Project description:After finding a QTL hotspot in a fission yeast cross of strains 968xY0036 that was apparently driven by frame shift mutation in swc5 (swc5-fs), we have determined the genome-wide occupancy of the histone variant H2AZ (PhT1). Indeed swc5 has been shown to affect H2AZ occupancy. To test the impact of swc5-fs on H2A.Z deposition, we performed genome-wide chromatin immuno-precipitation of H2A.Z coupled with deep sequencing (ChIP-seq) in the two parental strains (968, Y0036) and in a swc5 deletion strain. We also assed the histone H3 occupancy as a positive control. We generated pht1-myc tagged strains to precipitate H2AZ with Myc antibody. Several negative controls have been performed, in particular pulldowns with the non tagged strains. Results show a reduced H2A.Z occupancy at the +1 histone in both Y0036 and swc5-deletion strains.
Project description:We generated the first recombinant strain library for fission yeast and conducted an RNA-seq based QTL study of the coding, non-coding, and antisense transcriptomes. We cross the lab strain 968 with the lab strain Y0036 to generate segregant. We used RNA-seq for both expression profiling and gentoyping of the segregant and DNA resequencing of the parental strains for variation detection in the whole library.
Project description:Genome wide map of heterochromatin state in fission yeast Schizosaccharomyces pombe via 4 different strains Examination of a single histone modification in 4 different 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, ago1d, mmi1d and dcr1d strains. Overall design: RNA expression profiles of Schizosacccharomyces pombe strains containing deletions were compared to the wild type to generate differences in gene expression.
Project description:Novak1997 - Cell Cycle
Modeling the control of DNA replication in fission yeast.
This model is described in the article:
Modeling the control of DNA replication in fission yeast.
Novak B., Tyson JJ.
Proc. Natl. Acad. Sci. U.S.A. 1997:94(17):9147-52
A central event in the eukaryotic cell cycle is the decision to commence DNA replication (S phase). Strict controls normally operate to prevent repeated rounds of DNA replication without intervening mitoses ("endoreplication") or initiation of mitosis before DNA is fully replicated ("mitotic catastrophe"). Some of the genetic interactions involved in these controls have recently been identified in yeast. From this evidence we propose a molecular mechanism of "Start" control in Schizosaccharomyces pombe. Using established principles of biochemical kinetics, we compare the properties of this model in detail with the observed behavior of various mutant strains of fission yeast: wee1(-) (size control at Start), cdc13Delta and rum1(OP) (endoreplication), and wee1(-) rum1Delta (rapid division cycles of diminishing cell size). We discuss essential features of the mechanism that are responsible for characteristic properties of Start control in fission yeast, to expose our proposal to crucial experimental tests.
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Project description:Investigation of whole genome gene expression level changes in red2∆, compared to the parental wild-type strain. The red2 deletion cells analyzed in this study will be described in Sugiyama and Sugioka-Sugiyama. An mRNA profiling study using total RNA recovered from vegetatively growing wild-type culture of fission yeast and red2 deletion cultures of fission yeast. Each chip measures the expression level of 4.997 genes from S.pombe with fourteen 60-mer probe pairs (PM/MM) per gene, with seven-fold technical redundancy.
Project description:We have used micrococcal nuclease (MNase) digestion followed by deep sequencing in order to obtain a higher-resolution map than previously available of nucleosome positions in the fission yeast, Schizosaccharomyces pombe. Our data confirm an unusually short average nucleosome repeat length, ~152 bp, in fission yeast and that transcriptional start sites (TSSs) are associated with nucleosome-depleted regions (NDRs), ordered nucleosome arrays downstream and less regularly spaced upstream nucleosomes. In addition, we found enrichments for associated function in four of eight groups of genes clustered according to chromatin configurations near TSSs. At replication origins, our data revealed asymmetric localization of Pre-Replication Complex (pre-RC) proteins within large NDRs—a feature that is conserved in fission and budding yeast and is therefore likely to be conserved in other eukaryotic organisms. Examination of nucleosome positioning in Schizosaccharomyces pombe
Project description:We report gene expression profiling in the fission yeast Schizosaccharomyces pombe. We performed high-throughput sequencing of RNA isolated from wild-type, erh1∆, and ccr4∆ strains. We find that many meiotic gene containing degradation sequence DSR are expressed in vegetative erh1∆, while these meiotic mRNAs do not increase in ccr4∆, indicating that Erh1 and Ccr4 target different set of genes during vegetative growth. Overall design: RNA sequencing in wild-type, erh1∆ and ccr4∆ strains. Two biological replicates for erh1∆ and ccr4∆, and one sample for wild-type because we already reported wild-type data previously.
Project description:We report the high-throughput profiling of H3K9me2 in fission yeast Schizosaccharomyces pombe. By obtaining 1-10 ng immunoprecipitated DNA, we generated genome-wide H3K9me2 maps in single deletions of the selected chromatin modulating genes, histone H3 mutants and ccp1Δepe1Δ double mutant in fission yeast. We find that the subtelomeric heterochromatin distribution is highly variable under different genetic perturbations and small heterochromatin islands are formed at clr4 and clr2 loci in ccp1Δepe1Δ. Overall design: Single deletions of the selected chromatin modulating genes, histone H3 mutants and ccp1Δepe1Δ double mutant were examined by anti-H3K9me2 ChIP-seq in fission yeast.