# Cellular quiescence uncouples the proteome from the transcriptome in neural stem cells

## TL;DR

Quiescent neural stem cells retain mRNAs in the nucleus, causing a mismatch between RNA and protein levels, which helps protect the cells.

## Contribution

Discovery of a conserved mechanism in quiescent neural stem cells where mRNAs are retained in the nucleus to repress translation.

## Key findings

- Quiescence causes transcripts from over 2000 genes to accumulate in the nucleus, leading to protein downregulation.
- GA-rich mRNAs relocalize to nuclear speckles enriched with SR-proteins, promoting their retention and translational repression.
- The mechanism is conserved from Drosophila to mammals and distinct from TOR-dependent translational repression.

## Abstract

Quiescence is a cellular state defined by reversible cell-cycle arrest and diminished biosynthesis, particularly of nucleic acids and proteins. These features protect stem cells from proliferation-induced mutations, self-renewal exhaustion, and environmental insults. Despite relevance to development, tissue homeostasis and cancer, we lack understanding about many aspects of quiescence regulation and unique molecular markers for this state. Here, we employ Drosophila and mammalian neural stem cells to reveal that a mechanism for inhibiting translation in quiescence is selective nuclear enrichment of transcripts from more than 2000 genes, resulting in uncoupling between transcriptome and proteome. Three-quarters of these transcripts become increasingly nuclear as quiescence deepens, and nuclear bias predicts protein downregulation for the large majority of targets. We find that a large fraction of nuclear-biased transcripts present GA-rich multivalency and relocalise to nuclear speckles with increased SR-protein enrichment, which we propose promotes their nuclear retention. Finally, our evidence for differing degrees of transcript processing in steady-state quiescence suggests regulated sequential deployment of factors towards cell-cycle reentry. In brief, we present a previously unappreciated layer of post-transcriptional control of quiescence.

Quiescent neural stem cells inhibit protein synthesis by selectively retaining many mRNAs in the nucleus. GA-rich multivalent transcripts accumulate in SR-protein–enriched nuclear speckles as quiescence deepens, reducing their cytoplasmic translation and producing a marked uncoupling of transcriptome and proteome.

Quiescence induces significant nucleocytoplasmic bias changes in transcripts from >2,000 genes, with ~75% becoming increasingly nuclear as NSCs enter deeper quiescence.Nuclear or cytoplasmic mRNA bias predicts protein down- or up-regulation with >80% concordance, explaining transcriptome–proteome uncoupling in qNSCs.Nuclear-biased mRNAs are specifically enriched for GA-rich multivalency and relocalise to SSRM2-positive nuclear speckles.Speckles in qNSCs show increased SR-protein signal, and GA-multivalent transcripts (e.g., EIF3A, MAP1B) preferentially accumulate there.The pathway is conserved from Drosophila to mammals and is distinct from TOR-dependent translational repression.

Quiescence induces significant nucleocytoplasmic bias changes in transcripts from >2,000 genes, with ~75% becoming increasingly nuclear as NSCs enter deeper quiescence.

Nuclear or cytoplasmic mRNA bias predicts protein down- or up-regulation with >80% concordance, explaining transcriptome–proteome uncoupling in qNSCs.

Nuclear-biased mRNAs are specifically enriched for GA-rich multivalency and relocalise to SSRM2-positive nuclear speckles.

Speckles in qNSCs show increased SR-protein signal, and GA-multivalent transcripts (e.g., EIF3A, MAP1B) preferentially accumulate there.

The pathway is conserved from Drosophila to mammals and is distinct from TOR-dependent translational repression.

GA-rich multivalent mRNAs accumulate in nuclear speckles to repress translation during NSC quiescence, a pathway conserved from Drosophila to mammals.