Unknown,Transcriptomics,Genomics,Proteomics

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Genomic Run On (GRO): determination of the nascent transcriptional rates in a spt16 mutant


ABSTRACT: We analyzed the effect of SPT16 on the transcription rates, mRNA stabilities and mRNA levels by doing GRO experiments in a thermosensitive spt16 point mutant (G132D) mutant at 35 ºC comparing with permisive temperature (30 ºC) and a wt treated in the same way. Cells (wt or spt16 mutant) were grown in SC-ura at 30 ºC to 0.25 OD600. At that time α factor was added and let to stand for 160 min in the same conditions. Then each sample (wt or mutant) was separated in two aliquots. One of them remain at 30ºC and the other was incubated at 35ºC. Both aliquots in the presence of α factor for 1h more. Finally, samples were processed for GRO experiment as described in Garcia-Marinez et al (2004). Three replicates of the whole experiment were done.

ORGANISM(S): Saccharomyces cerevisiae

SUBMITTER: Jose Perez-Ortin 

PROVIDER: E-GEOD-64006 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Publications

The cellular growth rate controls overall mRNA turnover, and modulates either transcription or degradation rates of particular gene regulons.

García-Martínez José J   Delgado-Ramos Lidia L   Ayala Guillermo G   Pelechano Vicent V   Medina Daniel A DA   Carrasco Fany F   González Ramón R   Andrés-León Eduardo E   Steinmetz Lars L   Warringer Jonas J   Chávez Sebastián S   Pérez-Ortín José E JE  

Nucleic acids research 20151229 8


We analyzed 80 different genomic experiments, and found a positive correlation between both RNA polymerase II transcription and mRNA degradation with growth rates in yeast. Thus, in spite of the marked variation in mRNA turnover, the total mRNA concentration remained approximately constant. Some genes, however, regulated their mRNA concentration by uncoupling mRNA stability from the transcription rate. Ribosome-related genes modulated their transcription rates to increase mRNA levels under fast  ...[more]

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