title: Comparative dynamic transcriptome analysis (cDTA) reveals mutual feedback between mRNA synthesis and degradation.
abstract: To monitor eukaryotic mRNA metabolism, we developed comparative dynamic transcriptome analysis (cDTA). cDTA provides absolute rates of mRNA synthesis and decay in Saccharomyces cerevisiae (Sc) cells with the use of Schizosaccharomyces pombe (Sp) as an internal standard. cDTA uses nonperturbing metabolic labeling that supersedes conventional methods for mRNA turnover analysis. cDTA reveals that Sc and Sp transcripts that encode orthologous proteins have similar synthesis rates, whereas decay rates are fivefold lower in Sp, resulting in similar mRNA concentrations despite the larger Sp cell volume. cDTA of Sc mutants reveals that a eukaryote can buffer mRNA levels. Impairing transcription with a point mutation in RNA polymerase (Pol) II causes decreased mRNA synthesis rates as expected, but also decreased decay rates. Impairing mRNA degradation by deleting deadenylase subunits of the Ccr4-Not complex causes decreased decay rates as expected, but also decreased synthesis rates. Extended kinetic modeling reveals mutual feedback between mRNA synthesis and degradation that may be achieved by a factor that inhibits synthesis and enhances degradation.
authors.affiliation: Gene Center Munich and Department of Biochemistry, Center for Integrated Protein Science CIPSM, Ludwig-Maximilians-Universität München, Munich, Germany.
authors.forename: Mai
authors.initials: M
authors.lastname: Sun
authors.forename: Björn
authors.initials: B
authors.lastname: Schwalb
authors.forename: Daniel
authors.initials: D
authors.lastname: Schulz
authors.forename: Nicole
authors.initials: N
authors.lastname: Pirkl
authors.forename: Stefanie
authors.initials: S
authors.lastname: Etzold
authors.forename: Laurent
authors.initials: L
authors.lastname: Larivière
authors.forename: Kerstin C
authors.initials: KC
authors.lastname: Maier
authors.forename: Martin
authors.initials: M
authors.lastname: Seizl
authors.forename: Achim
authors.initials: A
authors.lastname: Tresch
authors.forename: Patrick
authors.initials: P
authors.lastname: Cramer
mesh_terms: D002467:Cell Nucleus / Q000235:genetics / Q000378:metabolism; D025461:Feedback, Physiological; D020869:Gene Expression Profiling / Q000379:methods*; D015966:Gene Expression Regulation, Fungal; D016681:Genome, Fungal; D017354:Point Mutation; D020871:RNA Stability; D012331:RNA, Fungal / Q000235:genetics / Q000378:metabolism*; D012333:RNA, Messenger / Q000096:biosynthesis* / Q000235:genetics; D012260:Ribonucleases / Q000235:genetics / Q000378:metabolism; D012441:Saccharomyces cerevisiae / Q000235:genetics* / Q000378:metabolism; D029701:Saccharomyces cerevisiae Proteins / Q000235:genetics / Q000378:metabolism; D012568:Schizosaccharomyces / Q000235:genetics / Q000378:metabolism; D014158:Transcription, Genetic; D059467:Transcriptome
chemical_list: D012331:RNA, Fungal; D012333:RNA, Messenger; D029701:Saccharomyces cerevisiae Proteins; C078657:CCR4 protein, S cerevisiae; D012260:Ribonucleases