The DOI matches its Crossref record; 18 of the 18 references it cites were found in a registry or an index.
The demographics of the ubiquitin system
Overview
The claims and statistics of this paper haven’t been checked yet.
Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.
Integrity signals
Registry
Cites
Statistics
Verification
Claims the paper makes
The claims and statistics of this paper haven’t been checked yet.
Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.
Self-check
Percentages, sums and reported differences re-computed from the paper’s own numbers.
The self-check needs the paper’s full text.
Citations
Cites
Global quantification of mammalian gene expression control
Schwanhäusser, B., Busse, D., Li, N., Dittmar, G., Schuchhardt, J., Wolf, J., Chen, W., & Selbach, M. (2011) · Nature · doi:10.1038/nature10098 · Cited by 6,566
Komander, D., & Rape, M. (2012) · Annual Review of Biochemistry · doi:10.1146/annurev-biochem-060310-170328 · Cited by 3,679
A draft map of the human proteome
Kim, M.-S., Pinto, S. M., Getnet, D., Nirujogi, R. S., Manda, S. S., Chaerkady, R., Madugundu, A. K., Kelkar, D. S., Isserlin, R., Jain, S., et al. (2014) · Nature · doi:10.1038/nature13302 · Cited by 2,198
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
An inhibitor of NEDD8-activating enzyme as a new approach to treat cancer
Soucy, T. A., Smith, P. G., Milhollen, M. A., Berger, A. J., Gavin, J. M., Adhikari, S., Brownell, J. E., Burke, K. E., Cardin, D. P., Critchley, S., et al. (2009) · Nature · doi:10.1038/nature07884 · Cited by 1,990
Mass-spectrometry-based draft of the human proteome
Wilhelm, M., Schlegl, J., Hahne, H., Gholami, A. M., Lieberenz, M., Savitski, M. M., Ziegler, E., Butzmann, L., Gessulat, S., Marx, H., et al. (2014) · Nature · doi:10.1038/nature13319 · Cited by 1,820
Kulak, N. A., Pichler, G., Paron, I., Nagaraj, N., & Mann, M. (2014) · Nature Methods · doi:10.1038/nmeth.2834 · Cited by 1,719
Proteolysis: from the lysosome to ubiquitin and the proteasome
Ciechanover, A. (2005) · Nature Reviews Molecular Cell Biology · doi:10.1038/nrm1552 · Cited by 1,133
Deep proteome and transcriptome mapping of a human cancer cell line
Nagaraj, N., Wisniewski, J. R., Geiger, T., Cox, J., Kircher, M., Kelso, J., Pääbo, S., & Mann, M. (2011) · Molecular Systems Biology · doi:10.1038/msb.2011.81 · Cited by 979
The quantitative proteome of a human cell line
Beck, M., Schmidt, A., Malmstroem, J., Claassen, M., Ori, A., Szymborska, A., Herzog, F., Rinner, O., Ellenberg, J., & Aebersold, R. (2011) · Molecular Systems Biology · doi:10.1038/msb.2011.82 · Cited by 816
Research works printed but not linked: 86
- Clague, 2010, Ubiquitin: same molecule, different degradation pathways, Cell, 143, 682, 10.1016/j.cell.2010.11.012 · DOI · Paper page
- Grabbe, 2011, The spatial and temporal organization of ubiquitin networks, Nat. Rev. Mol. Cell Biol., 12, 295, 10.1038/nrm3099 · DOI · Paper page
- Ly, 2014, A proteomic chronology of gene expression through the cell cycle in human myeloid leukemia cells, Elife, 3, e01630, 10.7554/eLife.01630 · DOI
- Monia, 1989, Gene synthesis, expression, and processing of human ubiquitin carboxyl extension proteins, J. Biol. Chem., 264, 4093, 10.1016/S0021-9258(19)84967-0 · DOI
- Kaiser, 2011, Protein standard absolute quantification (PSAQ) method for the measurement of cellular ubiquitin pools, Nat. Methods, 8, 691, 10.1038/nmeth.1649 · DOI · Paper page
- Yang, 2013, Absolute quantification of E1, ubiquitin-like proteins and Nedd8-MLN4924 adduct by mass spectrometry, Cell. Biochem. Biophys., 67, 139, 10.1007/s12013-013-9625-5 · DOI
- Joo, 2007, Regulation of cell cycle progression and gene expression by H2A deubiquitination, Nature, 449, 1068, 10.1038/nature06256 · DOI · Paper page
- Dammer, 2011, Polyubiquitin linkage profiles in three models of proteolytic stress suggest the etiology of Alzheimer disease, J. Biol. Chem., 286, 10457, 10.1074/jbc.M110.149633 · DOI · Paper page
- Walczak, 2012, Generation and physiological roles of linear ubiquitin chains, BMC Biol., 10, 23, 10.1186/1741-7007-10-23 · DOI · Paper page
- Phu, 2011, Improved quantitative mass spectrometry methods for characterizing complex ubiquitin signals, Mol. Cell. Proteomics, 10, 10.1074/mcp.M110.003756 · DOI
- Xu, 2010, Global analysis of lysine ubiquitination by ubiquitin remnant immunoaffinity profiling, Nat. Biotechnol., 28, 868, 10.1038/nbt.1654 · DOI · Paper page
- Kim, 2011, Systematic and quantitative assessment of the ubiquitin-modified proteome, Mol. Cell, 44, 325, 10.1016/j.molcel.2011.08.025 · DOI · Paper page
- Rotin, 2009, Physiological functions of the HECT family of ubiquitin ligases, Nat. Rev. Mol. Cell Biol., 10, 398, 10.1038/nrm2690 · DOI · Paper page
- Smit, 2014, RBR E3-ligases at work, EMBO Rep., 15, 142, 10.1002/embr.201338166 · DOI
- Budhidarmo, 2012, RINGs hold the key to ubiquitin transfer, Trends Biochem. Sci., 37, 58, 10.1016/j.tibs.2011.11.001 · DOI · Paper page
- Schulman, 2011, Twists and turns in ubiquitin-like protein conjugation cascades, Protein Sci., 20, 1941, 10.1002/pro.750 · DOI
- Kleiger, 2014, Perilous journey: a tour of the ubiquitin-proteasome system, Trends Cell Biol., 24, 352, 10.1016/j.tcb.2013.12.003 · DOI · Paper page
- Streich, 2014, Structural and functional insights to ubiquitin-like protein conjugation, Annu. Rev. Biophys., 43, 357, 10.1146/annurev-biophys-051013-022958 · DOI · Paper page
- Schulman, 2009, Ubiquitin-like protein activation by E1 enzymes: the apex for downstream signalling pathways, Nat. Rev. Mol. Cell Biol., 10, 319, 10.1038/nrm2673 · DOI · Paper page
- Jin, 2007, Dual E1 activation systems for ubiquitin differentially regulate E2 enzyme charging, Nature, 447, 1135, 10.1038/nature05902 · DOI · Paper page
- Tokgoz, 2012, E1-E2 interactions in ubiquitin and Nedd8 ligation pathways, J. Biol. Chem., 287, 311, 10.1074/jbc.M111.294975 · doi:10.1074/jbc.m111.294975
- Chiu, 2007, E1-L2 activates both ubiquitin and FAT10, Mol. Cell, 27, 1014, 10.1016/j.molcel.2007.08.020 · DOI · Paper page
- Lee, 2011, Alternative ubiquitin activation/conjugation cascades interact with N-end rule ubiquitin ligases to control degradation of RGS proteins, Mol. Cell, 43, 392, 10.1016/j.molcel.2011.05.034 · DOI
- van Wijk, 2010, The family of ubiquitin-conjugating enzymes (E2s): deciding between life and death of proteins, FASEB J., 24, 981, 10.1096/fj.09-136259 · DOI · Paper page
- Ye, 2009, Building ubiquitin chains: E2 enzymes at work, Nat. Rev. Mol. Cell Biol., 10, 755, 10.1038/nrm2780 · DOI · Paper page
- Brown, 2014, Mechanism of polyubiquitination by human anaphase-promoting complex: RING repurposing for ubiquitin chain assembly, Mol. Cell, 56, 246, 10.1016/j.molcel.2014.09.009 · DOI
- Kelly, 2014, Ubiquitin chain elongation requires E3-dependent tracking of the emerging conjugate, Mol. Cell, 56, 232, 10.1016/j.molcel.2014.09.010 · DOI
- Andersen, 2005, Distinct regulation of Ubc13 functions by the two ubiquitin-conjugating enzyme variants Mms2 and Uev1A, J. Cell Biol., 170, 745, 10.1083/jcb.200502113 · DOI · Paper page
- Schumacher, 2013, The N-terminal extension of UBE2E ubiquitin-conjugating enzymes limits chain assembly, J. Mol. Biol., 425, 4099, 10.1016/j.jmb.2013.06.039 · DOI
- Wenzel, 2011, UBCH7 reactivity profile reveals parkin and HHARI to be RING/HECT hybrids, Nature, 474, 105, 10.1038/nature09966 · DOI · Paper page
- Doyle, 2010, MAGE-RING protein complexes comprise a family of E3 ubiquitin ligases, Mol. Cell, 39, 963, 10.1016/j.molcel.2010.08.029 · DOI · Paper page
- Xiao, 2014, MAGE proteins regulate KRAB zinc finger transcription factors and KAP1 E3 ligase activity, Arch. Biochem. Biophys., 563, 136, 10.1016/j.abb.2014.07.026 · DOI
- Gack, 2007, TRIM25 RING-finger E3 ubiquitin ligase is essential for RIG-I-mediated antiviral activity, Nature, 446, 916, 10.1038/nature05732 · DOI · Paper page
- Capon, 2008, Identification of ZNF313/RNF114 as a novel psoriasis susceptibility gene, Hum. Mol. Genet., 17, 1938, 10.1093/hmg/ddn091 · DOI · Paper page
- Tan, 2003, Human homologue of ariadne promotes the ubiquitylation of translation initiation factor 4E homologous protein, 4EHP, FEBS Lett., 554, 501, 10.1016/S0014-5793(03)01235-3 · DOI
- Bennett, 2010, Dynamics of cullin-RING ubiquitin ligase network revealed by systematic quantitative proteomics, Cell, 143, 951, 10.1016/j.cell.2010.11.017 · DOI · Paper page
- Clague, 2013, Deubiquitylases from genes to organism, Physiol. Rev., 93, 1289, 10.1152/physrev.00002.2013 · DOI · Paper page
- Yao, 2002, A cryptic protease couples deubiquitination and degradation by the proteasome, Nature, 419, 403, 10.1038/nature01071 · DOI · Paper page
- Beck, 2012, Near-atomic resolution structural model of the yeast 26S proteasome, Proc. Natl. Acad. Sci. U.S.A., 109, 14870, 10.1073/pnas.1213333109 · DOI · Paper page
- Koulich, 2008, Relative structural and functional roles of multiple deubiquitylating proteins associated with mammalian 26S proteasome, Mol. Biol. Cell, 19, 1072, 10.1091/mbc.E07-10-1040 · DOI · Paper page
- Finley, 2009, Recognition and processing of ubiquitin-protein conjugates by the proteasome, Ann. Rev. Biochem., 78, 477, 10.1146/annurev.biochem.78.081507.101607 · DOI · Paper page
- Clague, 2012, Governance of endocytic trafficking and signaling by reversible ubiquitylation, Dev. Cell, 23, 457, 10.1016/j.devcel.2012.08.011 · DOI · Paper page
- Wilkinson, 1995, Metabolism of the polyubiquitin degradation signal: structure, mechanism, and role of isopeptidase T, Biochemistry, 34, 14535, 10.1021/bi00044a032 · DOI · Paper page
- Reyes-Turcu, 2006, The ubiquitin binding domain ZnF UBP recognizes the C-terminal diglycine motif of unanchored ubiquitin, Cell, 124, 1197, 10.1016/j.cell.2006.02.038 · DOI · Paper page
- Juang, 2012, OTUB1 co-opts Lys48-linked ubiquitin recognition to suppress E2 enzyme function, Mol. Cell, 45, 384, 10.1016/j.molcel.2012.01.011 · DOI · Paper page
- Wiener, 2012, The mechanism of OTUB1-mediated inhibition of ubiquitination, Nature, 483, 618, 10.1038/nature10911 · DOI · Paper page
- Wiener, 2013, E2 ubiquitin-conjugating enzymes regulate the deubiquitinating activity of OTUB1, Nat. Struct. Mol. Biol., 20, 1033, 10.1038/nsmb.2655 · DOI
- Woodsmith, 2012, Systematic analysis of dimeric E3–RING interactions reveals increased combinatorial complexity in human ubiquitination networks, Mol. Cell. Proteomics, 11, 10.1074/mcp.M111.016162 · DOI
- Hayes, 2012, Direct and indirect control of mitogen-activated protein kinase pathway-associated components, BRAP/IMP E3 ubiquitin ligase and CRAF/RAF1 kinase, by the deubiquitylating enzyme USP15, J. Biol. Chem., 287, 43007, 10.1074/jbc.M112.386938 · DOI
- Sowa, 2009, Defining the human deubiquitinating enzyme interaction landscape, Cell, 138, 389, 10.1016/j.cell.2009.04.042 · DOI · Paper page
- Kouranti, 2010, A global census of fission yeast deubiquitinating enzyme localization and interaction networks reveals distinct compartmentalization profiles and overlapping functions in endocytosis and polarity, PLoS Biol., 8, e1000471, 10.1371/journal.pbio.1000471 · DOI
- Urbe, 2012, Systematic survey of deubiquitinase localisation identifies USP21 as a regulator of centrosome and microtubule associated functions, Mol. Biol. Cell, 23, 1095, 10.1091/mbc.E11-08-0668 · DOI
- Neutzner, 2007, Outer mitochondrial membrane protein degradation by the proteasome, Novartis Found Symp., 287, 4, 10.1002/9780470725207.ch2 · DOI
- David, 2010, The E2 ubiquitin-conjugating enzymes direct polyubiquitination to preferred lysines, J. Biol. Chem., 285, 8595, 10.1074/jbc.M109.089003 · DOI · Paper page
- Eddins, 2006, Mms2-Ubc13 covalently bound to ubiquitin reveals the structural basis of linkage-specific polyubiquitin chain formation, Nat. Struct. Mol. Biol., 13, 915, 10.1038/nsmb1148 · DOI · Paper page
- Matsumoto, 2010, K11-linked polyubiquitination in cell cycle control revealed by a K11 linkage-specific antibody, Mol. Cell, 39, 477, 10.1016/j.molcel.2010.07.001 · DOI · Paper page
- Liu, 2014, Dimeric Ube2g2 simultaneously engages donor and acceptor ubiquitins to form Lys48-linked ubiquitin chains, EMBO J., 33, 46, 10.1002/embj.201385315 · DOI
- Faesen, 2011, The differential modulation of USP activity by internal regulatory domains, interactors and eight ubiquitin chain types, Chem. Biol., 18, 1550, 10.1016/j.chembiol.2011.10.017 · DOI · Paper page
- Komander, 2009, Molecular discrimination of structurally equivalent Lys63-linked and linear polyubiquitin chains, EMBO Rep., 10, 466, 10.1038/embor.2009.55 · DOI · Paper page
- McCullough, 2006, Activation of the endosome-associated ubiquitin isopeptidase AMSH by STAM, a component of the multivesicular body-sorting machinery, Curr. Biol., 16, 160, 10.1016/j.cub.2005.11.073 · DOI · Paper page
- Cooper, 2009, K63-specific deubiquitination by two JAMM/MPN+ complexes: BRISC–associated Brcc36 and proteasomal Poh1, EMBO J., 28, 621, 10.1038/emboj.2009.27 · DOI · Paper page
- Mevissen, 2013, OTU deubiquitinases reveal mechanisms of linkage specificity and enable ubiquitin chain restriction analysis, Cell, 154, 169, 10.1016/j.cell.2013.05.046 · DOI · Paper page
- Edelmann, 2009, Structural basis and specificity of human otubain 1-mediated deubiquitination, Biochem. J., 418, 379, 10.1042/BJ20081318 · DOI · Paper page
- Wang, 2009, Evidence for bidentate substrate binding as the basis for the K48 linkage specificity of otubain 1, J. Mol. Biol., 386, 1011, 10.1016/j.jmb.2008.12.085 · DOI
- Keusekotten, 2013, OTULIN antagonizes LUBAC signaling by specifically hydrolyzing Met1-linked polyubiquitin, Cell, 153, 1312, 10.1016/j.cell.2013.05.014 · DOI · Paper page
- Rivkin, 2013, The linear ubiquitin-specific deubiquitinase gumby regulates angiogenesis, Nature, 498, 318, 10.1038/nature12296 · DOI · Paper page
- Johnston, 1999, Structural basis for the specificity of ubiquitin C-terminal hydrolases, EMBO J., 18, 3877, 10.1093/emboj/18.14.3877 · DOI · Paper page
- Misaghi, 2005, Structure of the ubiquitin hydrolase UCH-L3 complexed with a suicide substrate, J. Biol. Chem., 280, 1512, 10.1074/jbc.M410770200 · DOI · Paper page
- Larsen, 1998, Substrate specificity of deubiquitinating enzymes: ubiquitin C-terminal hydrolases, Biochemistry, 37, 3358, 10.1021/bi972274d · DOI · Paper page
- Tatham, 2013, Ube2W conjugates ubiquitin to alpha-amino groups of protein N-termini, Biochem. J., 453, 137, 10.1042/BJ20130244 · DOI
- Bett, 2014, Ubiquitin-C-terminal hydrolases cleave isopeptide and peptide-linked ubiquitin from structured proteins but do not edit ubiquitin homopolymers, Biochem. J., 466, 489, 10.1042/BJ20141349 · DOI
- Thrower, 2000, Recognition of the polyubiquitin proteolytic signal, EMBO J., 19, 94, 10.1093/emboj/19.1.94 · DOI · Paper page
- Rape, 2006, The processivity of multiubiquitination by the APC determines the order of substrate degradation, Cell, 124, 89, 10.1016/j.cell.2005.10.032 · DOI · Paper page
- Zeng, 2010, Reconstitution of the RIG-I pathway reveals a signaling role of unanchored polyubiquitin chains in innate immunity, Cell, 141, 315, 10.1016/j.cell.2010.03.029 · DOI · Paper page
- Boname, 2010, Efficient internalization of MHC I requires lysine-11 and lysine-63 mixed linkage polyubiquitin chains, Traffic, 11, 210, 10.1111/j.1600-0854.2009.01011.x · DOI
- Goto, 2010, Contribution of lysine 11-linked ubiquitination to MIR2-mediated major histocompatibility complex class I internalization, J. Biol. Chem., 285, 35311, 10.1074/jbc.M110.112763 · DOI
- Emmerich, 2013, Activation of the canonical IKK complex by K63/M1-linked hybrid ubiquitin chains, Proc. Natl. Acad. Sci. U.S.A., 110, 15247, 10.1073/pnas.1314715110 · DOI · Paper page
- Meyer, 2014, Enhanced protein degradation by branched ubiquitin chains, Cell, 157, 910, 10.1016/j.cell.2014.03.037 · DOI · Paper page
- Ohtake, 2014, Ubiquitin acetylation inhibits polyubiquitin chain elongation, EMBO Rep., 16, 192, 10.15252/embr.201439152 · DOI
- Zheng, 2014, Pink1, the first ubiquitin kinase, EMBO J., 33, 1621, 10.15252/embj.201489185 · DOI
- Ordureau, 2014, Quantitative proteomics reveal a feedforward mechanism for mitochondrial PARKIN translocation and ubiquitin chain synthesis, Mol. Cell, 56, 360, 10.1016/j.molcel.2014.09.007 · DOI · Paper page
- Wauer, 2014, Ubiquitin Ser65 phosphorylation affects ubiquitin structure, chain assembly and hydrolysis, EMBO J., 34, 307, 10.15252/embj.201489847 · DOI · Paper page
- Meierhofer, 2008, Quantitative analysis of global ubiquitination in HeLa cells by mass spectrometry, J. Proteome Res., 7, 4566, 10.1021/pr800468j · DOI · Paper page
- Jacobson, 2009, The lysine 48 and lysine 63 ubiquitin conjugates are processed differently by the 26s proteasome, J. Biol. Chem., 284, 35485, 10.1074/jbc.M109.052928 · DOI
- Xu, 2009, Quantitative proteomics reveals the function of unconventional ubiquitin chains in proteasomal degradation, Cell, 137, 133, 10.1016/j.cell.2009.01.041 · DOI · Paper page
- Larance, 2013, Global subcellular characterization of protein degradation using quantitative proteomics, Mol. Cell. Proteomics, 12, 638, 10.1074/mcp.M112.024547 · DOI
Cited by
Swatek, K. N., & Komander, D. (2016) · Cell Research · doi:10.1038/cr.2016.39 · Cited by 2,081
PROTACs: past, present and future
Li, K., & Crews, C. M. (2022) · Chemical Society Reviews · doi:10.1039/d2cs00193d · Cited by 869
Current strategies for the design of PROTAC linkers: a critical review
Troup, R. I., Fallan, C., & Baud, M. G. J. (2020) · Exploration of Targeted Anti-tumor Therapy · doi:10.37349/etat.2020.00018 · Cited by 424
“Over 600 E3 ligases have been identified in the human proteome [8, 28], but there is a general dearth of high affinity ligands available for them [29].”
BackgroundUSP7 small-molecule inhibitors interfere with ubiquitin binding.
Kategaya, L., Di Lello, P., Rougé, L., Pastor, R., Clark, K. R., Drummond, J., Kleinheinz, T., Lin, E., Upton, J.-P., Prakash, S., et al. (2017) · Nature · doi:10.1038/nature24006 · Cited by 333
Structural basis of indisulam-mediated RBM39 recruitment to DCAF15 E3 ligase complex
Bussiere, D. E., Xie, L., Srinivas, H., Shu, W., Burke, A., Be, C., Zhao, J., Godbole, A., King, D., Karki, R. G., et al. (2020) · Nature Chemical Biology · doi:10.1038/s41589-019-0411-6 · Cited by 257
Metadata
- Authors
- Clague, M. J., Heride, C., & Urbé, S.
- Venue
- Trends in Cell Biology
- Publisher
- Elsevier BV
- Published
- 2015-07
- Volume
- 25
- Issue
- 7
- Pages
- 417-426
- ISSN
- 0962-8924 (ISSN-L)
- OpenAlex
- W2047161080
- Cited by
- 373
- References
- 18
- FWCI
- 1.88
- Type
- journal article
- Language
- en
- Open access
- closed
- Licence
- www.elsevier.com/tdm/userlicense/1.0/ (tdm)
About these checks
Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.
Statistics and arithmetic are recomputed, not judged.
Confidence bands are shown only for fields calibrated on our annotated test set. None is calibrated yet, so no band is shown.
What counts as a claim ›How we measure confidence ›How we check this ›
Are you an author, or do you see a problem with this page? Request a review
How to cite
Cite CoChat for the checks on this page, and the paper for its own findings.
- This page
- CoChat. (2026). Citation check: The demographics of the ubiquitin system. https://app.cochat.ai/papers/10.1016/j.tcb.2015.03.002
- The paper
- Clague, M. J., Heride, C., & Urbé, S. (2015). The demographics of the ubiquitin system. Trends in Cell Biology. https://doi.org/10.1016/j.tcb.2015.03.002
Data sources
Bibliographic data: Semantic Scholar, OpenAlex, Crossref.
Contains information from the Semantic Scholar Academic Graph Datasets, made available under the ODC Attribution License (ODC-BY 1.0).
Semantic Scholar’s data is described in: Kinney, R., et al. (2023). The Semantic Scholar Open Data Platform. arXiv:2301.10140.