Transcription Templated Assembly of the Nucleolus in the Embryo

Overview

Journal bioRxiv

Date 2024 Jun 19

PMID 38895351

Authors

Nishant Kodan

Rabeya Hussaini

Stephanie C Weber

Jane Kondev

Lishibanya Mohapatra

Affiliations

Soon will be listed here.

Abstract

The nucleolus is a multicomponent structure made of RNA and proteins that serves as the site of ribosome biogenesis within the nucleus. It has been extensively studied as a prototype of a biomolecular condensate whose assembly is driven by phase separation. While the steady-state size of the nucleolus is quantitatively accounted for by the thermodynamics of phase separation, we show that experimental measurements of the assembly dynamics are inconsistent with a simple model of a phase-separating system relaxing to its equilibrium state. Instead, we show that the dynamics are well described by a model in which the transcription of ribosomal RNA actively drives nucleolar assembly. We find that our model of active transcription-templated assembly quantitatively accounts for the rapid kinetics observed in early embryos at different developmental stages, and for different RNAi perturbations of embryo size. Our model predicts a scaling of the time to assembly with the volume of the nucleus to the one-third power, which is confirmed by experimental data. Our study highlights the role of active processes such as transcription in controlling the placement and timing of assembly of membraneless organelles.

References

Mohapatra L, Lagny T, Harbage D, Jelenkovic P, Kondev J . The Limiting-Pool Mechanism Fails to Control the Size of Multiple Organelles. Cell Syst. 2017; 4(5):559-567.e14. PMC: 5906859. DOI: 10.1016/j.cels.2017.04.011. View

Geles K, Adam S . Germline and developmental roles of the nuclear transport factor importin alpha3 in C. elegans. Development. 2001; 128(10):1817-30. DOI: 10.1242/dev.128.10.1817. View

Lee J, Wang R, Xiong F, Krakowiak J, Liao Z, Nguyen P . Enhancer RNA m6A methylation facilitates transcriptional condensate formation and gene activation. Mol Cell. 2021; 81(16):3368-3385.e9. PMC: 8383322. DOI: 10.1016/j.molcel.2021.07.024. View

Sarov M, Murray J, Schanze K, Pozniakovski A, Niu W, Angermann K . A genome-scale resource for in vivo tag-based protein function exploration in C. elegans. Cell. 2012; 150(4):855-66. PMC: 3979301. DOI: 10.1016/j.cell.2012.08.001. View

Condon C, French S, Squires C, Squires C . Depletion of functional ribosomal RNA operons in Escherichia coli causes increased expression of the remaining intact copies. EMBO J. 1993; 12(11):4305-15. PMC: 413727. DOI: 10.1002/j.1460-2075.1993.tb06115.x. View

Banani S, Rice A, Peeples W, Lin Y, Jain S, Parker R . Compositional Control of Phase-Separated Cellular Bodies. Cell. 2016; 166(3):651-663. PMC: 4967043. DOI: 10.1016/j.cell.2016.06.010. View

Brangwynne C, Eckmann C, Courson D, Rybarska A, Hoege C, Gharakhani J . Germline P granules are liquid droplets that localize by controlled dissolution/condensation. Science. 2009; 324(5935):1729-32. DOI: 10.1126/science.1172046. View

Sulston J, Schierenberg E, White J, Thomson J . The embryonic cell lineage of the nematode Caenorhabditis elegans. Dev Biol. 1983; 100(1):64-119. DOI: 10.1016/0012-1606(83)90201-4. View

Kamath R, Fraser A, Dong Y, Poulin G, Durbin R, Gotta M . Systematic functional analysis of the Caenorhabditis elegans genome using RNAi. Nature. 2003; 421(6920):231-7. DOI: 10.1038/nature01278. View

10.

Hyman A, Weber C, Julicher F . Liquid-liquid phase separation in biology. Annu Rev Cell Dev Biol. 2014; 30:39-58. DOI: 10.1146/annurev-cellbio-100913-013325. View

11.

Schede H, Natarajan P, Chakraborty A, Shrinivas K . A model for organization and regulation of nuclear condensates by gene activity. Nat Commun. 2023; 14(1):4152. PMC: 10338548. DOI: 10.1038/s41467-023-39878-4. View

12.

French S, Osheim Y, Cioci F, Nomura M, Beyer A . In exponentially growing Saccharomyces cerevisiae cells, rRNA synthesis is determined by the summed RNA polymerase I loading rate rather than by the number of active genes. Mol Cell Biol. 2003; 23(5):1558-68. PMC: 151703. DOI: 10.1128/MCB.23.5.1558-1568.2003. View

13.

Wippich F, Bodenmiller B, Gustafsson Trajkovska M, Wanka S, Aebersold R, Pelkmans L . Dual specificity kinase DYRK3 couples stress granule condensation/dissolution to mTORC1 signaling. Cell. 2013; 152(4):791-805. DOI: 10.1016/j.cell.2013.01.033. View

14.

Yuan X, Zhou Y, Casanova E, Chai M, Kiss E, Grone H . Genetic inactivation of the transcription factor TIF-IA leads to nucleolar disruption, cell cycle arrest, and p53-mediated apoptosis. Mol Cell. 2005; 19(1):77-87. DOI: 10.1016/j.molcel.2005.05.023. View

15.

Morton E, Hall A, Cuperus J, Queitsch C . Substantial rDNA copy number reductions alter timing of development and produce variable tissue-specific phenotypes in C. elegans. Genetics. 2023; 224(1). PMC: 10474940. DOI: 10.1093/genetics/iyad039. View

16.

Goehring N, Hyman A . Organelle growth control through limiting pools of cytoplasmic components. Curr Biol. 2012; 22(9):R330-9. DOI: 10.1016/j.cub.2012.03.046. View

17.

Weber S, Brangwynne C . Inverse size scaling of the nucleolus by a concentration-dependent phase transition. Curr Biol. 2015; 25(5):641-6. PMC: 4348177. DOI: 10.1016/j.cub.2015.01.012. View

18.

Berry J, Weber S, Vaidya N, Haataja M, Brangwynne C . RNA transcription modulates phase transition-driven nuclear body assembly. Proc Natl Acad Sci U S A. 2015; 112(38):E5237-45. PMC: 4586886. DOI: 10.1073/pnas.1509317112. View

19.

Pologruto T, Sabatini B, Svoboda K . ScanImage: flexible software for operating laser scanning microscopes. Biomed Eng Online. 2003; 2:13. PMC: 161784. DOI: 10.1186/1475-925X-2-13. View

20.

Sonnichsen B, Koski L, Walsh A, Marschall P, Neumann B, Brehm M . Full-genome RNAi profiling of early embryogenesis in Caenorhabditis elegans. Nature. 2005; 434(7032):462-9. DOI: 10.1038/nature03353. View