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Genetic and Environmental Determinants of Multicellular-like Phenotype Formation in Fission Yeast

ABSTRACT: MLP formation in S. pombe

PROVIDER: PRJEB69522 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	ERR12366424_1.fastq.gz	Fastqsanger.gz
	ERR12366424_2.fastq.gz	Fastqsanger.gz
	ERR12366425_1.fastq.gz	Fastqsanger.gz
	ERR12366425_2.fastq.gz	Fastqsanger.gz
	ERR12366426_1.fastq.gz	Fastqsanger.gz

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The fission yeast Schizosaccharomyces pombe

Project description:The fission yeast Schizosaccharomyces pombe

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A conserved membrane curvature-generating protein is crucial for autophagosome formation in fission yeast

Project description:Organelles are shaped by curvature-generating proteins, which include the reticulons and REEPs that are involved in forming the endoplasmic reticulum (ER). A conserved REEP subfamily differs from the ER-shaping REEPs in abundance and membrane topology and has unidentified functions. Here, we show that Rop1, the single member of this family in the fission yeast Schizosacharomyces pombe, is crucial for the macroautophagy of organelles and cytosolic proteins. Rop1 is needed for the formation of phagophores, cup-like structures consisting of two closely apposed membrane sheets that encapsulate cargo. It is recruited at early stages to phagophores and is required for their maturation into autophagosomes. Rop1 function relies on its ability to generate high membrane curvature and on its colocalization with the autophagy component Atg2 that is thought to reside at the phagophore rim. We propose that Rop1 facilitates the formation and growth of the double-membrane structure of the autophagosome.

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FYPO: the fission yeast phenotype ontology.

Project description:MotivationTo provide consistent computable descriptions of phenotype data, PomBase is developing a formal ontology of phenotypes observed in fission yeast.ResultsThe fission yeast phenotype ontology (FYPO) is a modular ontology that uses several existing ontologies from the open biological and biomedical ontologies (OBO) collection as building blocks, including the phenotypic quality ontology PATO, the Gene Ontology and Chemical Entities of Biological Interest. Modular ontology development facilitates partially automated effective organization of detailed phenotype descriptions with complex relationships to each other and to underlying biological phenomena. As a result, FYPO supports sophisticated querying, computational analysis and comparison between different experiments and even between species.AvailabilityFYPO releases are available from the Subversion repository at the PomBase SourceForge project page (https://sourceforge.net/p/pombase/code/HEAD/tree/phenotype_ontology/). The current version of FYPO is also available on the OBO Foundry Web site (http://obofoundry.org/).

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RNAi mediates post-transcriptional repression of gene expression in fission yeast Schizosaccharomyces pombe [Affymetrix]

Project description:RNA interference (RNAi) is a gene silencing mechanism conserved from fungi to mammals. Small interfering RNAs are products and mediators of the RNAi pathway and act as specificity factors in recruiting effector complexes. The Schizosaccharomyces pombe genome encodes one of each of the core RNAi proteins, Dicer, Argonaute and RNA-dependent RNA polymerase (dcr1, ago1, rdp1). Even though the function of RNAi in heterochromatin assembly in S. pombe is established, its role in controlling gene expression is elusive. Here, we report the identification of small RNAs mapped anti-sense to protein coding genes in fission yeast. We demonstrate that these genes are up-regulated at the protein level in RNAi mutants, while their mRNA levels are not significantly changed. We show that the repression by RNAi is not a result of heterochromatin formation. Thus, we conclude that RNAi is involved in post-transcriptional gene silencing in S. pombe.

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Expression profilings of fission yeast strains

Project description:We report gene expression profiling in the fission yeast Schizosaccharomyces pombe. We performed high-throughput sequencing of RNA isolated from wild-type, mmi1(W112A) mutant, erh1∆, and mmi1∆ strains. We find that mmi1(W112A) and erh1∆ derepress a shared subset of mmi1-repressed genes during vegetative growth.

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Regulation of transcriptome, translation, and proteome in response to environmental stress in fission yeast

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Highly condensed chromatins are formed adjacent to subtelomeric and decondensed silent chromatin in fission yeast

Project description:It is generally believed that silent chromatin is condensed and transcriptionally active chromatin is decondensed. However, little is known about the relationship between condensation levels and gene expression. Here we report condensation levels of interphase chromatin in the fission yeast Schizosaccharomyces pombe examined by super-resolution fluorescence microscopy. Unexpectedly, silent chromatin was observed to be less condensed than the euchromatin. Furthermore, the telomeric silent regions were flanked by highly condensed chromatin bodies, or “knobs”. Knob regions span approximately 50 kb of sequence devoid of methylated histones. Knob condensation was independent of HP1 homolog Swi6 and other gene silencing factors. Disruption of methylation at lysine 36 of histone H3 (H3K36) eliminated knob formation and gene repression at the subtelomeric and adjacent knob regions. Thus, epigenetic marks atH3K36 play crucial roles in the formation of a unique chromatin structure and in gene regulation at those regions in S. pombe.

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Project description:RNA-seq analysis compares gene expression of the STF6 (asp1-W386*), STF9 (asp1-W493*), kcs1-R332T, kcs1-L338R, and kcs1-E834K mutants to the wild-type fission yeast (Schizosaccharomyces pombe).

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RNAi mediates post-transcriptional repression of gene expression in fission yeast Schizosaccharomyces pombe [Illumina Genome Analyzer]

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Genome wide map of H3K9me2 in fission yeast Schizosaccharomyces pombe.

Project description:Genome wide map of H3K9me2 in 4 different strains of fission yeast Schizosaccharomyces pombe.

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