Saccharomyces cerevisiae
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA138995 | ENA |
REPOSITORIES: ENA
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Project description:Background: Recent studies have demonstrated that antisense transcription is pervasive in budding yeasts and is conserved between Saccharomyces cerevisiae and S. paradoxus. While studies have examined antisense transcripts of S. cerevisiae for inverse transcription in stationary phase and stress conditions, there is a lack of comprehensive analysis of the conditional specific evolutionary characteristics of antisense transcription between yeasts. Here we attempt to decipher the evolutionary relationship of antisense transcription of S. cerevisiae and S. paradoxus cultured in mid log, early stationary phase, and heat shock conditions. Results: Massively parallel sequencing of sequence strand-specific cDNA library was performed from RNA isolated from S. cerevisiae and S. paradoxus cells at mid log, stationary phase and heat shock conditions. We performed this analysis using a stringent set of sense ORF transcripts and non-coding antisense transcripts that were expressed in all the three conditions, as well as in both species. We found the divergence of the condition specific anti-sense transcription levels is higher than that in condition specific sense transcription levels, suggesting that antisense transcription played a potential role in adapting to different conditions. Furthermore, 43% of sense-antisense pairs demonstrated inverse transcription in either stationary phase or heat shock conditions relative to the mid log conditions. In addition, a large part of sense-antisense pairs (67%), which demonstrated inverse transcription, were highly conserved between the two species. Our results were also concordant with known functional analyses from previous studies and with the evidence from mechanistic experiments of role of individual genes. Conclusions: This study provides a comprehensive picture of the role of antisense transcription mediating sense transcription in different conditions across yeast species. We can conclude from our findings that antisense regulation could act like an on-off switch on sense regulation in different conditions.
2014-06-09 | GSE58319 | GEO
Project description:Background: Recent studies have demonstrated that antisense transcription is pervasive in budding yeasts and is conserved between Saccharomyces cerevisiae and S. paradoxus. While studies have examined antisense transcripts of S. cerevisiae for inverse transcription in stationary phase and stress conditions, there is a lack of comprehensive analysis of the conditional specific evolutionary characteristics of antisense transcription between yeasts. Here we attempt to decipher the evolutionary relationship of antisense transcription of S. cerevisiae and S. paradoxus cultured in mid log, early stationary phase, and heat shock conditions. Results: Massively parallel sequencing of sequence strand-specific cDNA library was performed from RNA isolated from S. cerevisiae and S. paradoxus cells at mid log, stationary phase and heat shock conditions. We performed this analysis using a stringent set of sense ORF transcripts and non-coding antisense transcripts that were expressed in all the three conditions, as well as in both species. We found the divergence of the condition specific anti-sense transcription levels is higher than that in condition specific sense transcription levels, suggesting that antisense transcription played a potential role in adapting to different conditions. Furthermore, 43% of sense-antisense pairs demonstrated inverse transcription in either stationary phase or heat shock conditions relative to the mid log conditions. In addition, a large part of sense-antisense pairs (67%), which demonstrated inverse transcription, were highly conserved between the two species. Our results were also concordant with known functional analyses from previous studies and with the evidence from mechanistic experiments of role of individual genes. Conclusions: This study provides a comprehensive picture of the role of antisense transcription mediating sense transcription in different conditions across yeast species. We can conclude from our findings that antisense regulation could act like an on-off switch on sense regulation in different conditions. Transcriptomes of two yeast species under mid-log phase, early stationary phase, and after heat shock treatment were generated by Illumina HiSeq 2000 paired-end sequencing
2014-06-09 | E-GEOD-58319 | biostudies-arrayexpress
Project description:To identify yeast proteins associated with Ty1 integrase (IN) that could regulate Ty1 replication, we co-purified IN partners using the tandem chromatin affinity purification procedure after in vivo cross-link (TChAP), which we developed previously (Nguyen et al. 2014). We first identified RNA Pol I and Pol III complexes and also a small subset of additional evolutionary conserved complexes, including PAF1 (Polymerase-Associated Factor 1),FACT (FAcilitates Chromatin Transcription), the proteasome and the CK2 kinase. We next confirmed that CK2 interacts with Ty1 integrase in vivo and repress Ty1 retromobility. We showed that Ty1 IN is a substrate of CK2 in vitro and identified 12 phosphorylated residues. In vivo approaches showed that only part of the protein was phosphorylated in the cells and did not demonstrate any direct evidence between Ty1 IN phosphorylation and retromobility inhibition.
2022-11-17 | PXD027420 | Pride
Project description:Retrotransposon Ty1 integration targets specifically positioned asymmetric nucleosomal DNA segments in tRNA hotspots
| PRJNA150613 | ENA
Project description:Sense Cryptic transcription in histone H3 K36A, K56R and K36AK56R mutant yeast strain compared to wild-type
| PRJNA158263 | ENA
Project description:<p>High throughput RNA Sequencing has revealed that the human genome is widely transcribed. However, the extent of natural antisense transcription, the molecular mechanisms by which natural antisense transcripts (NATs) might affect their cognate sense genes, and the role of NATs in cancer are less well understood. Here, we use strand-specific paired-end RNA sequencing (ssRNASeq) on a cohort of 376 cancer patients covering 9 tissue types to comprehensively characterize the landscape of antisense expression. Our results reveal that greater than 60% of annotated transcripts have measureable antisense expression and the expression of sense and antisense transcript pairs is in general positively correlated. Furthermore, by studying the expression of sense/antisense pairs across tissues we identify lineage-specific, ubiquitous and cancer-specific antisense loci. Our results raise the possibility that NATs participate in the regulation of well-known tumor suppressors and oncogenes. Finally, this study provides a catalogue of cancer related genes with significant antisense transcription (oncoNAT). This resource will allow researchers to investigate the molecular mechanisms of sense/antisense regulation and further advance our understanding of their role in cancer.</p>
| phs000937 | dbGaP
Project description:In this work, we show that under specific conditions, defect in AMP deaminase activity strongly impairs yeast cell growth and we establish that AMP deaminase is required for correct balance between adenylic and guanylic nucleotides. Study of the Amd1p homologs, Yjl070p and Ybr284p, reveals that overexpression of these proteins cannot suppress phenotypes associated to /amd1/ deletion but instead mimic in a wild-type strain a loss of Amd1p function. Data presented combined global transcription analyses to measurements of intracellular nucleotides pools by HPLC. Keywords: yeast strains implied in purines interconversion.
2009-10-30 | GSE9557 | GEO
Project description:This study addresses the effect of mutations related to sense and antisense transcription of Saccharomyces cerevisiae phosphate genes using strand-specific RNAseq. Replacement of the transcriptional terminator of PHO84 by that of CYC1 resulted, unexpectedly, in an increased antisense transcription and a strongly reduced sense transcription of PHO84. Also RNA levels of SPL2 were strongly reduced. Deletion of the PHO84 coding region did not markedly affect the expression of SPL2, suggesting that antisense transcription of PHO84 and not the Pho84 transporter affects the expression of SPL2. Deletion of the two putative binding sites for the transcriptional regulator Ume6 in the SPL2 promoter resulted in a slightly increased level of SPL2 RNA, whereas deletion of the UME6 gene resulted in a decreased level of SPL2 and PHO84 RNA. These results suggests that Ume6 is involved in the regulation of SPL2 by a mechanism different from a simple binding to the putative Ume6 binding sites.
2024-03-06 | GSE226971 | GEO
Project description:H2A.Z marks antisense promoters and has positive effects on antisense transcript levels in budding yeast
| PRJNA235191 | ENA
Project description:Antisense Cryptic transcription in histone H3 K36A, K56R and K36AK56R mutant yeast strain compared to wild-type
| PRJNA158293 | ENA