Project ID CM-HD2024_56


Co Supervisor 1A Institute of Psychiatry, Psychology & Neuroscience, School of Neuroscience, Centre for Developmental NeurobiologyWebsite

Co Supervisor 1B Faculty of Life Sciences & Medicine, School of Basic & Medical Biosciences, Department of Medical & Molecular GeneticsWebsite

Regulation of neural stem cell quiescence by ribosomal activity

Neural stem cells (NSCs) are self-renewing multipotent progenitors that generate various cell types in the central nervous system (CNS). It is crucial to understand how NSCs regulate proliferation as this controls development, maintenance, and repair of the CNS, as well as learning, memory and mood.
Stem cells pause divisions by entering a state called quiescence, reversible cell-cycle arrest accompanied by diminished biosynthetic activity. Quiescence protects cells against environmental insults, replicative exhaustion, and proliferation-induced mutations. Cancer stem cells also undergo quiescence, which renders them refractory to therapies. Mechanisms governing quiescence are therefore of great biological and clinical interest but only partially understood.
We recently found that quiescent NSCs display nuclear biasing of many mRNAs relative to active NSCs, as well as smaller-scale cytoplasmic biasing of others. Nuclear or cytoplasmic biasing of mRNA was associated with decreased or increased protein synthesis (>80% cases), as determined by proteomics, leading to uncoupling between the transcriptome and proteome in quiescence (Fig. 1).
Here, we further exploit our expertise in NSCs, RNA biology and genome-scale technologies to investigate how gene expression is regulated in the transition between quiescent and active NSCs at the level of mRNA nuclear export and translation to understand how this contributes to reversible alterations in stem cell behaviour.
Aim 1: To determine which transcripts are being actively translated in quiescent versus active NSCs (mouse hippocampal NSC cultures, polysome fractionation, RNA-seq, bioinformatics)
Aim 2: To determine if ribosome composition changes in quiescent versus active NSCs (mouse hippocampal NSC cultures, polysome fractionation, RNA-seq, RNA modification profiling, bioinformatics, proteomics).
Aim 3: To validate mechanisms of regulation for the model produced in Aims 1 and 2 (gene perturbations in mouse NSCs and Drosophila in vivo, stainings, microscopy, image analyses).

Representative Publications

Rossi A, Coum A, Madelenat M, Harris L, Miedzik A, Strohbuecker S, Chai A, Fiaz H, Chaouni R, Grey W, Bonnet D, Hamid F, Makeyev EV, Faull P, Snijders AP, Kelly G, Guillemot F, Sousa-Nunes R Cellular quiescence uncouples the proteome from the transcriptome, bioRxiv DOI: https//doi.org10.1101/2021.01.06.425462v2 (in revision). Shaw RE, Kottler, B, Ludlow ZN, Buhl E, Kim S, Morais da Silva S, Miedzik A, Coum A, Hodge JJL, Hirth F, Sousa-Nunes R (2018) In vivo expansion of functionally integrated GABAergic interneurons by targeted increase of neural progenitors. EMBO J 37:e98163. DOI: 10.15252/embj.201798163 Sousa-Nunes R, Yee LL, Gould AP (2011) Fat cells reactivate quiescent neuroblasts via TOR and glial Insulin relays in Drosophila. Nature 471(7339):508-12. DOI: 10.1038/nature09867
Rodriguez-Algarra F, Seaborne RAE, Danson AF, Yildizoglu S, Yoshikawa H, Law PP, Ahmad Z, Maudsley VA, Brew A, Holmes N, Ochoa M, Hodgkinson A, Marzi SJ, Pradeepa MM, Loose M, Holland ML*, Rakyan VK* (2022) Genome Biol. 23:54 Genetic variation at mouse and human ribosomal DNA influences associated epigenetic states. DOI: 10.1186/s13059-022-02617-x Danson AF, Marzi SJ, Lowe R, Holland ML*, Rakyan VK* (2018) BMC Biology 16:51 Early life diet conditions the molecular response to post-weaning protein restriction in mice. DOI: 10.1186/s12915-018-0516-5 *Holland ML, Lowe R, Caton PW, Gemma C, Carbajosa G, Danson AF, Carpenter AA, Loche E, Ozanne SE, *Rakyan VK (2016) Science 353:495 Early-life nutrition modulates the epigenetic state of specific rDNA genetic variants in mice. DOI: 10.1126/science.aaf7040