Unknown,Transcriptomics,Genomics,Proteomics

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Control of Cdc28 CDK1 by a stress-induced lncRNA

ABSTRACT: Genomic analysis has revealed the existence of a large number of long non-coding RNAs (lncRNAs) in a variety of organisms, including yeast. lncRNAs might have several biological functions during normal cell growth and development. Cells are subject to dramatic changes of gene expression in response to environmental changes. Using whole-genome tiling arrays, we found that a set of lncRNAs are induced specifically by the Hog1 stress-activated protein kinase (SAPK) in response to stress. Cdc28 kinase controls the cell cycle in yeast and there is a stress-induced lncRNA in the antisense orientation in CDC28, which permits Hog1 and RSC to induce CDC28 gene expression by remodeling the +1 nucleosome. Increased levels of Cdc28 mediate a more efficient cell cycle re-entry after stress. Therefore, Hog1 mediates changes on the level of Cdc28 protein by induction of a specific lncRNA.

ORGANISM(S): Saccharomyces cerevisiae

SUBMITTER: Chenchen Zhu

PROVIDER: E-MTAB-1686 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Project description:In budding yeast, this signaling pathway— the high-osmolarity glycerol (HOG) response —culminates in dual phosphorylation and nuclear translocation of the MAPK, Hog1 (ortholog of mammalian p38/SAPK). Induction of at least 50 genes requires nuclear Hog1, implying that transcriptional up-regulation is necessary to cope with hyperosmotic stress. Contrary to this expectation, we found that cells lacking the karyopherin (Nmd5) required for Hog1 nuclear import or in which Hog1 was permanently anchored at the plasma membrane(HOG1-CCAAX) (or both) withstood hyperosmotic challenge by three different solutes (1 M sorbitol, KCl or NaCl). In cells where activated Hog1 is excluded from the nucleus, there was little change in transcriptional program after exposure to hyperosmotic shock (comparable to hog1∆ cells), as judged by examining several diagnostic mRNAs and by global transcript measurements using microarrays. Systematic genetic analysis ruled out the need for any transcription factor known to be influenced by Hog1 (Hot1, Msn2, Msn4, Sko1 and Smp1). Keywords: Time course of stress response gene expression array The transcriptomes' of HOG1-GFP, hog1del, and HOG1-CCAAX strains before and after 60 min hyperosmotic shock with 1M sorbitol at 25C were compared. Three biological replicates were done, with the first biological replicate done in technical triplicate, and the final two biological replicates beind done in technical duplicate by in slide duplication of features. Several supplementary files attached to the Series are summarized below: GSE8703 B1, B2, B3 Tscombined_matrix files show the averages of the technical replicates for each biological replicate. GSE8703 B1, B2, B3 norm_to_0_matrix files show the fold change over the time course (log2 time 60 - log2 time 0) for each of the three strains in each biological replicate. GSE8703 Figure_S6 shows the 30 genes with the most significant difference between the HOG1-GFP strain and the hog1del strain as determined by SAM. Genes were identified as: >3 fold induction in HOG1-GFP over 60 minute hyperosmotic shock and <3 fold induction in hog1del over 60 minute hyperosmotic shock.

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Control of Cdc28 CDK1 by a stress-induced lncRNA

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