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Expression profiling of mmi1 delta cells, using tiling microarray in S. pombe

ABSTRACT: We used tiling microarrays to identify up-regulated genes in mmi1 delta cells. Because these cells grow very poorly due to misexpression of mei4 gene, we combined mmi1 delta mutation to a partial deletion of mei4. Cells carrying only mei4 partial deletion were also analyzed in our transcriptomics to verify that variations observed in mmi1 delta cells are not due mei4 mutation.

ORGANISM(S): Schizosaccharomyces pombe

PROVIDER: GSE31119 | GEO | 2012/08/31

SECONDARY ACCESSION(S): PRJNA144665

REPOSITORIES: GEO

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Expression profiling of mmi1 delta cells, using tiling microarray in S. pombe

Project description:We used tiling microarrays to identify up-regulated genes in mmi1 delta cells. Because these cells grow very poorly due to misexpression of mei4 gene, we combined mmi1 delta mutation to a partial deletion of mei4. Cells carrying only mei4 partial deletion were also analyzed in our transcriptomics to verify that variations observed in mmi1 delta cells are not due mei4 mutation. RNA levels from S. pombe cells with only mei4 partial deletion (SPV481) or with mei4 partial deletion in combination with mmi1 delta deletion (SPV903) were compared to wild type cells (SPV8), using Affymetrix S. pombe Tiling 1.0FR microarrays. Two biological replicates were analyzed for each experiment.

2012-08-31 | E-GEOD-31119 | biostudies-arrayexpress

Stability of meiosis-specific messenger RNA provides a novel paradigm for the regulation of meiosis

Project description:Compared to mitosis, much remains to be elucidated about molecular regulation of meiosis, although increasing light has been shed recently on its signal transduction, cell cycle regulation and chromosome dynamics. Here we show that some transcripts required exclusively for meiosis in fission yeast, such as mei4 mRNA encoding a transcription factor or rec8 mRNA encoding a cohesin subunit, are highly unstable if expressed during the mitotic cell cycle. These transcripts carry a cis-acting region responsible for the mitotic instability, which we name DSR. A YTH-family protein encoded by the mmi1 gene is essential for manifestation of their instability. Deletion of mmi1 impairs cell growth severely, apparently due to detriments brought by untimely expression of meiotic messages. Microarray analysis using a temperature-sensitive mmi1 mutant has revealed that at least a dozen of meiosis-specific transcripts are governed by the DSR-mmi1 system. Thus, regulation of mRNA stability appears to play a crucial role in differentiating the mitotic and the meiotic cell cycles. Keywords: Keywards: Time course, Temperature-sensitive mutant, mmi1

2006-07-06 | GSE3314 | GEO

The fission yeast Schizosaccharomyces pombe: H3K9me2, Erh1-GFP and CFP-Mmi1 ChIP-chip

Project description:ChIP-chip analyses of H3K9me2 (in WT, erh1∆, mmi1∆ and ccr4∆), Erh1-GFP (in WT and mmi1∆) and CFP-Mmi1 (in WT)

2016-06-15 | GSE76111 | GEO

Genome-wide data of RNAs associated to Mmi1 in wild type Schizosaccharomyces pombe cells

Project description:Mmi1 is a YTH domain containing protein. We used Solexa Deep Sequencing to identify the mRNas and lncRNAs specifically associated to Mmi1.

2017-07-27 | GSE90688 | GEO

Identification of transcripts simultaneously bound by Mmi1 and Mei2

Project description:We determined the repertoire of transcripts simultaneously bound by Mmi1 and Mei2 through sequential immunoprecipitations followed by high-throughput sequencing of associated RNAs (seqRIP-seq)

2020-12-21 | GSE152383 | GEO

The fission yeast Schizosaccharomyces pombe: H3K9me2, Erh1-GFP and CFP-Mmi1 ChIP-chip

Project description:ChIP-chip analyses of H3K9me2 (in WT, erh1â??, mmi1â?? and ccr4â??), Erh1-GFP (in WT and mmi1â??) and CFP-Mmi1 (in WT) H3K9me2: WT vs erh1â??, WT vs mmi1â?? and WT vs ccr4â??; Erh1-GFP: WT vs mmi1â??; CFP-Mmi1 in WT, Biological replicates: 2

2016-06-15 | E-GEOD-76111 | biostudies-arrayexpress

Identification of transcripts simultaneously bound by Mmi1 and Mei2

Project description:Identification of transcripts simultaneously bound by Mmi1 and Mei2

| PRJNA639146 | ENA

Regulation of mRNA Levels by Suicidal Introns that Induce Nuclear Decay

Project description:In eukaryotic cells, inefficient splicing is surprisingly common and leads to degradation of transcripts with retained introns. How pre-mRNAs are committed to nuclear decay is unknown. Here we uncover a mechanism by which intronic transcripts are targeted for nuclear degradation in fission yeast. Surprisingly, sequence elements within âsuicidalâ introns co-transcriptionally recruit the exosome adaptor Mmi1 not only to degrade unspliced precursor, but also to downregulate levels of the resulting mRNA. Under conditions permissive for fast splicing, Mmi1 is no longer recruited and negative expression regulation is relieved. This mechanism negatively regulates levels of the RNA-helicase DDX5/Dbp2 to ensure cell survival in response to stress. We propose that suicidal introns are maintained because they facilitate regulation of gene expression. We identify multiple novel Mmi1 targets including mRNAs, non-coding RNAs, and sn/snoRNAs. We suggest a general role in RNA regulation for Mmi1 beyond degradation of meiotic transcripts. Two biological replicates of CRAC experiments (Control and Mmi1-HTP). Six RNAseq datasets in total: three biological replicates of wt and delta Mmi1 strain.

2015-11-19 | E-GEOD-73144 | biostudies-arrayexpress

Transcription profiling of Enterococcus faecalis wild type, delta-relA and delta-relAsp (partial deletion) strains

Project description:Two mutants of the relA gene of Enterococcus faecalis were constructed, one (delta-relA) carrying a whole deletion of the gene, the other (delta-relAsp) carrying a partial deletion of its 3' extremity. the 3 strains were cultured to mid exponential growth phase in M17 medium, and RNAs were extracted using the RNeasy Midi Kit (QIAGEN). <br>RNAs were subjected to 2 DNase treatments, and prepared for chips hybridization.

2009-12-29 | E-MEXP-2112 | biostudies-arrayexpress

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.

2019-01-03 | GSE119605 | GEO

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