Coupled evolution of transcription and mRNA degradation.
Ontology highlight
ABSTRACT:
ORGANISM(S): Saccharomyces cerevisiae Saccharomyces cerevisiae x Saccharomyces paradoxus Saccharomyces paradoxus
PROVIDER: GSE28849 | GEO | 2011/08/01
SECONDARY ACCESSION(S): PRJNA140675
REPOSITORIES: GEO
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Project description:The rates of mRNA synthesis and degradation determine cellular mRNA levels and can be monitored by comparative Dynamic Transcriptome Analysis (cDTA) that uses non-perturbing metabolic RNA labeling. Here we present cDTA data for 46 yeast strains lacking genes involved in mRNA degradation and metabolism. In these strains, changes in mRNA degradation rates are generally compensated by changes in mRNA synthesis rates, resulting in a buffering of mRNA levels. We show that buffering of mRNA levels requires the RNA exonuclease Xrn1. The buffering is rapidly established when mRNA synthesis is impaired, but is delayed when mRNA degradation is impaired, apparently due to Xrn1-dependent transcription repressor induction. Cluster analysis of the data defines the general mRNA degradation machinery, reveals different substrate preferences for the two mRNA deadenylase complexes Ccr4-Not and Pan2-Pan3, and unveils an interwoven cellular mRNA surveillance network. For this purpose, cDTA was carried out as described in Sun et.al. Genome Res. 2012 (DOI:10.1101/gr.130161.111). S. cerevisiae cultures were grown at 30¡ãC in 50 ml aliquots of YPD medium. S. pombe cultures were grown at 32¡ãC in YES medium. For inhibitor perturbation, BY4741 cells (OD600=0.1) were inoculated from a saturated overnight culture in two 100 ml aliquots of YPD liquid medium, incubated at 30¡ãC and grown to early-log phase (OD600=0.8). Cells were labeled for 6 minutes (sample 0 min). Then cycloheximide was added and cells were labeled for 10 minutes and 60 minutes. Cells were harvested and treated as described in Sun et.al. Genome Res. 2012 (DOI:10.1101/gr.130161.111). 1,10-Phenanthroline was added to the culture to a final concentration of 25 _g/ml as described (Dori-Bachash et al., 2012), and labeled for 6 minutes after 18 minutes treatment. Cells were treated as above. For the anchor-away analysis, S. cerevisiae cells (OD600=0.1) were cultured in two 200 ml aliquots of YPD containing 1_g/ml rapamycin and incubated at 30¡ãC untill OD600 reached 0.8. Due to the instability of rapamycin, we added 1_g/ml rapamycin every two hours. Then a 20 ml sample was taken and labeled with 4sU. The cells were then treated as described in Sun et.al. Genome Res. 2012 (DOI:10.1101/gr.130161.111).
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Project description:Coupled evolution of transcription and mRNA degradation.
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Project description:To comprehend the profile of rice gene expression at reproductive stage under high temperature, Agilent 4x44k rice oligo microarray experiments were carried out using rice panicle of developmental stage 7-9 at 0min, 10min, 20min, 60min, and 2hr after the treatment of 40 degree centigrade, and the significantly expressed genes mainly involved in transcriptional regulation, transport, cellular homeostasis, and stress response were identified. Among them, the predominant transcription factor gene families were Hsf, NAC, AP2/ERF, WRKY, MYB, and C2H2. KMC analysis discovered the time-dependent gene expression pattern under heat. The results of motif co-occurrence on the promoters of genes from an early up-regulated cluster showed the important roles of GCC box, HSE, ABRE, and CE3, and unraveled the possible cross-talk mechanism during heating. The response model central to ROS combined with transcriptome data indicated the great importance to maintain ROS balance in heat response in rice panicle and the wide existing of cross-talks. Heat shock induced gene expression in rice panicle of late developmental stage was measured at 0min, 10min, 20min, 60min, and 2hr after the treatment of 40 degree centigrade in plant growth chamber. Two independent replicate experiments were performed at each time point.
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