FRAP) is an important tool used by cell biologists to study the diffusion and binding kinetics of vesicles, proteins, and other molecules in the cytoplasm, nucleus, or cell membrane. Although many FRAP models have been developed over the past decades, the influence of the complex boundaries of 3D cellular geometries on the recovery curves, in conjunction with regions of interest and optical effects (imaging, photobleaching, photoswitching, and scanning), has not been well studied...
March 13, 2018: Biophysical Journal
https://www.readbyqxmd.com/read/29535210/rapid-production-of-pure-recombinant-actin-isoforms-in-pichia-pastoris
#11
Tomoyuki Hatano, Salvatore Alioto, Emanuele Roscioli, Saravanan Palani, Scott T Clarke, Anton Kamnev, Juan Ramon Hernandez-Fernaud, Lavanya Sivashanmugam, Bernardo Chapa-Y-Lazo, Alexandra M E Jones, Robert C Robinson, Karuna Sampath, Masanori Mishima, Andrew D McAinsh, Bruce L Goode, Mohan K Balasubramanian
Actins are major eukaryotic cytoskeletal proteins, and they are involved in many important cell functions, including cell division, cell polarity, wound healing and muscle contraction. Despite obvious drawbacks, muscle actin, which is easily purified, is used extensively for biochemical studies of the non-muscle actin cytoskeleton. Here, we report a rapid and cost-effective method to purify heterologous actins expressed in the yeast Pichia pastoris Actin is expressed as a fusion with the actin-binding protein thymosin β4 and purified by means of an affinity tag introduced in the fusion...
April 23, 2018: Journal of Cell Science
https://www.readbyqxmd.com/read/29473861/nutrient-limitation-inactivates-mrc1-to-cds1-checkpoint-signalling-in-schizosaccharomyces-pombe
#12
Jessica Fletcher, Liam Griffiths, Thomas Caspari
The S. pombe checkpoint kinase, Cds1, protects the integrity of stalled DNA replication forks after its phosphorylation at threonine-11 by Rad3 (ATR). Modified Cds1 associates through its N-terminal forkhead-associated domain (FHA)-domain with Mrc1 (Claspin) at stalled forks. We report here that nutrient starvation results in post-translational changes to Cds1 and the loss of Mrc1. A drop in glucose after a down-shift from 3% to 0.1-0.3%, or when cells enter the stationary phase, triggers a sharp decline in Mrc1 and the accumulation of insoluble Cds1...
February 23, 2018: Cells
https://www.readbyqxmd.com/read/29464330/the-interplay-of-histone-h2b-ubiquitination-with-budding-and-fission-yeast-heterochromatin
#13
REVIEW
Alexis Zukowski, Aaron M Johnson
Mono-ubiquitinated histone H2B (H2B-Ub) is important for chromatin regulation of transcription, chromatin assembly, and also influences heterochromatin. In this review, we discuss the effects of H2B-Ub from nucleosome to higher-order chromatin structure. We then assess what is currently known of the role of H2B-Ub in heterochromatic silencing in budding and fission yeasts (S. cerevisiae and S. pombe), which have distinct silencing mechanisms. In budding yeast, the SIR complex initiates heterochromatin assembly with the aid of a H2B-Ub deubiquitinase, Ubp10...
February 20, 2018: Current Genetics
https://www.readbyqxmd.com/read/29458562/the-fission-yeast-schizosaccharomyces-pombe-mtf2-is-required-for-mitochondrial-cox1-gene-expression
#14
Jinyu Liu, Yan Li, Jie Chen, Yirong Wang, Mengting Zou, Ruyue Su, Ying Huang
Mitochondrial gene expression is essential for adenosine triphosphate synthesis via oxidative phosphorylation, which is the universal energy currency of cells. Here, we report the identification and characterization of a homologue of Saccharomyces cerevisiae Mtf2 (also called Nam1) in Schizosaccharomyces pombe. The Δmtf2 mutant with the intron-containing mitochondrial DNA (mtDNA) exhibited impaired growth on a rich medium containing the non-fermentable carbon source glycerol, suggesting that mtf2 is involved in mitochondrial function...
March 2018: Microbiology
https://www.readbyqxmd.com/read/29432178/general-amino-acid-control-in-fission-yeast-is-regulated-by-a-nonconserved-transcription-factor-with-functions-analogous-to-gcn4-atf4
#15
Caia D S Duncan, María Rodríguez-López, Phil Ruis, Jürg Bähler, Juan Mata
Eukaryotes respond to amino acid starvation by enhancing the translation of mRNAs encoding b-ZIP family transcription factors ( GCN4 in Saccharomyces cerevisiae and ATF4 in mammals), which launch transcriptional programs to counter this stress. This pathway involves phosphorylation of the eIF2 translation factor by Gcn2-protein kinases and is regulated by upstream ORFs (uORFs) in the GCN4 / ATF4 5' leaders. Here, we present evidence that the transcription factors that mediate this response are not evolutionarily conserved...
February 20, 2018: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/29423861/schizosaccharomyces-pombe-isolation-protocol
#16
Ángel Benito, Fernando Calderón, Santiago Benito
This chapter describes a methodology to isolate yeast strains from Schizosaccharomyces pombe species. The method is based on a selective-differential medium that notably facilitates the isolation of S. pombe. The main difficulty in isolating microorganisms from this genus is their extremely low incidence in nature when they are compared to other microorganisms. The proposed methodology allows isolating and selecting strains from this species for industrial purposes. Methodologies allows detecting the presence of those yeasts when they are considered spoilage microorganisms...
2018: Methods in Molecular Biology
https://www.readbyqxmd.com/read/29423860/schizosaccharomyces-pombe-biotechnological-applications-in-winemaking
#17
Ángel Benito, Fernando Calderón, Santiago Benito
The traditional way of producing wine is through the use of Saccharomyces cerevisiae in order to convert glucose and fructose into alcohol. In the case of red wines, after this alcoholic fermentation lactic bacteria Oenococus oeni is used to stabilize wine from a microbiological point of view by converting malic acid into lactic acid that it is not a microbiological substract. The yeast species Schizosaccharomyces pombe was traditionally considered spoilage yeast. Nevertheless, during the last decade it started to be used due to its unique malic acid deacidification ability to reduce the harsh acidity of wines from northern Europe, by converting malic acid to ethanol and CO2 without producing lactic acid as lactic bacteria does...
2018: Methods in Molecular Biology
https://www.readbyqxmd.com/read/29423856/high-frequency-lithium-acetate-transformation-of-schizosaccharomyces-pombe
#18
Sudhir Kumar Rai, Angela Atwood-Moore, Henry L Levin
The introduction of ectopic DNA, such as plasmids, into yeast cells has for decades been a critical protocol for the study of this eukaryotic model system. We describe here an efficient transformation procedure for use in the fission yeast Schizosaccharomyces pombe. This method relies on chemical agents (lithium acetate, and polyethylene glycol) and temperature stresses, which ultimately facilitate transfer of the genetic material through the cell wall and plasma membrane without significant impact on the transferred DNA or the recipient cell...
2018: Methods in Molecular Biology
https://www.readbyqxmd.com/read/29423855/in-situ-chromatin-binding-assay-using-epifluorescent-microscopy-in-s-pombe
#19
Jinpu Yang, Fei Li
Chromatin-associated proteins play critical roles in many cellular processes, including gene expression, epigenetic regulation, DNA repair, recombination, and replication. Especially, epigenetic landscape, shaped by a variety of chromatin-binding proteins, is dynamic and regulated in a context-dependent manner. In situ chromatin-binding assay is a powerful but simple tool to investigate how proteins, such as epigenetic components, associate with chromatin. This approach relies on the fact that chromatin bound proteins are more resistant to detergent extraction...
2018: Methods in Molecular Biology
https://www.readbyqxmd.com/read/29423854/wide-band-electrical-impedance-spectroscopy-eis-measures-s-pombe-cell-growth-in-vivo
#20
Zhen Zhu, Olivier Frey, Andreas Hierlemann
This chapter describes a microfluidic device that enables immobilization and culturing of single rod-shaped S. pombe cells in a stand-up mode. The wide-band electrical impedance spectroscopy (EIS) has been integrated in the microfluidic device to continuously measure cell growth of single S. pombe cells. Cell growth curves showing cellular and intracellular features at high spatiotemporal resolution can be obtained from EIS signals. The features include longitudinal cell elongation in the G2 phase, mitosis, and cell division during an entire cell cycle of S...
2018: Methods in Molecular Biology
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