How to get the most from fission yeast genome data: a report from the 2006 European Fission Yeast Meeting computing workshop

Yeast ◽  
2006 ◽  
Vol 23 (13) ◽  
pp. 905-912 ◽  
Author(s):  
Valerie Wood
Keyword(s):  
Fission Yeast ◽  
Yeast Genome ◽  
Genome Data

scholarly journals Website Review: How to Get the Best From Fission Yeast Genome Data

2002 ◽  
Vol 3 (3) ◽  
pp. 282-288 ◽  
Author(s):  
Valerie Wood ◽  
Jürg Bähler
Keyword(s):  
Functional Genomics ◽  
Schizosaccharomyces Pombe ◽  
Fission Yeast ◽  
Model Organism ◽  
Research Community ◽  
Yeast Genome ◽  
Biological Databases ◽  
Genome Data ◽  
Internet Resources ◽  
Continuous Feedback

Researchers are increasingly depending on various centralized resources to access the vast amount of information reported in the literature and generated by systematic sequencing and functional genomics projects. Biological databases have become everyday working tools for many researchers. This dependency goes both ways in that the databases require continuous feedback from the research community to maintain accurate, reliable, and upto- date information. The fission yeastSchizosaccharomyces pombehas recently been sequenced, setting the stage for the post-genome era of this popular model organism. Here, we provide an overview of relevant databases available, or being developed, together with a compilation of Internet resources containing useful information and tools for fission yeast.

scholarly journals Phosphorylation of Arp2 is not essential for Arp2/3 complex activity in fission yeast

2018 ◽  
Vol 1 (5) ◽  
pp. e201800202 ◽  
Author(s):  
Alexander E Epstein ◽  
Sofia Espinoza-Sanchez ◽  
Thomas D Pollard
Keyword(s):  
Mass Spectrometry ◽  
Amino Acids ◽  
Fission Yeast ◽  
Aspartic Acid ◽  
Actin Filaments ◽  
Yeast Genome ◽  
Complex Activity ◽  
Actin Patch

LeClaire et al presented evidence that phosphorylation of three sites on the Arp2 subunit activates the Arp2/3 complex to nucleate actin filaments. We mutated the homologous residues of Arp2 (Y198, T233, and T234) in the fission yeast genome to amino acids that preclude or mimic phosphorylation. Arp2/3 complex is essential for the viability of fission yeast, yet strains unable to phosphorylate these sites grew normally. Y198F/T233A/T234A Arp2 was only nonfunctional if GFP-tagged, as observed by LeClaire et al in Drosophila cells. Replacing both T233 and T234 with aspartic acid was lethal, suggesting that phosphorylation might be inhibitory. Nevertheless, blocking phosphorylation at these sites had the same effect as mimicking it: slowing assembly of endocytic actin patches. Mass spectrometry revealed phosphorylation at a fourth conserved Arp2 residue, Y218, but both blocking and mimicking phosphorylation of Y218 only slowed actin patch assembly slightly. Therefore, phosphorylation of Y198, T233, T234, and Y218 is not required for the activity of fission yeast Arp2/3 complex.

scholarly journals G-rich telomeric and ribosomal DNA sequences from the fission yeast genome form stable G-quadruplex DNA structuresin vitroand are unwound by the Pfh1 DNA helicase

2016 ◽  
Vol 44 (13) ◽  
pp. 6213-6231 ◽  
Author(s):  
Marcus Wallgren ◽  
Jani B. Mohammad ◽  
Kok-Phen Yan ◽  
Parham Pourbozorgi-Langroudi ◽  
Mahsa Ebrahimi ◽  
...  
Keyword(s):  
Fission Yeast ◽  
Ribosomal Dna ◽  
Dna Sequences ◽  
Dna Helicase ◽  
Yeast Genome ◽  
Quadruplex Dna ◽  
G Quadruplex

scholarly journals Chromosome domain architecture and dynamic organization of the fission yeast genome

FEBS Letters ◽  
2015 ◽  
Vol 589 (20PartA) ◽  
pp. 2975-2986 ◽  
Author(s):  
Takeshi Mizuguchi ◽  
Jemima Barrowman ◽  
Shiv I.S. Grewal
Keyword(s):  
Fission Yeast ◽  
Domain Architecture ◽  
Yeast Genome ◽  
Dynamic Organization

scholarly journals Phosphorylation of Arp2 is not essential for Arp2/3 complex activity in fission yeast

2018 ◽  
Author(s):  
Alexander E. Epstein ◽  
Sofia Espinoza-Sanchez ◽  
Thomas D. Pollard
Keyword(s):  
Mass Spectrometry ◽  
Amino Acids ◽  
Fission Yeast ◽  
Aspartic Acid ◽  
Actin Filaments ◽  
Yeast Genome ◽  
Complex Activity ◽  
Actin Patch

AbstractLeClaire et al. presented evidence that phosphorylation of three sites on the Arp2 subunit activates Arp2/3 complex to nucleate actin filaments. We mutated the homologous residues of Arp2 (Y198, T233 and T234) in the fission yeast genome to amino acids that preclude or mimic phosphorylation. Arp2/3 complex is essential for the viability of fission yeast, yet strains unable to phosphorylate these sites grew normally. Y198F/T233A/T234A Arp2 was only nonfunctional if GFP-tagged, as observed by LeClaire et al. in Drosophila cells. Replacing both T233 and T234 with aspartic acid was lethal, suggesting that phosphorylation might be inhibitory. Nevertheless, blocking phosphorylation at these sites had the same effect as mimicking it: slowing assembly of endocytic actin patches. Mass spectrometry revealed phosphorylation at a fourth conserved Arp2 residue, Y218, but both blocking and mimicking phosphorylation of Y218 only slowed actin patch assembly slightly. Therefore, phosphorylation of Y198, T233, T234 and Y218 is not required for the activity of fission yeast Arp2/3 complex.SummaryPrevious research concluded that phosphorylation at three sites on Arp2 is necessary to activate Arp2/3 complex. Epstein et al. make genomic substitutions blocking or mimicking phosphorylation to demonstrate that phosphorylation of these three sites does not regulate Arp2/3 complex in fission yeast.

Comprehensive analysis of heterochromatin- and RNAi-mediated epigenetic control of the fission yeast genome

2005 ◽  
Vol 37 (8) ◽  
pp. 809-819 ◽  
Author(s):  
Hugh P Cam ◽  
Tomoyasu Sugiyama ◽  
Ee Sin Chen ◽  
Xi Chen ◽  
Peter C FitzGerald ◽  
...  
Keyword(s):  
Fission Yeast ◽  
Comprehensive Analysis ◽  
Yeast Genome ◽  
Epigenetic Control

scholarly journals lncRNA transcription induces meiotic recombination through chromatin remodelling in fission yeast

2021 ◽  
Vol 4 (1) ◽  
Author(s):  
Satoshi Senmatsu ◽  
Ryuta Asada ◽  
Arisa Oda ◽  
Charles S. Hoffman ◽  
Kunihiro Ohta ◽  
...  
Keyword(s):  
Fission Yeast ◽  
Chromatin Remodeling ◽  
Meiotic Recombination ◽  
Consensus Sequence ◽  
Metabolic Stress ◽  
Strand Break ◽  
Upstream Region ◽  
Yeast Genome ◽  
Regulation Of Transcription ◽  
Dependent Manner

AbstractNoncoding RNAs (ncRNAs) are involved in various biological processes, including gene expression, development, and disease. Here, we identify a novel consensus sequence of a cis-element involved in long ncRNA (lncRNA) transcription and demonstrate that lncRNA transcription from this cis-element activates meiotic recombination via chromatin remodeling. In the fission yeast fbp1 gene, glucose starvation induces a series of promoter-associated lncRNAs, referred to as metabolic-stress-induced lncRNAs (mlonRNAs), which contribute to chromatin remodeling and fbp1 activation. Translocation of the cis-element required for mlonRNA into a well-characterized meiotic recombination hotspot, ade6-M26, further stimulates transcription and meiotic recombination via local chromatin remodeling. The consensus sequence of this cis-element (mlon-box) overlaps with meiotic recombination sites in the fission yeast genome. At one such site, the SPBC24C6.09c upstream region, meiotic double-strand break (DSB) formation is induced in an mlon-box-dependent manner. Therefore, mlonRNA transcription plays a universal role in chromatin remodeling and the regulation of transcription and recombination.

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