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

  1. García-Martínez, J. 1
  2. Delgado-Ramos, L. 5
  3. Ayala, G. 1
  4. Pelechano, V. 4
  5. Medina, Daniel A. 1
  6. Carrasco, F. 1
  7. González, R. 6
  8. Andrés-León, E. 5
  9. Steinmetz, L. 478
  10. Warringer, J. 3
  11. Chávez, S. 5
  12. Pérez-Ortín, J.E. 1
  1. 1 Universitat de València
    info

    Universitat de València

    Valencia, España

    ROR https://ror.org/043nxc105

  2. 2 Universidad de Sevilla
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    Universidad de Sevilla

    Sevilla, España

    ROR https://ror.org/03yxnpp24

  3. 3 University of Gothenburg
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    University of Gothenburg

    Gotemburgo, Suecia

    ROR https://ror.org/01tm6cn81

  4. 4 European Molecular Biology Laboratory (EMBL), Genome Biology Unit, Meyerhofstrasse 1, Heidelberg, Germany
  5. 5 Instituto de Biomedicina de Sevilla
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    Instituto de Biomedicina de Sevilla

    Sevilla, España

    ROR https://ror.org/031zwx660

  6. 6 Instituto de Ciencias de la Vid y del Vino
    info

    Instituto de Ciencias de la Vid y del Vino

    Logroño, España

    ROR https://ror.org/01rm2sw78

  7. 7 Stanford Genome Technology Center, 3165 Porter Dr., Palo Alto, CA, United States
  8. 8 Stanford University
    info

    Stanford University

    Stanford, Estados Unidos

    ROR https://ror.org/00f54p054

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Revista:
Nucleic Acids Research

ISSN: 0305-1048

Año de publicación: 2016

Volumen: 44

Número: 8

Páginas: 3643-3658

Tipo: Artículo

DOI: 10.1093/NAR/GKV1512 SCOPUS: 2-s2.0-84966359514 WoS: WOS:000376389000023 GOOGLE SCHOLAR

Otras publicaciones en: Nucleic Acids Research

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Resumen

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 growth. In contrast, mitochondria-related and stress-induced genes lowered mRNA levels by reducing mRNA stability or the transcription rate, respectively. We also detected these regulations within the heterogeneity of a wild-type cell population growing in optimal conditions. The transcriptomic analysis of sorted microcolonies confirmed that the growth rate dictates alternative expression programs by modulating transcription and mRNA decay. The regulation of overall mRNA turnover keeps a constant ratio between mRNA decay and the dilution of [mRNA] caused by cellular growth. This regulation minimizes the indiscriminate transmission of mRNAs from mother to daughter cells, and favors the response capacity of the latter to physiological signals and environmental changes. We also conclude that, by uncoupling mRNA synthesis from decay, cells control the mRNA abundance of those gene regulons that characterize fast and slow growth. © The Author(s) 2015. Published by Oxford University Press on behalf of Nucleic Acids Research.