Cell-fate determination by ubiquitin-dependent regulation of translation
Open accessAbstract
Metazoan development depends on the accurate execution of differentiation programs that allow pluripotent stem cells to adopt specific fates. Differentiation requires changes to chromatin architecture and transcriptional networks, yet whether other regulatory events support cell-fate determination is less well understood. Here we identify the ubiquitin ligase CUL3 in complex with its vertebrate-specific substrate adaptor KBTBD8 (CUL3(KBTBD8)) as an essential regulator of human and Xenopus tropicalis neural crest specification. CUL3(KBTBD8) monoubiquitylates NOLC1 and its paralogue TCOF1, the mutation of which underlies the neurocristopathy Treacher Collins syndrome. Ubiquitylation drives formation of a TCOF1-NOLC1 platform that connects RNA polymerase I with ribosome modification enzymes and remodels the translational program of differentiating cells in favour of neural crest specification. We conclude that ubiquitin-dependent regulation of translation is an important feature of cell-fate determination.
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EGR1 is implicated in cranial development in animal models, and its promoter has been shown to feature a bivalent state in human embryonic cranial neural crest.
“which is implicated in cranial development (in animal models) (33, 34) and whose promoter has been recently shown to feature a bivalent state in human embryonic cranial NC (23, 35).”
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Cites
Differential expression analysis for sequence count data
Anders, S., & Huber, W. (2010) · Genome Biology · doi:10.1186/gb-2010-11-10-r106 · Cited by 15,581 · see citing works
Highly efficient neural conversion of human ES and iPS cells by dual inhibition of SMAD signaling
Chambers, S. M., Fasano, C. A., Papapetrou, E. P., Tomishima, M., Sadelain, M., & Studer, L. (2009) · Nature Biotechnology · doi:10.1038/nbt.1529 · Cited by 3,620 · see citing works
Function and regulation of cullin–RING ubiquitin ligases
Petroski, M. D., & Deshaies, R. J. (2005) · Nature Reviews Molecular Cell Biology · doi:10.1038/nrm1547 · Cited by 2,148 · see citing works
Exome sequencing identifies recurrent SPOP, FOXA1 and MED12 mutations in prostate cancer
Barbieri, C. E., Baca, S. C., Lawrence, M. S., Demichelis, F., Blattner, M., Theurillat, J.-P. P., White, T. A., Stojanov, P., Allen, E. M. V., Stransky, N., et al. (2012) · Nature Genetics · doi:10.1038/ng.2279 · Cited by 1,550 · see citing works
Defining the Human Deubiquitinating Enzyme Interaction Landscape
Sowa, M. E., Bennett, E. J., Gygi, S. P., & Harper, J. W. (2009) · Cell · doi:10.1016/j.cell.2009.04.042 · Cited by 1,512 · see citing works
Ingolia, N. T., Brar, G. A., Rouskin, S., McGeachy, A. M., & Weissman, J. S. (2012) · Nature Protocols · doi:10.1038/nprot.2012.086 · Cited by 1,240 · see citing works
Self-citationWelcker, M., & Clurman, B. E. (2008) · Nature Reviews Cancer · doi:10.1038/nrc2290 · Cited by 1,084 · see citing works
Specialized ribosomes: a new frontier in gene regulation and organismal biology
Xue, S., & Barna, M. (2012) · Nature Reviews Molecular Cell Biology · doi:10.1038/nrm3359 · Cited by 687 · see citing works
Mechanisms and function of substrate recruitment by F-box proteins
Skaar, J. R., Pagan, J. K., & Pagano, M. (2013) · Nature Reviews Molecular Cell Biology · doi:10.1038/nrm3582 · Cited by 671 · see citing works
Ribosome-Mediated Specificity in Hox mRNA Translation and Vertebrate Tissue Patterning
Kondrashov, N., Pusic, A. D., Stumpf, C. R., Shimizu, K., Hsieh, A. C., Xue, S., Ishijima, J., Shiroishi, T., & Barna, M. (2011) · Cell · doi:10.1016/j.cell.2011.03.028 · Cited by 581 · see citing works
Mechanism of Ubiquitin-Chain Formation by the Human Anaphase-Promoting Complex
Jin, L., Williamson, A. P., Banerjee, S., Philipp, I., & Rapé, M. (2008) · Cell · doi:10.1016/j.cell.2008.04.012 · Cited by 536 · see citing works
Prevention of the neurocristopathy Treacher Collins syndrome through inhibition of p53 function
Jones, N. C., Lynn, M. L., Gaudenz, K., Sakai, D., Aoto, K., Rey, J., Glynn, E. F., Ellington, L. R., Du, C., Dixon, J., et al. (2008) · Nature Medicine · doi:10.1038/nm1725 · Cited by 426 · see citing works
Impaired Control of IRES-Mediated Translation in X-Linked Dyskeratosis Congenita
Yoon, A., Peng, G., Brandenburg, Y., Zollo, O., Xu, W. G., Rego, E. M., & Ruggero, D. (2006) · Science · doi:10.1126/science.1123835 · Cited by 423 · see citing works
Positional cloning of a gene involved in the pathogenesis of Treacher Collins syndrome
Colla, T. T. C. S., Dixon, J., Edwards, S. J., et al. (1996) · Nature Genetics · doi:10.1038/ng0296-130 · Cited by 406 · see citing works
Cullin-3 targets cyclin E for ubiquitination and controls S phase in mammalian cellsPreprint
Singer, J. D., Gurian-West, M., Clurman, B. E., & Roberts, J. M. (1999) · Genes & Development · doi:10.1101/gad.13.18.2375 · Cited by 404 · see citing works
Dixon, J., Jones, N. C., Sandell, L. J., Jayasinghe, S. M., Crane, J. F., Rey, J., Dixon, M. J., & Trainor, P. A. (2006) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0603730103 · Cited by 379 · see citing works
Mutations in genes encoding subunits of RNA polymerases I and III cause Treacher Collins syndrome
Dauwerse, J. G., Dixon, J., Seland, S., Ruivenkamp, C. A. L., van Haeringen, A., Hoefsloot, L. H., Peters, D. J. M., Boers, A. C.-D., Daumer‐Haas, C., Maiwald, R., et al. (2010) · Nature Genetics · doi:10.1038/ng.724 · Cited by 369 · see citing works
Analysis of proteome dynamics in the mouse brain
Price, J. C., Guan, S., Burlingame, A., Prusiner, S. B., & Ghaemmaghami, S. (2010) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1006551107 · Cited by 357 · see citing works
Louis-Dit-Picard, H., Barc, J., Trujillano, D., Miserey‐Lenkei, S., Bouatia‐Naji, N., Pylypenko, O., Beaurain, G., Bonnefond, A., Sand, O., Simian, C., et al. (2012) · Nature Genetics · doi:10.1038/ng.2218 · Cited by 337 · see citing works
Ubiquitin-dependent regulation of COPII coat size and function
Jin, L., Pahuja, K. B., Wickliffe, K. E., Gorur, A., Baumgärtel, C., Schekman, R., & Rape, M. (2012) · Nature · doi:10.1038/nature10822 · Cited by 330 · see citing works
Jack, K. D., Bellodi, C., Landry, D. M., Niederer, R. O., Meškauskas, A., Musalgaonkar, S., Kopmar, N. E., Krasnykh, O., Dean, A. M., Thompson, S. R., et al. (2011) · Molecular Cell · doi:10.1016/j.molcel.2011.09.017 · Cited by 318 · see citing works
The Processivity of Multiubiquitination by the APC Determines the Order of Substrate Degradation
Rapé, M., Reddy, S., & Kirschner, M. W. (2006) · Cell · doi:10.1016/j.cell.2005.10.032 · Cited by 280 · see citing works
Systems-wide Proteomic Analysis in Mammalian Cells Reveals Conserved, Functional Protein Turnover
Cambridge, S. B., Gnad, F., Nguyen, C., Bermejo, J. L., Krüger, M., & Mann, M. (2011) · Journal of Proteome Research · doi:10.1021/pr101183k · Cited by 277 · see citing works
Techniques and probes for the study of <i>Xenopus tropicalis</i> development
Khokha, M. K., Chung, C., Bustamante, E. L., Gaw, L. W. K., Trott, K. A., Yeh, J., Lim, N., Lin, J. C. Y., Taverner, N., Amaya, E., et al. (2002) · Developmental Dynamics · doi:10.1002/dvdy.10184 · Cited by 241 · see citing works
A Transcriptome-wide Atlas of RNP Composition Reveals Diverse Classes of mRNAs and lncRNAs
Tuck, A., & Tollervey, D. W. (2013) · Cell · doi:10.1016/j.cell.2013.07.047 · Cited by 231 · see citing works
Yanai, I., Peshkin, L., Jorgensen, P., & Kirschner, M. W. (2011) · Developmental Cell · doi:10.1016/j.devcel.2011.03.015 · Cited by 204 · see citing works
Targeted disruption of <i>p185/Cul7</i> gene results in abnormal vascular morphogenesis
Arai, T., Kasper, J. S., Skaar, J. R., Ali, S. H., Takahashi, C., & DeCaprio, J. A. (2003) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1733908100 · Cited by 145 · see citing works
The F-box protein Ppa is a common regulator of core EMT factors Twist, Snail, Slug, and Sip1
Lander, R. M., Nordin, K., & LaBonne, C. (2011) · The Journal of Cell Biology · doi:10.1083/jcb.201012085 · Cited by 142 · see citing works
Deletion of the Cul1 gene in mice causes arrest in early embryogenesis and accumulation of cyclin E
Wang, Y., Penfold, S. S., Tang, X., Hattori, N., Riley, P. R., Harper, J. W., Cross, J. C., & Tyers, M. (1999) · Current Biology · doi:10.1016/s0960-9822(00)80024-x · Cited by 137 · see citing works
McCann, K. L., & Baserga, S. J. (2013) · Science · doi:10.1126/science.1244156 · Cited by 112 · see citing works
Freed, E. F., Prieto, J.-L., McCann, K. L., McStay, B., & Baserga, S. J. (2012) · PLoS Genetics · doi:10.1371/journal.pgen.1002892 · Cited by 99 · see citing works
SCF ubiquitin ligases in the maintenance of genome stability
Silverman, J. S., Skaar, J. R., & Pagano, M. (2011) · Trends in Biochemical Sciences · doi:10.1016/j.tibs.2011.10.004 · Cited by 89 · see citing works
Jiang, B., Zhao, W., Yuan, J., Qian, Y., Sun, W., Zou, Y., Guo, C., Chen, B., Shao, C., & Gong, Y. (2012) · PLoS ONE · doi:10.1371/journal.pone.0037070 · Cited by 77 · see citing works
Human diseases of the SSU processome
Sondalle, S. B., & Baserga, S. J. (2013) · Biochimica et Biophysica Acta (BBA) - Molecular Basis of Disease · doi:10.1016/j.bbadis.2013.11.004 · Cited by 43 · see citing works
The egg and the nucleus: a battle for supremacy
Gurdon, J. B. (2013) · Development · doi:10.1242/dev.097170 · Cited by 40 · see citing works
Voigt, J., & Papalopulu, N. (2006) · Development · doi:10.1242/dev.02201 · Cited by 20 · see citing works
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Yau, R., & Rape, M. (2016) · Nature Cell Biology · doi:10.1038/ncb3358 · Cited by 1,054 · see citing works
Self-citationDual proteome-scale networks reveal cell-specific remodeling of the human interactome
Huttlin, E. L., Bruckner, R. J., Navarrete-Perea, J., Cannon, J. R., Baltier, K., Gebreab, F., Gygi, M. P., Thornock, A., Zarraga, G., Tam, S., et al. (2020) · doi:10.1101/2020.01.19.905109 · Cited by 960 · see citing works
Principles of Ubiquitin-Dependent Signaling
Oh, E., Akopian, D., & Rape, M. (2018) · Annual Review of Cell and Developmental Biology · doi:10.1146/annurev-cellbio-100617-062802 · Cited by 339 · see citing works
Regulation of the CUL3 Ubiquitin Ligase by a Calcium-Dependent Co-adaptor
McGourty, C. A., Akopian, D., Walsh, C., Gorur, A., Werner, A., Schekman, R., Bautista, D., & Rape, M. (2016) · Cell · doi:10.1016/j.cell.2016.09.026 · Cited by 126 · see citing works
Self-citationZanella, M., Vitriolo, A., Andirko, A., Martins, P. T., Sturm, S., O’Rourke, T., Laugsch, M., Malerba, N., Skaros, A., Trattaro, S., et al. (2019) · Science Advances · doi:10.1126/sciadv.aaw7908 · Cited by 101 · see citing works
Cullin 3, a cellular scripter of the non-proteolytic ubiquitin code
Jerabkova, K., & Sumara, I. (2019) · Seminars in Cell & Developmental Biology · doi:10.1016/j.semcdb.2018.12.007 · Cited by 33 · see citing works
- Authors
- Werner, A., Iwasaki, S., McGourty, C. A., Medina-Ruiz, S., Teerikorpi, N., Fedrigo, I., Ingolia, N. T., & Rape, M.
- Affiliations
- Howard Hughes Medical Institute (US)
- University of California, Berkeley (US)
- Venue
- Nature
- Published
- 2015-09
- Volume
- 525
- Issue
- 7570
- Pages
- 523-527
- ISSN
- 0028-0836 (ISSN-L)
- 1476-4687
- PMC
- PMC4602398
- OpenAlex
- W2173122519
- Cited by
- 184
- References
- 36
- Citations by year
- 2026: 4 · 2025: 20 · 2024: 21 · 2023: 13 · 2022: 24 · 2021: 18 · 2020: 18 · 2019: 14 · 2018: 16 · 2017: 21 · 2016: 12 · 2015: 1
- FWCI
- 7.23
- Type
- journal article
- Language
- en
- Open access
- green
- www.ncbi.nlm.nih.gov
- Licence
- www.springer.com/tdm (tdm)
- Locations
- Nature (publishedVersion)
- PubMed (publishedVersion)
- Europe PMC (PubMed Central) (acceptedVersion)
- PubMed Central (acceptedVersion)
- RePEc: Research Papers in Economics (submittedVersion)
- eScholarship (California Digital Library) (submittedVersion)
- Funders
- Howard Hughes Medical Institute
- National Institutes of Health (1s10rr025622-01)
- National Institute of General Medical Sciences (GM 42341, R01GM042341, R01GM083064)
- National Institute of Dental and Craniofacial Research (K99DE025314)
- National Center for Research Resources (S10 RR025622, S10RR029668, S10RR027303)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Developmental Biology and Gene Regulation
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Ubiquitin and proteasome pathways
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › RNA and protein synthesis mechanisms
- Keywords
- ubiquitin ligase, CUL3, NOLC1, TCOF1, Treacher Collins syndrome, neural crest specification, cell fate determination, post-transcriptional regulation, translational regulation, ribosome biogenesis, RNA polymerase I, embryonic stem cell differentiation, Xenopus tropicalis, ubiquitination
- MeSH terms
- Animals, Cell Differentiation, Humans, Mandibulofacial Dysostosis, Neural Crest, Nuclear Proteins, Phosphoproteins, Ribosomes, RNA Polymerase I, Protein Biosynthesis, Xenopus, Ubiquitin, Proteomics, Cullin Proteins, Adaptor Proteins, Signal Transducing, Embryonic Stem Cells, Ubiquitination
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