Browse
Submit Data
Databases
API
Help

Dataset Information

30 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

The translational landscape of fission-yeast meiosis and sporulation.

ABSTRACT: Sexual development in Schizosaccharomyces pombe culminates in meiosis and sporulation. We used ribosome profiling to investigate the translational landscape of this process. We show that the translation efficiency of hundreds of genes is regulated in complex patterns, often correlating with changes in RNA levels. Ribosome-protected fragments show a three-nucleotide periodicity that identifies translated sequences and their reading frame. Using this property, we identified 46 new translated genes and found that 24% of noncoding RNAs are actively translated. We also detected 19 nested antisense genes, in which both DNA strands encode translated mRNAs. Finally, we identified 1,735 translated upstream open reading frames (ORFs) in leader sequences. In S. pombe, in contrast with Saccharomyces cerevisiae, sexual development is not accompanied by large increases in upstream ORF use, thus suggesting that this is an organism-specific adaptation, not a general feature of developmental processes.

SUBMITTER: Duncan CD

PROVIDER: S-EPMC4082408 | biostudies-literature | 2014 Jul

REPOSITORIES: biostudies-literature

ACCESS DATA

Json Xml

Publications

The translational landscape of fission-yeast meiosis and sporulation.

Duncan Caia D S CD Mata Juan J

Nature structural & molecular biology 20140615 7

Sexual development in Schizosaccharomyces pombe culminates in meiosis and sporulation. We used ribosome profiling to investigate the translational landscape of this process. We show that the translation efficiency of hundreds of genes is regulated in complex patterns, often correlating with changes in RNA levels. Ribosome-protected fragments show a three-nucleotide periodicity that identifies translated sequences and their reading frame. Using this property, we identified 46 new translated genes ...[more]

PMID: 24929437

Similar Datasets

The dynamic landscape of fission yeast meiosis alternative-splice isoforms.

Project description:Alternative splicing increases the diversity of transcriptomes and proteomes in metazoans. The extent to which alternative splicing is active and functional in unicellular organisms is less understood. Here, we exploit a single-molecule long-read sequencing technique and develop an open-source software program called SpliceHunter to characterize the transcriptome in the meiosis of fission yeast. We reveal 14,353 alternative splicing events in 17,669 novel isoforms at different stages of meiosis, including antisense and read-through transcripts. Intron retention is the major type of alternative splicing, followed by alternate "intron in exon." Seven hundred seventy novel transcription units are detected; 53 of the predicted proteins show homology in other species and form theoretical stable structures. We report the complexity of alternative splicing along isoforms, including 683 intra-molecularly co-associated intron pairs. We compare the dynamics of novel isoforms based on the number of supporting full-length reads with those of annotated isoforms and explore the translational capacity and quality of novel isoforms. The evaluation of these factors indicates that the majority of novel isoforms are unlikely to be both condition-specific and translatable but consistent with the possibility of biologically functional novel isoforms. Moreover, the co-option of these unusual transcripts into newly born genes seems likely. Together, the results of this study highlight the diversity and dynamics at the isoform level in the sexual development of fission yeast.

| S-EPMC5204338 | biostudies-literature

Transcription profiling of fission yeast meiosis and sporulation

Project description:Fission yeast cells undergo meiosis and sporulation under conditions of nutritional stress, most frequently nitrogen starvation. This is a complex developmental process, which results in the formation of four spores that are highly resistant to environmental stress. We have carried out time course experiments with diploid fission yeast cells undergoing meiosis and sporulation. In this experiment we have used wild type diploids, and induced meiosis by removal of nitrogen from the medium. As a reference we used a pool consisting of equal amount of RNA from all time points of the experiments. This experiment is part of a series, with accession numbers E-SNGR-2 to E-SNGR-7.

2002-08-05 | E-SNGR-3 | biostudies-arrayexpress

Transcription profiling of fission yeast meiosis and sporulation

Project description:Transcriptional profile of fission yeast meiosis and sporulation. Fission yeast cells undergo meiosis and sporulation under conditions of nutritional stress, most frequently nitrogen starvation. This is a complex developmental process, which results in the formation of four spores that are highly resistant to environmental stress. We have carried out time courses of diploid fission yeast cells undergoing meiosis and sporulation. To achieve the best possible synchrony we have used thermosensitive mutants in the meiotic inhibitor pat1. We first pre-synchronized the cells in G1 by removal of nitrogen at the permissive temperature for pat1, and then induced meiosis by inactivating pat1 with a temperature shift. pat1-induced meiosis is a standard technique, resulting in a highly synchronous meiosis that is very similar to the normal process. The use of pat1 mutants and a temperature-shift may cause some artifacts, so these results should be viewed together with temperature shift controls and especially with the results of the time course done with wild type diploids, available under accession numbers E-SNGR-3 to E-SNGR-7. In all cases we used as reference a pool consisting of equal amounts of RNA from all time points of the experiment. This experiment describes the first biological replicate for pat1 using array design A-SNGR-2. Note that there are three other biological replicates, which use array design A-SNGR-1 in experiment E-SNGR-2.

2002-08-05 | E-SNGR-7 | biostudies-arrayexpress

Transcription profiling of fission yeast meiosis and sporulation

Project description:Study of the meiotic transcriptional profile of transcription factor mutants. The transcription factors atf21 and atf31 are highly induced during the meiotic divisions and required for proper spore formation. To identify possible targets of these transcription factors we compared the transcriptional profile of atf21 and atf31 mutants with that of wild type cells undergoing meiosis. We used haploid h90 cells for this experiment. Removal of nitrogen from the medium induces mating to form diploids, which immediately undergo meiosis and sporulation. This type of meiosis is not very synchronous. This experiment is part of a series, E-SNGR-2 to E-SNGR-7.

2002-08-05 | E-SNGR-4 | biostudies-arrayexpress

Transcription profiling of fission yeast meiosis and sporulation

Project description:pat1 meiosis is very synchronous (see E-SNGR-2), but the use of a temperature shift and the prolonged nitrogen starvation can lead to artifacts. As a control for the pat1 experiment,non-sporulating pat1+ diploids were treated exactly as in the protocol for pat1 cells, with the exception that no nitrogen was added at the time of the temperature shift. Under these conditions the cells remain blocked in G1. As a reference we used a pool consisting of equal amount of RNA from all time points of the experiments. This experiment is part of a series, E-SNGR-2 to E-SNGR-7.

2002-08-05 | E-SNGR-6 | biostudies-arrayexpress

Transcription profiling of fission yeast meiosis and sporulation

Project description:pat1 meiosis is very synchronous (see E-SNGR-2), but the use of a temperature shift and the prolonged nitrogen starvation can lead to artifacts. As a control for the E-SNGR-2 experiment, non-sporulating pat1+ diploids were treated exactly as in the protocol for E-SNGR-2 cells. Under these conditions the cells re-enter the mitotic cycle. As a reference we used a pool consisting of equal amount of RNA from all time points of the experiments. This experiment is part of a series, E-SNGR-2 to E-SNGR-7.

2002-08-05 | E-SNGR-5 | biostudies-arrayexpress

Yeast (S. cerevisiae SK1) Sporulation/Meiosis

Project description:Transription profile of Saccharomyces cerevisiae SK1 cultures undergoing synchronous sporulation. We have measured mRNA levels in synchronized SK1 cells immediately upon transfer to the sporulation medium and every 30 minutes after that for 6 hours. mRNA extracted from these cultures were converted to cDNA and hybridized to microarrays and log2 ratios of hybridization signal of each time point was compared to that of time zero (immediately prior to transfer to the sporulation medium). Keywords: Time course

2008-01-16 | GSE8506 | GEO

The dynamic landscape of fission yeast meiosis alternative-splice isoforms

Project description:Alternative splicing increases the diversity of transcriptomes and proteomes in metazoans. The extent to which alternative splicing is active and functional in unicellular organisms is less understood. Here we exploit a single-molecule long-read sequencing technique and develop a computational tool, SpliceHunter, to characterize the transcriptome in the meiosis of fission yeast. We reveal 17017 alternative splicing events in 19741 novel isoforms at different stages of meiosis, including antisense and read-through transcripts. Intron retention is the major type of alternative splicing, followed by “alternate intron in exon”. 887 novel transcription units are detected; 60 of the predicted proteins show homology in other species and form theoretical stable structures. We compare the dynamics of novel isoforms based on the number of supporting full-length reads with those of annotated isoforms and explore the translational capacity and quality of novel isoforms. The evaluation of these factors indicates that the majority of novel isoforms are unlikely to be both condition-specific and translatable but the possibility of functional novel isoforms is not excluded. Together, this study highlights the diversity and dynamics at the isoform level in the sexual development of fission yeast.

2016-11-10 | GSE79802 | GEO

Regulation of wee1(+) expression during meiosis in fission yeast.

Project description:In eukaryotes, the cyclin-dependent kinase Cdk1p (Cdc2p) plays a central role in entry into and progression through nuclear division during mitosis and meiosis. Cdk1p is activated during meiotic nuclear divisions by dephosphorylation of its tyrosine-15 residue. The phosphorylation status of this residue is largely determined by the Wee1p kinase and the Cdc25p phosphatase. In fission yeast, the forkhead-type transcription factor Mei4p is essential for entry into the first meiotic nuclear division. We recently identified cdc25(+) as an essential target of Mei4p in the control of entry into meiosis I. Here, we show that wee1(+) is another important target of Mei4p in the control of entry into meiosis I. Mei4p bound to the upstream region of wee1(+) in vivo and in vitro and inhibited expression of wee1(+), whereas Mei4p positively regulated expression of the adjacent pseudogene. Overexpression of Mei4p inhibited expression of wee1(+) and induced that of the pseudogene. Conversely, deletion of Mei4p did not decrease expression of wee1(+) but inhibited that of the pseudogene. In addition, deletion of Mei4p-binding regions delayed repression of wee1(+) expression as well as induction of expression of the pseudogene. These results suggest that repression of wee1(+) expression is primarily owing to Mei4p-mediated transcriptional interference.

| S-EPMC4612672 | biostudies-literature

Lipid droplets are central organelles for meiosis II progression during yeast sporulation.

Project description:Neutral lipids, predominantly triacylglycerol (TAG) and sterol ester, are stored within the cellular organelles termed lipid droplets (LDs). Although it is believed that the major function of LDs is to supply the cell with energy and membranes, little is known about the cellular events directly involving LDs and their contents. In this study, we provide cytological evidence that LDs form direct contacts with the prospore membrane (PSM) that is synthesized de novo during meiosis II to sequester the dividing nuclei in sporulating yeast. Lipidomic analyses indicate that TAG lipolysis releases free fatty acids at a time that correlates well with meiosis II progression, concomitant with phospholipid remodeling. Mutants lacking TAG or impaired of TAG hydrolysis show spore wall assembly defects, supporting a role for TAG and/or its metabolites in spore wall morphogenesis. Not only does LD integrity influence spore wall assembly, LDs are also essential for other aspects of spore development. Yeast cells lacking LDs are severely defective in PSM growth and organization and display disrupted spindles, producing dead spores or even failing to form spores. Together these results link LD physiology directly to a unique membrane morphogenesis process critical for development.

| S-EPMC5341727 | biostudies-literature

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data