Dynamic Regulation of Ribosome Biogenesis and Its Role in Early Brain Development

Abstract

Chapter 1, including figures and a substantial amount of text, has been re-used, with or without modifications, from the following previous published works: [1] Ni, C., and Buszczak, M. (2023a). The homeostatic regulation of ribosome biogenesis. Semin Cell Dev Biol 136, 13-26. [2] Ni, C., and Buszczak, M. (2023b). Ribosome biogenesis and function in development and disease. Development 150.Chapter 2, including figures and a substantial amount of text, has been re-used, with or without modifications, from the following previous published work: Ni, C., Schmitz, D.A., Lee, J., Pawłowski, K., Wu, J., and Buszczak, M. (2022). Labeling of heterochronic ribosomes reveals C1ORF109 and SPATA5 control a late step in human ribosome assembly. Cell Reports 38, 110597.Chapter 3, including figures and a substantial amount of text, has been re-used, with or without modifications, from the following previous pre-print work: Chunyang Ni , Leqian Yu, Barbara Vona, Dayea Park, Yulei Wei, Daniel A Schmitz, Yudong Wei, Yi Ding, Masahiro Sakurai, Emily Ballard, Yan Liu, Ashwani Kumar, Chao Xing, Hyung-Goo Kim, Cumhur Ekmekci, Ehsan Ghayoor Karimiani, Shima Imannezhad, Fatemeh Eghbal, Reza Shervin Badv, Eva Maria Christina Schwaibold, Mohammadreza Dehghani, Mohammad Yahya Vahidi Mehrjardi, Zahra Metanat, Hosein Eslamiyeh, Ebtissal Khouj, Saleh Mohammed Nasser Alhajj, Aziza Chedrawi, César Augusto Pinheiro Ferreira Alves, Henry Houlden, Michael Kruer, Fowzan S. Alkuraya, Can Cenik, Reza Maroofian, Jun Wu, and Michael Buszczak (2023) Dynamic ribosome biogenesis shapes early brain development (Submitted).While features of ribosome assembly are shared between species, our understanding of the diversity, complexity, dynamics, and regulation of ribosome production in multicellular organisms remains incomplete. To gain insights into ribosome biogenesis in human cells, we performed a genome wide loss of function screen combined with differential labeling of pre-existing and newly assembled ribosomes. These efforts identified two functionally uncharacterized genes, C1ORF109 and SPATA5. We provide evidence that these factors, together with CINP and SPATA5L1, control a late step of human pre-60S maturation in the cytoplasm. Loss of either C1ORF109 or SPATA5 impairs global protein synthesis. These results raise the possibility that neurodevelopmental disorders associated with recessive SPATA5 mutations are caused by defects in ribosome assembly. Based on these findings, we propose the expanded repertoire of ribosome biogenesis factors likely enables multicellular organisms to regulate ribosome production in different ways in response to different developmental and environmental stimuli. Lineage specific transcriptional programs orchestrate human brain development. Many neural developmental defects, however, are linked to mutations in general regulators of housekeeping genes, such as those encoding ribosome biogenesis and mRNA translation factors, suggesting additional layers of regulation. The molecular and cellular mechanisms by which minor disruptions in global protein synthesis capacity cause neurodevelopmental disorders and when these defects first arise remain unclear. Using cerebral organoids in combination with proteomic analysis, single-cell transcriptome analysis across multiple developmental stages, and single organoid translatome analysis, we discovered a previously unappreciated mechanism linking changes in ribosome levels and the timing of cell fate specification during early brain development. We find ribosome levels decrease during neuroepithelial differentiation, and differentiating cells are particularly vulnerable to defective ribosome biogenesis during this time. Reduced ribosome availability more profoundly impacts the translation of specific transcripts, disrupting both survival and cell fate commitment of transitioning neuroepithelia. Enhancing global protein synthesis ameliorates the growth and developmental defects associated with microcephaly linked variants. Together, these findings reveal that dynamic changes in ribosome levels regulate early development of central nervous system and provide insights into how disruptions in protein synthesis machinery can result in brain-specific malformations