Differential regulation of mRNA stability modulates transcriptional memory and facilitates environmental adaptation

Bingnan Li, Patrice Zeis, Yujie Zhang, Alisa Alekseenko, Eliska Fürst, Yerma Pareja Sanchez, Gen Lin, Manu M. Tekkedil, Ilaria Piazza, Lars M. Steinmetz and Vicent Pelechano ()
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Bingnan Li: Shandong University
Patrice Zeis: Genome Biology Unit
Yujie Zhang: Karolinska Institutet
Alisa Alekseenko: Karolinska Institutet
Eliska Fürst: Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC Berlin)
Yerma Pareja Sanchez: Karolinska Institutet
Gen Lin: Genome Biology Unit
Manu M. Tekkedil: Genome Biology Unit
Ilaria Piazza: Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC Berlin)
Lars M. Steinmetz: Genome Biology Unit
Vicent Pelechano: Karolinska Institutet

Nature Communications, 2023, vol. 14, issue 1, 1-17

Abstract: Abstract Transcriptional memory, by which cells respond faster to repeated stimuli, is key for cellular adaptation and organism survival. Chromatin organization has been shown to play a role in the faster response of primed cells. However, the contribution of post-transcriptional regulation is not yet explored. Here we perform a genome-wide screen to identify novel factors modulating transcriptional memory in S. cerevisiae in response to galactose. We find that depletion of the nuclear RNA exosome increases GAL1 expression in primed cells. Our work shows that gene-specific differences in intrinsic nuclear surveillance factor association can enhance both gene induction and repression in primed cells. Finally, we show that primed cells present altered levels of RNA degradation machinery and that both nuclear and cytoplasmic mRNA decay modulate transcriptional memory. Our results demonstrate that mRNA post-transcriptional regulation, and not only transcription regulation, should be considered when investigating gene expression memory.

Date: 2023
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DOI: 10.1038/s41467-023-36586-x

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