Ubiquitin (-like) signaling and Proteomics

Main Scientific Articles from the group :

1               Salas-Lloret, D. et al. BRCA1/BARD1 ubiquitinates PCNA in unperturbed conditions to promote continuous DNA synthesis. Nature communications 15, 4292 (2024). https://doi.org/10.1038/s41467-024-48427-6

2               Salas-Lloret, D. et al. SUMO-activated target traps (SATTs) enable the identification of a comprehensive E3-specific SUMO proteome. Sci Adv 9, eadh2073 (2023). https://doi.org/10.1126/sciadv.adh2073

3               Salas-Lloret, D. & Gonzalez-Prieto, R. Insights in Post-Translational Modifications: Ubiquitin and SUMO. Int J Mol Sci 23 (2022). https://doi.org/10.3390/ijms23063281

4               Gonzalez-Prieto, R. et al. Global non-covalent SUMO interaction networks reveal SUMO-dependent stabilization of the non-homologous end joining complex. Cell Rep 34, 108691 (2021). https://doi.org/10.1016/j.celrep.2021.108691

5               Salas-Lloret, D., Agabitini, G. & Gonzalez-Prieto, R. TULIP2: An Improved Method for the Identification of Ubiquitin E3-Specific Targets. Front Chem 7, 802 (2019). https://doi.org/10.3389/fchem.2019.00802

6               Kumar, R., Gonzalez-Prieto, R., Xiao, Z., Verlaan-de Vries, M. & Vertegaal, A. C. O. The STUbL RNF4 regulates protein group SUMOylation by targeting the SUMO conjugation machinery. Nature communications 8, 1809 (2017). https://doi.org/10.1038/s41467-017-01900-x

7               Gonzalez-Prieto, R., Cuijpers, S. A., Luijsterburg, M. S., van Attikum, H. & Vertegaal, A. C. SUMOylation and PARylation cooperate to recruit and stabilize SLX4 at DNA damage sites. EMBO reports 16, 512-519 (2015). https://doi.org/10.15252/embr.201440017

8               Gonzalez-Prieto, R., Cuijpers, S. A., Kumar, R., Hendriks, I. A. & Vertegaal, A. C. c-Myc is targeted to the proteasome for degradation in a SUMOylation-dependent manner, regulated by PIAS1, SENP7 and RNF4. Cell Cycle 14, 1859-1872 (2015). https://doi.org/10.1080/15384101.2015.1040965

9               Gonzalez-Prieto, R., Munoz-Cabello, A. M., Cabello-Lobato, M. J. & Prado, F. Rad51 replication fork recruitment is required for DNA damage tolerance. The EMBO journal 32, 1307-1321 (2013). https://doi.org/10.1038/emboj.2013.73

10            Gañán-Calvo, A. M., González-Prieto, R., Riesco-Chueca, P., Herrada, M. A. & Flores-Mosquera, M. Focusing capillary jets close to the continuum limit. Nat Phys 3, 737-742 (2007). https://doi.org/10.1038/nphys710

Collaborations from the last 5 years:

1               Nguyen, B. A. et al. Structural polymorphism of amyloid fibrils in ATTR amyloidosis revealed by cryo-electron microscopy. Nature communications 15, 581 (2024). https://doi.org/10.1038/s41467-024-44820-3

2               Rodrigues, J. S. et al. dsRNAi-mediated silencing of PIAS2beta specifically kills anaplastic carcinomas by mitotic catastrophe. Nature communications 15, 3736 (2024). https://doi.org/10.1038/s41467-024-47751-1

3               Yanez-Vilches, A. et al. Physical interactions between specifically regulated subpopulations of the MCM and RNR complexes prevent genetic instability. PLoS genetics 20, e1011148 (2024). https://doi.org/10.1371/journal.pgen.1011148

4               Yalcin, Z. et al. UBE2D3 facilitates NHEJ by orchestrating ATM signalling through multi-level control of RNF168. Nature communications 15, 5032 (2024). https://doi.org/10.1038/s41467-024-49431-6

5               Condezo, Y. B. et al. RNF212B E3 ligase is essential for crossover designation and maturation during male and female meiosis in the mouse. Proceedings of the National Academy of Sciences of the United States of America 121, e2320995121 (2024). https://doi.org/10.1073/pnas.2320995121

6               Yalcin, Z. et al. Ubiquitinome Profiling Reveals in Vivo UBE2D3 Targets and Implicates UBE2D3 in Protein Quality Control. Molecular & cellular proteomics : MCP 22, 100548 (2023). https://doi.org/10.1016/j.mcpro.2023.100548

7               van den Heuvel, D. et al. A disease-associated XPA allele interferes with TFIIH binding and primarily affects transcription-coupled nucleotide excision repair. Proceedings of the National Academy of Sciences of the United States of America 120, e2208860120 (2023). https://doi.org/10.1073/pnas.2208860120

8               Fan, C. et al. The lncRNA LETS1 promotes TGF-beta-induced EMT and cancer cell migration by transcriptionally activating a TbetaR1-stabilizing mechanism. Sci Signal 16, eadf1947 (2023). https://doi.org/10.1126/scisignal.adf1947

9               van Dinther, M. et al. CD44 acts as a coreceptor for cell-specific enhancement of signaling and regulatory T cell induction by TGM1, a parasite TGF-beta mimic. Proceedings of the National Academy of Sciences of the United States of America 120, e2302370120 (2023). https://doi.org/10.1073/pnas.2302370120

10            Tessier, S. et al. Exploration of nuclear body-enhanced sumoylation reveals that PML represses 2-cell features of embryonic stem cells. Nature communications 13, 5726 (2022). https://doi.org/10.1038/s41467-022-33147-6

11            Blessing, C. et al. XPC-PARP complexes engage the chromatin remodeler ALC1 to catalyze global genome DNA damage repair. Nature communications 13, 4762 (2022). https://doi.org/10.1038/s41467-022-31820-4

12            Kamp, J. A. et al. THO complex deficiency impairs DNA double-strand break repair via the RNA surveillance kinase SMG-1. Nucleic acids research 50, 6235-6250 (2022). https://doi.org/10.1093/nar/gkac472

13            Salas-Lloret, D. & Gonzalez-Prieto, R. Insights in Post-Translational Modifications: Ubiquitin and SUMO. Int J Mol Sci 23 (2022). https://doi.org/10.3390/ijms23063281

14            Kumar, S. et al. Targeting pancreatic cancer by TAK-981: a SUMOylation inhibitor that activates the immune system and blocks cancer cell cycle progression in a preclinical model. Gut 71, 2266-2283 (2022). https://doi.org/10.1136/gutjnl-2021-324834

15            Tessier, S. et al. Unbiased <em>in vivo</em> exploration of nuclear bodies-enhanced sumoylation reveals that PML orchestrates embryonic stem cell fate. bioRxiv, 2021.2006.2029.450368 (2021). https://doi.org/10.1101/2021.06.29.450368

16            Apelt, K. et al. ERCC1 mutations impede DNA damage repair and cause liver and kidney dysfunction in patients. J Exp Med 218 (2021). https://doi.org/10.1084/jem.20200622

17            Goossens, R. et al. A proteomics study identifying interactors of the FSHD2 gene product SMCHD1 reveals RUVBL1-dependent DUX4 repression. Sci Rep 11, 23642 (2021). https://doi.org/10.1038/s41598-021-03030-3

18            van den Heuvel, D. et al. A CSB-PAF1C axis restores processive transcription elongation after DNA damage repair. Nature communications 12, 1342 (2021). https://doi.org/10.1038/s41467-021-21520-w

19            van der Weegen, Y. et al. ELOF1 is a transcription-coupled DNA repair factor that directs RNA polymerase II ubiquitylation. Nature cell biology 23, 595-607 (2021). https://doi.org/10.1038/s41556-021-00688-9

20            Cabello-Lobato, M. J. et al. Physical interactions between MCM and Rad51 facilitate replication fork lesion bypass and ssDNA gap filling by non-recombinogenic functions. Cell Rep 36, 109440 (2021). https://doi.org/10.1016/j.celrep.2021.109440

21            Singh, J. K. et al. Zinc finger protein ZNF384 is an adaptor of Ku to DNA during classical non-homologous end-joining. Nature communications 12, 6560 (2021). https://doi.org/10.1038/s41467-021-26691-0

22            Koedoot, E. et al. Splicing factors control triple-negative breast cancer cell mitosis through SUN2 interaction and sororin intron retention. J Exp Clin Cancer Res 40, 82 (2021). https://doi.org/10.1186/s13046-021-01863-4

23            Cano-Linares, M. I. et al. Non-recombinogenic roles for Rad52 in translesion synthesis during DNA damage tolerance. EMBO reports 22, e50410 (2021). https://doi.org/10.15252/embr.202050410

24            van den Heuvel, D. et al. A CSB-PAF1C axis restores processive transcription elongation after DNA damage repair. bioRxiv, 2020.2001.2004.894808 (2020). https://doi.org/10.1101/2020.01.04.894808

25            van der Weegen, Y. et al. The cooperative action of CSB, CSA, and UVSSA target TFIIH to DNA damage-stalled RNA polymerase II. Nature communications 11, 2104 (2020). https://doi.org/10.1038/s41467-020-15903-8

26            Liu, S. et al. Deubiquitinase Activity Profiling Identifies UCHL1 as a Candidate Oncoprotein That Promotes TGFbeta-Induced Breast Cancer Metastasis. Clin Cancer Res 26, 1460-1473 (2020). https://doi.org/10.1158/1078-0432.CCR-19-1373

27            Gjonaj, L. et al. USP7: combining tools towards selectivity. Chem Commun (Camb) 55, 5075-5078 (2019). https://doi.org/10.1039/c9cc00969h

28            Sha, Z., Blyszcz, T., Gonzalez-Prieto, R., Vertegaal, A. C. O. & Goldberg, A. L. Inhibiting ubiquitination causes an accumulation of SUMOylated newly synthesized nuclear proteins at PML bodies. The Journal of biological chemistry 294, 15218-15234 (2019). https://doi.org/10.1074/jbc.RA119.009147

Book Chapters:

1. Gonzalez-Prieto, R.#, Vertegaal, A.C.O.# (2019) Wilson, V. G. (ed.), SUMOylation and Ubiquitination: Current and Emerging Concepts. Caister Academic Press, U.K., pp.147-160.
2. Gonzalez-Prieto, R., Cabello-Lobato, M.J., and Prado, F. (2021). In Vivo Binding of Recombination Proteins to Non-DSB DNA Lesions and to Replication Forks. Methods in molecular biology 2153, 447-458.