Investigating the essential roles of Ubiquitin-like molecules and the Ubiquitin Proteasome System

 

 

 

 

 

   
 2013
 
 

Amore A, Wals K, Koekoek E, Hoppes R, Toebes M, Schumacher TN, Rodenko B, Ovaa H. Development of a hypersensitive periodate-cleavable amino acid that is methionine- and disulfide-compatible and its application in MHC exchange reagents for T cell characterisation. Chembiochem. 2013 Jan 2;14(1):123-31. doi: 10.1002/cbic.201200540.

Bai Z, Cai L, Umemoto E, Takeda A, Tohya K, Komai Y, Veeraveedu PT, Hata E, Sugiura Y, Kubo A, Suematsu M, Hayasaka H, Okudaira S, Aoki J, Tanaka T, Albers HM, Ovaa H, Miyasaka M. Constitutive lymphocyte transmigration across the basal lamina of high endothelial venules is regulated by the autotaxin/lysophosphatidic acid axis. J Immunol. 2013 Mar 1;190(5):2036-48. doi: 10.4049/jimmunol.1202025. Epub 2013 Jan 30.

Bett JS, Ibrahim AF, Garg AK, Kelly V, Pedrioli P, Rocha S, Hay RT. The P-body component USP52/PAN2 is a novel regulator of HIF1A mRNA stability. Biochem J. 2013 Apr 15;451(2):185-94.

Bonne-Andrea C, Kahli M, Mechali F, Lemaitre J-M, Bossis G, Coux O. SUMO2/3 modification of cyclin E contributes to the control of replication origin firing. Nat. Commun. 2013;4:1850.

Campagna M, Marcos-Villar L, Arnoldi F, de la Cruz-Herrera CF, Gallego P, González-Santamaría J, González D, Lopitz-Otsoa F, Rodriguez MS, Burrone OR, Rivas C. Rotavirus viroplasm proteins interact with the cellular SUMOylation system: implications for viroplasm-like structure formation. J Virol. 2013 Jan;87(2):807-17. doi: 10.1128/JVI.01578-12. Epub 2012 Oct 31. PMID: 23115286

Carreras Puigvert J, von Stechow L, Siddappa R, Pines A, Bahjat M, Haazen LC, Olsen JV, Vrieling H, Meerman JH, Mullenders LH, van de Water B, Danen EH. Systems biology approach identifies the kinase Csnk1a1 as a regulator of the DNA damage response in embryonic stem cells. Sci Signal. 2013 Jan 22;6(259):ra5. doi: 10.1126/scisignal.2003208. PMID: 23354688 

Crosetto N, Mitra A, Silva MJ, Bienko M, Dojer N, Wang Q, Karaca E, Chiarle R, Skrzypczak M, Ginalski K, Pasero P, Rowicka M, Dikic I. Nucleotide-resolution DNA double-strand break mapping by next-generation sequencing. Nat Methods. 2013 Apr;10(4):361-5.

den Hoed M, Eijgelsheim M, Esko T, Brundel BJ, Peal DS, Evans DM, Nolte IM, Segrè AV, Holm H, Handsaker RE, Westra HJ, Johnson T, Isaacs A, Yang J, Lundby A, …, Olsen JV, Visscher PM, Willer C, Franke L; Global BPgen Consortium; CARDIoGRAM Consortium, Erdmann J, Thompson JR; PR GWAS Consortium, Pfeufer A; QRS GWAS Consortium, Sotoodehnia N; QT-IGC Consortium, Newton-Cheh C; CHARGE-AF Consortium, Ellinor PT, Stricker BH, Metspalu A, Perola M, Beckmann JS, Smith GD, Stefansson K, Wareham NJ, Munroe PB, Sibon OC, Milan DJ, Snieder H, Samani NJ, Loos RJ. Identification of heart rate-associated loci and their effects on cardiac conduction and rhythm disorders. Nat Genet. 2013 Jun;45(6):621-31.

Echalier A, Pan Y, Birol M, Tavernier N, Pintard L, Hoh F, Ebel C, Galophe N, Claret FX, Dumas C. Insights into the regulation of the human COP9 signalosome catalytic subunit, CSN5/Jab1. PNAS U S A. 2013 Jan 22;110(4):1273-8.

Ekkebus R, van Kasteren SI, Kulathu Y, Scholten A, Berlin I, Geurink PP, de Jong A, Goerdayal S, Neefjes J, Heck AJ, Komander D, Ovaa H. On terminal alkynes that can react with active-site cysteine nucleophiles in proteases. J Am Chem Soc. 2013 Feb 27;135(8):2867-70. doi: 10.1021/ja309802n. Epub 2013 Feb 15.

Fiškin E, Dikic I. Parkin promotes cell survival via linear ubiquitination. EMBO J. 2013 Apr 17;32(8):1072-4.

Francavilla C, Rigbolt KTG, Emdal KB, Carraro G, Vernet E, Bekker-Jensen DB, Streicher W, Wikström M, Sundström M, Bellusci S, Cavallaro U, Blagoev B, Olsen JV. Functional proteomics defines the molecular switch underlying FGF receptor trafficking and cellular outputs. Mol Cell. 2013 Sept 4; doi:pii: S1097-2765(13)00575-3. 10.1016/j.molcel.2013.08.002. [Epub ahead of print]

Hay RT. Decoding the SUMO signal. Biochem Soc Trans. 2013 Apr;41(2):463-73.

Hekmat O, Munk S, Fogh L, Yadav R, Francavilla C, Horn H, Würtz SO, Schrohl AS, Damsgaard B, Rømer MU, Belling KC, Jensen NF, Gromova I, Bekker-Jensen DB, Moreira JM, Jensen LJ, Gupta R, Lademann U, Brünner N, Olsen JV, Stenvang J. TIMP-1 Increases Expression and Phosphorylation of Proteins Associated with Drug Resistance in Breast Cancer Cells. J Proteome Res. 2013 Sep 6;12(9):4136-51.

Helfricht A, Wiegant WW, Thijssen PE, Vertegaal AC, Luijsterburg MS, van Attikum H. Remodeling and spacing factor 1 (RSF1) deposits centromere proteins at DNA double-strand breaks to promote non-homologous end-joining. Cell Cycle. 2013 Aug 20;12(18). Epub

Kohlhase J, Barrio R, Sutherland JD. SALL1 and the Townes-Brocks syndrome. Inborn Errors in Development, 2013 Oxford University Press USA Chapter 25, in press.

Kohlhase J, Barrio R, Sutherland JD. SALL4 and the Duane Radial-Ray/ Okihiro and Acro-renal-ocular syndromes. Inborn Errors in Development 2013 Oxford University Press USA Chapter 123, in press.

Korac J, Schaeffer V, Kovacevic I, Clement AM, Jungblut B, Behl C, Terzic J, Dikic I. Ubiquitin-independent function of optineurin in autophagic clearance of protein aggregates. J Cell Sci. 2013 Jan 15;126(Pt 2):580-92.

Kulathu Y, Garcia FJ, Mevissen TE, Busch M, Arnaudo N, Carroll KS, Barford D, Komander D. Regulation of A20 and other OTU deubiquitinases by reversible oxidation. Nat Commun. 2013 Mar 5;4:1569. doi: 10.1038/ncomms2567. PMID: 23463012 

Landré V, Pion E, Narayan V, Xirodimas DP, Ball KL. DNA-binding regulates site-specific ubiquitination of IRF-1. Biochem J. 2013; 449(3):707-17.

Lundby A, Andersen MN, Steffensen AB, Horn H, Kelstrup CD, Francavilla C, Jensen LJ, Schmitt N, Thomsen MB, Olsen JV. In vivo phosphoproteomics analysis reveals the cardiac targets of β-adrenergic receptor signaling. Sci Signal. 2013 Jun 4;6(278):rs11.

Lundby A, Olsen JV. Phosphoproteomics taken to heart. Cell Cycle. 2013 Sep 1;12(17):2707-2708.

M, McEwan DG, Löhr F, Güntert P, Dikic I, Wakatsuki S, Dötsch V.Structural basis for phosphorylation-triggered autophagic clearance of Salmonella. Rogov VV, Suzuki H, Fiskin E, Wild P, Kniss A, Rozenknop A, Kato R, Kawasaki. Biochem J. 2013 Jun 28. [Epub ahead of print]

Marcos-Villar L, Gallego P, Muñoz-Fontela C, de la Cruz-Herrera CF, Campagna M, González D, Lopitz-Otsoa F, Rodríguez MS, Rivas C. Kaposi's sarcoma-associated herpesvirus lana2 protein interacts with the pocket proteins and inhibits their sumoylation. Oncogene. 2013 Jan 14. doi: 10.1038/onc.2012.603. PMID: 23318443 

Mevissen TE, Hospenthal MK, Geurink PP, Elliott PR, Akutsu M, Arnaudo N, Ekkebus R, Kulathu Y, Wauer T, El Oualid F, Freund SM, Ovaa H, Komander D. OTU deubiquitinases reveal mechanisms of linkage specificity and enable ubiquitin chain restriction analysis. Cell. 2013 Jul 3;154(1):169-84. doi: 10.1016/j.cell.2013.05.046.

Min M, Mayor U, Lindon C. Ubiquitination site preferences in anaphase promoting complex/cyclosome (APC/C) substrates. Open Biol. 2013 Sep 4;3(9):130097. doi:10.1098/rsob.130097

Miyabe Y, Miyabe C, Iwai Y, Takayasu A, Fukuda S, Yokoyama W, Nagai J, Jona M, Tokuhara Y, Ohkawa R, Albers HM, Ovaa H, Aoki J, Chun J, Yatomi Y, Ueda H, Miyasaka M, Miyasaka N, Nanki T. Necessity of lysophosphatidic Acid receptor 1 for development of arthritis. Arthritis Rheum. 2013 Aug;65(8):2037-47. doi: 10.1002/art.37991.

Nasser R, Pelegrin M, Plays M, Gros L, Piechaczyk M. Control of regulatory T cells is necessary for vaccine-like effects of antiviral immunotherapy by monoclonal antibodies. Blood 2013;121(7):1102-11.

Olma MH, Dikic I. Cullins getting undressed by the protein exchange factor Cand1. Cell. 2013 Mar 28;153(1):14-6.

Orlando L, Ginolhac A, Zhang G, Froese D, Albrechtsen A, Stiller M, Schubert M, Cappellini E, Petersen B, Moltke I, Johnson PL, Fumagalli M, Vilstrup JT, Raghavan M, Korneliussen T, Malaspinas AS, Vogt J, Szklarczyk D, Kelstrup CD, Vinther J, Dolocan A, Stenderup J, Velazquez AM, Cahill J, Rasmussen M, Wang X, Min J, Zazula GD, Seguin-Orlando A, Mortensen C, Magnussen K, Thompson JF, Weinstock J, Gregersen K, Røed KH, Eisenmann V, Rubin CJ, Miller DC, Antczak DF, Bertelsen MF, Brunak S, Al-Rasheid KA, Ryder O, Andersson L, Mundy J, Krogh A, Gilbert MT, Kjær K, Sicheritz-Ponten T, Jensen LJ, Olsen JV, Hofreiter M, Nielsen R, Shapiro B, Wang J, Willerslev E. Recalibrating Equus evolution using the genome sequence of an early Middle Pleistocene horse. Nature. 2013 Jul 4;499(7456):74-8.

Orre M, Kamphuis W, Dooves S, Kooijman L, Chan ET, Kirk CJ, Dimayuga Smith V, Koot S, Mamber C, Jansen AH, Ovaa H, Hol EM. Reactive glia show increased immunoproteasome activity in Alzheimer's disease. Brain. 2013 May;136(Pt 5):1415-31. doi: 10.1093/brain/awt083. Epub 2013 Apr 19.

Pang B, Qiao X, Janssen L, Velds A, Groothuis T, Kerkhoven R, Nieuwland M, Ovaa H, Rottenberg S, van Tellingen O, Janssen J, Huijgens P, Zwart W, Neefjes J. Drug-induced histone eviction from open chromatin contributes to the chemotherapeutic effects of doxorubicin. Nat Commun. 2013;4:1908. doi: 10.1038/ncomms2921.

Pelegrin M, Gros L, Piechaczyk M. Des effets vaccinaux pour les anticorps monoclonaux antiviraux Medecine/Science 2013;29(5):457-60.

Puigvert JC, von Stechow L, Siddappa R, Pines A, Bahjat M, Haazen LCJM, Olsen JV, Vrieling H, Meerman JHN, Mullenders LHF, van de Water B, and Danen EHJ Systems approach identifies Csnk1a1 as a novel regulator of the DNA damage response in embryonic stem cells Sci Signal. 2013 Jan 22;6(259):ra5.

Salem T, Gomard T, Court F, Moquet-Torcy G, Brockly F, Forné T, Piechaczyk M. Chromatin loop organization of the junb locus in murine dendritic cells. Nucl. Acids Res. 2013;in press.

Shaid S, Brandts CH, Serve H, Dikic I. Ubiquitination and selective autophagy. Cell Death Differ. 2013 Jan;20(1):21-30. doi: 10.1038/cdd.2012.72. Epub 2012 Jun 22. PMID: 22722335 

Soundararajan M, Roos AK, Savitsky P, Filippakopoulos P, Kettenbach AN, Olsen JV, Gerber SA, Eswaran J, Knapp S, Elkins JM. Structures of Down syndrome kinases, DYRKs, reveal mechanisms of kinase activation and substrate recognition. Structure. 2013 Jun 4;21(6):986-96.

Talamillo A, Herboso L, Pirone L, Pérez C, González M, Sánchez J, Mayor U, Lopitz-Otsoa F, Rodriguez MS, Sutherland JD, Barrio R. Scavenger receptors mediate the role of SUMO and Ftz-f1 in Drosophila steroidogenesis. PLoS Genet. 2013 Apr;9(4):e1003473.

Tatham MH, Plechanovová A, Jaffray EG, Salmen H, Hay RT. Ube2W conjugates ubiquitin to α-amino groups of protein N-termini. Biochem J. 2013 Jul 1;453(1):137-45.

Tempé D, Vives E, Brockly F, Brooks H, de Rossi S, Piechaczyk M, Bossis G. SUMOylation of the inducible (c-Fos:c-Jun)/AP-1 transcriptional complex occurs on target promoters to limit transcription. Oncogene 2013;doi: 10.1038/onc.2013.4.

Thoresen SB, Perdios L, Daigaku R, Francis RE, Futter C, Dikic I, Braga VM.The TBC/RabGAP Armus coordinates Rac1 and Rab7 functions during autophagy. Carroll B, Mohd-Naim N, Maximiano F, Frasa MA, McCormack J, Finelli M, Dev Cell. 2013 Apr 15;25(1):15-28.

Tinti M, Kiemer L, Costa S, Miller ML, Sacco F, Olsen JV, Carducci M, Paoluzi S, Langone F, Workman CT, Blom N, Machida K, Thompson CM, Schutkowski M, Brunak S, Mann M, Mayer BJ, Castagnoli L, Cesareni G. The SH2 domain interaction landscape. Cell Rep. 2013 Apr 25;3(4):1293-305.

Tyanova S, Cox J, Olsen JV, Mann M, Frishman D. Phosphorylation Variation during the Cell Cycle Scales with Structural Propensities of Proteins. PLoS Comput Biol. 2013 Jan;9(1):e1002842.

van Loosdregt J, Fleskens V, Fu J, Brenkman AB, Bekker CP, Pals CE, Meerding J, Berkers CR, Barbi J, Gröne A, Sijts AJ, Maurice MM, Kalkhoven E, Prakken BJ, Ovaa H, Pan F, Zaiss DM, Coffer PJ. Stabilization of the Transcription Factor Foxp3 by the Deubiquitinase USP7 Increases Treg-Cell-Suppressive Capacity. Immunity. 2013 Aug 22;39(2):259-71. doi: 10.1016/j.immuni.2013.05.018.

van Wijk SJ, Fiškin E, Dikic I. Selective monitoring of ubiquitin signals with genetically encoded ubiquitin chain-specific sensors. Nat Protoc. 2013 Jul;8(7):1449-58.

von Muhlinen N, Akutsu M, Ravenhill BJ, Foeglein A, Bloor S, Rutherford TJ, Freund SM, Komander D, Randow F. An essential role for the ATG8 ortholog LC3C in antibacterial autophagy. Autophagy. 2013 Feb 22;9(5). PMID: 23434839 

Vyas R, Kumar R, Clermont F, Helfricht A, Kalev P, Sotiropoulou P, Hendriks IA, Radaelli E, Hochepied T, Blanpain C, Sablina A, van Attikum H, Olsen JV, Jochemsen AG, Vertegaal AC, Marine JC. RNF4 is required for DNA double-strand break repair in vivo. Cell Death Differ. 2013 Mar;20(3):490-502.

Wang B, Lançon P, Bienvenu C, Vierling P, Di Giorgio C, Bossis G. A general approach for the microrheology of cancer cells by atomic force microscopy. Micron. 2013 Jan;44:287-97. doi: 10.1016/j.micron.2012.07.006. Epub 2012 Aug 7. PMID: 22951283 

Xirodimas DP. DUBs "found in translation": USP15 controls stability of newly synthesized REST. Cell Cycle. 2013; 12(16) [Epub ahead of print].

Zhu Y, Massen S, Terenzio M, Lang V, Chen-Lindner S, Eils R, Novak I, Dikic I, Hamacher-Brady A, Brady NR. Modulation of serines 17 and 24 in the LC3-interacting region of Bnip3 determines pro-survival mitophagy versus apoptosis. J Biol Chem. 2013 Jan 11;288(2):1099-113.

 
 2012    
 

Absalom N, Eghorn LF, Villumsen IS, Karim N, Bay T, Olsen JV, Knudsen GM, Bräuner-Osborne H, Frølund B, Clausen RP, Chebib M, Wellendorph P. α4βδ GABA(A) receptors are high-affinity targets for γ-hydroxybutyric acid (GHB). Proc Natl Acad Sci U S A. 2012 Aug 14;109(33):13404-9. doi: 10.1073/pnas.1204376109. Epub 2012 Jul 2. PMID: 22753476

Aillet F, Lopitz-Otsoa F, Egaña I, Hjerpe R, Fraser P, Hay RT, Rodriguez MS, Lang V. Heterologous SUMO-2/3-ubiquitin chains optimize IκBα degradation and NF-κB activity. PLoS One. 2012;7(12):e51672. doi: 10.1371/journal.pone.0051672. Epub 2012 Dec 20. PMID: 23284737 

Aillet F, Lopitz-Otsoa F, Hjerpe R, Torres-Ramos M, Lang V, Rodríguez MS. Isolation of ubiquitylated proteins using tandem ubiquitin-binding entities. Methods Mol Biol. 2012;832:173-83. doi: 10.1007/978-1-61779-474-2_12. PMID: 22350885 

Albers HM, Ovaa H. Chemical evolution of autotaxin inhibitors. Chem Rev. 2012 May 9;112(5):2593-603. doi: 10.1021/cr2003213. Epub 2012 Feb 15. Review. PMID: 22335786 

Allan C, Burel JM, Moore J, Blackburn C, Linkert M, Loynton S, Macdonald D, Moore WJ, Neves C, Patterson A, Porter M, Tarkowska A, Loranger B, Avondo J, Lagerstedt I, Lianas L, Leo S, Hands K, Hay RT, Patwardhan A, Best C, Kleywegt GJ, Zanetti G, Swedlow JR. OMERO: flexible, model-driven data management for experimental biology. Nat Methods. 2012 Feb 28;9(3):245-53. doi: 10.1038/nmeth.1896. PMID: 22373911 

Belgnaoui SM, Paz S, Samuel S, Goulet ML, Sun Q, Kikkert M, Iwai K, Dikic I, Hiscott J, Lin R. Linear ubiquitination of NEMO negatively regulates the interferon antiviral response through disruption of the MAVS-TRAF3 complex. Cell Host Microbe. 2012 Aug 16;12(2):211-22. doi: 10.1016/j.chom.2012.06.009. PMID: 22901541 

Belguise K, Milord S, Galtier F, Moquet-Torcy G, Piechaczyk M, Chalbos D. The PKCθ pathway participates in the aberrant accumulation of Fra-1 protein in invasive ER-negative breast cancer cells. Oncogene. 2012 Nov 22;31(47):4889-97. doi: 10.1038/onc.2011.659. Epub 2012 Jan 30. PMID: 22286759 

Beli P, Lukashchuk N, Wagner SA, Weinert BT, Olsen JV, Baskcomb L, Mann M, Jackson SP, Choudhary C. Proteomic investigations reveal a role for RNA processing factor THRAP3 in the DNA damage response. Mol Cell. 2012 Apr 27;46(2):212-25. doi: 10.1016/j.molcel.2012.01.026. Epub 2012 Mar 15. PMID: 22424773 

Berkers CR, Leestemaker Y, Schuurman KG, Ruggeri B, Jones-Bolin S, Williams M, Ovaa H. Probing the specificity and activity profiles of the proteasome inhibitors bortezomib and delanzomib. Mol Pharm. 2012 May 7;9(5):1126-35. doi: 10.1021/mp2004143. Epub 2012 Apr 16. PMID: 22432738 

Biard-Piechaczyk M, Borel S, Espert L, de Bettignies G, Coux O. HIV-1, ubiquitin and ubiquitin-like proteins: the dialectic interactions of a virus with a sophisticated network of post-translational modifications. Biol Cell. 2012 Mar;104(3):165-87. doi: 10.1111/boc.201100112. Epub 2012 Jan 23. Review. PMID: 22188301 

Boulon S, Bertrand E, Pradet-Balade B. HSP90 and the R2TP co-chaperone complex: building multi-protein machineries essential for cell growth and gene expression. RNA Biol. 2012 Feb;9(2):148-54. doi: 10.4161/rna.18494. Epub 2012 Feb 1. PMID: 22418846 

Bremm A, Komander D. Synthesis and analysis of K11-linked ubiquitin chains. Methods Mol Biol. 2012;832:219-28. doi: 10.1007/978-1-61779-474-2_15. PMID: 22350888 

Burns KE, McAllister FE, Schwerdtfeger C, Mintseris J, Cerda-Maira F, Noens EE, Wilmanns M, Hubbard SR, Melandri F, Ovaa H, Gygi SP, Darwin KH. Mycobacterium tuberculosis prokaryotic ubiquitin-like protein-deconjugating enzyme is an unusual aspartate amidase. J Biol Chem. 2012 Oct 26;287(44):37522-9. doi: 10.1074/jbc.M112.384784. Epub 2012 Aug 31. PMID: 22942282 

Camus S, Ménendez S, Fernandes K, Kua N, Liu G, Xirodimas DP, Lane DP, Bourdon JC. The p53 isoforms are differentially modified by Mdm2. Cell Cycle. 2012 Apr 15;11(8):1646-55. doi: 10.4161/cc.20119. Epub 2012 Apr 15. PMID: 2248768 

Cappellini E, Jensen LJ, Szklarczyk D, Ginolhac A, da Fonseca RA, Stafford TW, Holen SR, Collins MJ, Orlando L, Willerslev E, Gilbert MT, Olsen JV. Proteomic analysis of a pleistocene mammoth femur reveals more than one hundred ancient bone proteins. J Proteome Res. 2012 Feb 3;11(2):917-26. doi: 10.1021/pr200721u. Epub 2011 Dec 14. PMID: 22103443 

Da Silva-Ferrada E, Lopitz-Otsoa F, Lang V, Rodríguez MS, Matthiesen R. Strategies to Identify Recognition Signals and Targets of SUMOylation. Biochem Res Int. 2012;2012:875148. doi: 10.1155/2012/875148. Epub 2012 Jul 1. PMID: 22811915 

de Jong A, Merkx R, Berlin I, Rodenko B, Wijdeven RH, El Atmioui D, Yalçin Z, Robson CN, Neefjes JJ, Ovaa H. Ubiquitin-based probes prepared by total synthesis to profile the activity of deubiquitinating enzymes. Chembiochem. 2012 Oct 15;13(15):2251-8. doi: 10.1002/cbic.201200497. Epub 2012 Sep 25. PMID: 23011887 

Dikic I, Daly RJ. Signalling through the grapevine. EMBO Rep. 2012 Mar 1;13(3):178-80. doi: 10.1038/embor.2012.16. PMID: 22354089 

Dikic I, Robertson M. Ubiquitin ligases and beyond. BMC Biol. 2012 Mar 15;10:22. doi: 10.1186/1741-7007-10-22. No abstract available. PMID: 22420755 

Echalier A, Cot E, Camasses A, Hodimont E, Hoh F, Jay P, Sheinerman F, Krasinska L, Fisher D. An integrated chemical biology approach provides insight into Cdk2 functional redundancy and inhibitor sensitivity. Chem Biol. 2012 Aug 24;19(8):1028-40. doi: 10.1016/j.chembiol.2012.06.015. PMID: 22921070 

Egerod KL, Engelstoft MS, Grunddal KV, Nøhr MK, Secher A, Sakata I, Pedersen J, Windeløv JA, Füchtbauer EM, Olsen J, Sundler F, Christensen JP, Wierup N, Olsen JV, Holst JJ, Zigman JM, Poulsen SS, Schwartz TW. A major lineage of enteroendocrine cells coexpress CCK, secretin, GIP, GLP-1, PYY, and neurotensin but not somatostatin. Endocrinology. 2012 Dec;153(12):5782-95. doi: 10.1210/en.2012-1595. Epub 2012 Oct 12. PMID: 23064014 

Embade N, Fernández-Ramos D, Varela-Rey M, Beraza N, Sini M, Gutiérrez de Juan V, Woodhoo A, Martínez-López N, Rodríguez-Iruretagoyena B, Bustamante FJ, de la Hoz AB, Carracedo A, Xirodimas DP, Rodríguez MS, Lu SC, Mato JM, Martínez-Chantar ML. Murine double minute 2 regulates Hu antigen R stability in human liver and colon cancer through NEDDylation. Hepatology. 2012 Apr;55(4):1237-48. doi: 10.1002/hep.24795. Epub 2012 Mar 1. PMID: 22095636 

Federico L, Ren H, Mueller PA, Wu T, Liu S, Popovic J, Blalock EM, Sunkara M, Ovaa H, Albers HM, Mills GB, Morris AJ, Smyth SS. Autotaxin and its product lysophosphatidic acid suppress brown adipose differentiation and promote diet-induced obesity in mice. Mol Endocrinol. 2012 May;26(5):786-97. doi: 10.1210/me.2011-1229. Epub 2012 Apr 3. PMID: 22474126 

Ferreiro MJ, Rodríguez-Ezpeleta N, Pérez C, Hackenberg M, Aransay AM, Barrio R, Cantera R. Whole transcriptome analysis of a reversible neurodegenerative process in Drosophila reveals potential neuroprotective genes. BMC Genomics. 2012 Sep 15;13:483. doi: 10.1186/1471-2164-13-483. PMID: 22978642 

Fulda S, Rajalingam K, Dikic I. Ubiquitylation in immune disorders and cancer:  EMBO Mol Med. 2012 Jul;4(7):545-56. doi: 10.1002/emmm.201100707. Epub 2012 Jun 25. Review. PMID: 22730341 

Geurink PP, El Oualid F, Jonker A, Hameed DS, Ovaa H. A general chemical ligation approach towards isopeptide-linked ubiquitin and ubiquitin-like assay reagents. Chembiochem. 2012 Jan 23;13(2):293-7. doi: 10.1002/cbic.201100706. Epub 2011 Dec 23. No abstract available. PMID: 22213387 

González-Santamaría J, Campagna M, Ortega-Molina A, Marcos-Villar L, de la Cruz-Herrera CF, González D, Gallego P, Lopitz-Otsoa F, Esteban M, Rodríguez MS, Serrano M, Rivas C. Regulation of the tumor suppressor PTEN by SUMO. Cell Death Dis. 2012 Sep 27;3:e393. doi: 10.1038/cddis.2012.135. PMID: 23013792 

Guerra-Rebollo M, Mateo F, Franke K, Huen MS, Lopitz-Otsoa F, Rodríguez MS, Plans V, Thomson TM. Nucleolar exit of RNF8 and BRCA1 in response to DNA damage. Exp Cell Res. 2012 Nov 1;318(18):2365-76. doi: 10.1016/j.yexcr.2012.07.003. Epub 2012 Jul 16. PMID: 22814251 

Haglund K, Dikic I. The role of ubiquitylation in receptor endocytosis and endosomal sorting. J Cell Sci. 2012 Jan 15;125(Pt 2):265-75. doi: 10.1242/jcs.091280. PMID: 22357968 

Husnjak K, Dikic I. Ubiquitin-binding proteins: decoders of ubiquitin-mediated cellular functions. Annu Rev Biochem. 2012;81:291-322. doi: 10.1146/annurev-biochem-051810-094654. Epub 2012 Apr 5. Review. PMID: 22482907 

Kelstrup CD, Young C, Lavallee R, Nielsen ML, Olsen JV. Optimized Fast and Sensitive Acquisition Methods for Shotgun Proteomics on a Quadrupole Orbitrap Mass Spectrometer. J Proteome Res. 2012 May 10. PMID: 22537090 

Kensche T, Tokunaga F, Ikeda F, Goto E, Iwai K, Dikic I. Analysis of nuclear factor-κB (NF-κB) essential modulator (NEMO) binding to linear and lysine-linked ubiquitin chains and its role in the activation of NF-κB. J Biol Chem. 2012 Jul 6;287(28):23626-34. doi: 10.1074/jbc.M112.347195. Epub 2012 May 17. PMID: 22605335 

Keusekotten K, Komander D. New tools for ubiquitin signaling. J Mol Biol. 2012 May 4;418(3-4):129-30. doi: 10.1016/j.jmb.2012.02.032. Epub 2012 Feb 27. No abstract available. PMID: 22381406 

Klionsky DJ,… Dikic I…et al. Guidelines for the use and interpretation of assays for monitoring autophagy. Autophagy. 2012 Apr;8(4):445-544. PMID: 22966490 

Komander D, Rape M. The ubiquitin code. Annu Rev Biochem. 2012;81:203-29. doi: 10.1146/annurev-biochem-060310-170328. Epub 2012 Apr 10. Review. PMID: 22524316 

Korac J, Schaeffer V, Kovacevic I, Clement AM, Jungblut B, Behl C, Terzic J, Dikic I. Ubiquitin-independent function of optineurin in autophagic clearance of protein aggregates. J Cell Sci. 2012 Nov 23. [Epub ahead of print] PMID: 23178947 

Kulathu Y, Komander D. Atypical ubiquitylation - the unexplored world of polyubiquitin beyond Lys48 and Lys63 linkages. Nat Rev Mol Cell Biol. 2012 Jul 23;13(8):508-23. doi: 10.1038/nrm3394. Review. PMID: 22820888 

Lai SL, Yao WL, Tsao KC, Houben AJ, Albers HM, Ovaa H, Moolenaar WH, Lee SJ. Autotaxin/Lpar3 signaling regulates Kupffer's vesicle formation and left-right asymmetry in zebrafish. Development. 2012 Dec 1;139(23):4439-48. doi: 10.1242/dev.081745. Epub 2012 Oct 24. PMID: 2309589 

Larance M, Kirkwood KJ, Xirodimas DP, Lundberg E, Uhlen M, Lamond AI. Characterization of MRFAP1 turnover and interactions downstream of the NEDD8 pathway. Mol Cell Proteomics. 2012 Mar;11(3):M111.014407. doi: 10.1074/mcp.M111.014407. Epub 2011 Oct 29. PMID: 22038470 

Leidecker O, Matic I, Mahata B, Pion E, Xirodimas DP. The ubiquitin E1 enzyme Ube1 mediates NEDD8 activation under diverse stress  conditions. Cell Cycle. 2012 Mar 15;11(6):1142-50. doi: 10.4161/cc.11.6.19559. Epub 2012 Mar 15. PMID: 22370482 

Leidecker O, Xirodimas DP. Isolation of NEDDylated proteins in human cells. Methods Mol Biol. 2012;832:133-40. doi: 10.1007/978-1-61779-474-2_8. PMID: 22350881 

Lopitz-Otsoa F, Rodriguez-Suarez E, Aillet F, Casado-Vela J, Lang V, Matthiesen R, Elortza F, Rodriguez MS. Integrative analysis of the ubiquitin proteome isolated using Tandem Ubiquitin Binding Entities (TUBEs). J Proteomics. 2012 Jun 6;75(10):2998-3014. doi: 10.1016/j.jprot.2011.12.001. Epub 2011 Dec 10. PMID: 22178446 

Lundby A, Lage K, Weinert BT, Bekker-Jensen DB, Secher A, Skovgaard T, Kelstrup CD, Dmytriyev A, Choudhary C, Lundby C, Olsen JV. Proteomic analysis of lysine acetylation sites in rat tissues reveals organ specificity and subcellular patterns. Cell Rep. 2012 Aug 30;2(2):419-31. doi: 10.1016/j.celrep.2012.07.006. Epub 2012 Aug 16. PMID: 22902405 

Lundby A, Secher A, Lage K, Nordsborg NB, Dmytriyev A, Lundby C, Olsen JV. Quantitative maps of protein phosphorylation sites across 14 different rat organs and tissues. Nat Commun. 2012 Jun 6;3:876. doi: 10.1038/ncomms1871. PMID: 22673903 

Magnet C, Kuzhir P, Bossis G, Meunier A, Suloeva L, Zubarev A. Haloing in bimodal magnetic colloids: the role of field-induced phase separation. Phys Rev E Stat Nonlin Soft Matter Phys. 2012 Jul;86(1 Pt 1):011404. Epub 2012 Jul 13. PMID: 23005414 

Mahata B, Sundqvist A, Xirodimas DP. Recruitment of RPL11 at promoter sites of p53-regulated genes upon nucleolar stress through NEDD8 and in an Mdm2-dependent manner. Oncogene. 2012 Jun 21;31(25):3060-71. doi: 10.1038/onc.2011.482. Epub 2011 Nov 14. PMID: 22081073 

Matic I, Ahel I, Hay RT. Reanalysis of phosphoproteomics data uncovers ADP-ribosylation sites. Nat Methods. 2012 Jul 30;9(8):771-2. doi: 10.1038/nmeth.2106. No abstract available. PMID: 22847107 

Matic I, Hay RT. Detection and quantitation of SUMO chains by mass spectrometry. Methods Mol Biol. 2012;832:239-47. doi: 10.1007/978-1-61779-474-2_17. PMID: 22350890 

Mayor U, Peng J. Deciphering tissue-specific ubiquitylation by mass spectrometry. Methods Mol Biol. 2012;832:65-80. doi: 10.1007/978-1-61779-474-2_3. PMID: 22350876 

Merkx R, Burns KE, Slobbe P, El Oualid F, El Atmioui D, Darwin KH, Ovaa H. Synthesis and evaluation of a selective fluorogenic Pup derived assay reagent for Dop, a potential drug target in Mycobacterium tuberculosis. Chembiochem. 2012 Sep 24;13(14):2056-60. doi: 10.1002/cbic.201200460. Epub 2012 Aug 24. PMID: 22927162 

Nagaraj N, D'Souza RC, Cox J, Olsen JV, Mann M. Correction to Feasibility of Large-Scale Phosphoproteomics with Higher Energy Collisional Dissociation Fragmentation. J Proteome Res. 2012 May 21. [Epub ahead of print] No abstract available. PMID: 22612759 

Oualid FE, Hameed DS, Atmioui DE, Hilkmann H, Ovaa H. Synthesis of atypical diubiquitin chains. Methods Mol Biol. 2012;832:597-609. doi: 10.1007/978-1-61779-474-2_42. PMID: 22350915 

Pareja F, Ferraro DA, Rubin C, Cohen-Dvashi H, Zhang F, Aulmann S, Ben-Chetrit N, Pines G, Navon R, Crosetto N, Köstler W, Carvalho S, Lavi S, Schmitt F, Dikic I, Yakhini Z, Sinn P, Mills GB, Yarden Y. Deubiquitination of EGFR by Cezanne-1 contributes to cancer progression. Oncogene. 2012 Oct 25;31(43):4599-608. doi: 10.1038/onc.2011.587. Epub 2011 Dec 19. PMID: 22179831 

Pérez-Benavente B, García JL, Rodríguez MS, Pineda-Lucena A, Piechaczyk M, Font de Mora J, Farràs R. GSK3-SCF(FBXW7) targets JunB for degradation in G2 to preserve chromatid cohesion before anaphase. Oncogene. 2012 Jun 18. doi: 10.1038/onc.2012.235. PMID: 22710716 

Plechanovová A, Jaffray EG, Tatham MH, Naismith JH, Hay RT. Structure of a RING E3 ligase and ubiquitin-loaded E2 primed for catalysis. Nature. 2012 Sep 6;489(7414):115-20. doi: 10.1038/nature11376. PMID: 22842904

Pohl C, Dikic I. Fighting mycobacteria through ISGylation. EMBO Rep. 2012 Oct;13(10):872-3. doi: 10.1038/embor.2012.129. Epub 2012 Aug 31. PMID: 22940737 

Popovic D, Akutsu M, Novak I, Harper JW, Behrends C, Dikic I. Rab GTPase-activating proteins in autophagy: regulation of endocytic and autophagy pathways by direct binding to human ATG8 modifiers. Mol Cell Biol. 2012 May;32(9):1733-44. doi: 10.1128/MCB.06717-11. Epub 2012 Feb 21. PMID: 22354992 

Rahighi S, Dikic I. Selectivity of the ubiquitin-binding modules. FEBS Lett. 2012 Aug 14;586(17):2705-10. doi: 10.1016/j.febslet.2012.04.053. Epub 2012 May 5. Review. PMID: 22569095 

Rizvi H, Paterson JC, Tedoldi S, Ramsay A, Calaminici M, Natkunam Y, Lonardi S, Tan SY, Campbell L, Hansmann ML, Jones D, Dikic I, Shaw AS, Pileri SA, Stein H, Mason DY, Facchetti F, Marafioti T. Expression of the CD2AP adaptor molecule in normal, reactive and neoplastic human tissue. Pathologica. 2012 Apr;104(2):56-64. PMID: 22953501 

Rogov VV, Rozenknop A, Rogova NY, Löhr F, Tikole S, Jaravine V, Güntert P, Dikic I, Dötsch V. A universal expression tag for structural and functional studies of proteins. Chembiochem. 2012 May 7;13(7):959-63. doi: 10.1002/cbic.201200045. Epub 2012 Mar 20. PMID: 22434781 

Rohaim A, Kawasaki M, Kato R, Dikic I, Wakatsuki S. Structure of a compact conformation of linear diubiquitin. Acta Crystallogr D Biol Crystallogr. 2012 Feb;68(Pt 2):102-8. doi: 10.1107/S0907444911051195. Epub 2012 Jan 13. PMID: 22281738 

Rosenzweig R, Bronner V, Zhang D, Fushman D, Glickman MH. Rpn1 and Rpn2 coordinate ubiquitin processing factors at proteasome. J Biol Chem. 2012 Apr 27;287(18):14659-71. doi: 10.1074/jbc.M111.316323. Epub 2012 Feb 8. PMID: 22318722 

Sayan AE, Stanford R, Vickery R, Grigorenko E, Diesch J, Kulbicki K, Edwards R, Pal R, Greaves P, Jariel-Encontre I, Piechaczyk M, Kriajevska M, Mellon JK, Dhillon AS, Tulchinsky E. Fra-1 controls motility of bladder cancer cells via transcriptional upregulation of the receptor tyrosine kinase AXL. Oncogene. 2012 Mar 22;31(12):1493-503. doi: 10.1038/onc.2011.336. Epub 2011 Aug 8. PMID: 21822309 

Schreiner S, Martinez R, Groitl P, Rayne F, Vaillant R, Wimmer P, Bossis G, Sternsdorf T, Marcinowski L, Ruzsics Z, Dobner T, Wodrich H. Transcriptional activation of the adenoviral genome is mediated by capsid protein VI. PLoS Pathog. 2012 Feb;8(2):e1002549. doi: 10.1371/journal.ppat.1002549. Epub 2012 Feb 23. PMID: 22427750 

Schulz S, Chachami G, Kozaczkiewicz L, Winter U, Stankovic-Valentin N, Haas P, Hofmann K, Urlaub H, Ovaa H, Wittbrodt J, Meulmeester E, Melchior F. Ubiquitin-specific protease-like 1 (USPL1) is a SUMO isopeptidase with essential, non-catalytic functions. EMBO Rep. 2012 Oct;13(10):930-8. doi: 10.1038/embor.2012.125. Epub 2012 Aug 10. PMID: 22878415 

Stieglitz B, Haire LF, Dikic I, Rittinger K. Structural analysis of SHARPIN, a subunit of a large multi-protein E3 ubiquitin ligase, reveals a novel dimerization function for the pleckstrin homology superfold. J Biol Chem. 2012 Jun 15;287(25):20823-9. doi: 10.1074/jbc.M112.359547. Epub 2012 May 1. PMID: 22549881 

Sturrock M, Terry AJ, Xirodimas DP, Thompson AM, Chaplain MA. Influence of the nuclear membrane, active transport, and cell shape on the Hes1 and p53-Mdm2 pathways: insights from spatio-temporal modelling. Bull Math Biol. 2012 Jul;74(7):1531-79. doi: 10.1007/s11538-012-9725-1. Epub 2012 Apr 20. PMID: 22527944 

van Wijk SJ, Bienko M, Dikic I. Role of UbL family modifiers and their binding proteins in cell signaling. Methods Mol Biol. 2012;832:163-71. doi: 10.1007/978-1-61779-474-2_11. PMID: 22350884 

van Wijk SJ, Fiskin E, Putyrski M, Pampaloni F, Hou J, Wild P, Kensche T, Grecco HE, Bastiaens P, Dikic I. Fluorescence-based sensors to monitor localization and functions of linear and K63-linked ubiquitin chains in cells. Mol Cell. 2012 Sep 14;47(5):797-809. doi: 10.1016/j.molcel.2012.06.017. Epub 2012 Jul 19. PMID: 22819327 

Verhelst K, Carpentier I, Kreike M, Meloni L, Verstrepen L, Kensche T, Dikic I, Beyaert R. A20 inhibits LUBAC-mediated NF-κB activation by binding linear polyubiquitin chains via its zinc finger 7. EMBO J. 2012 Oct 3;31(19):3845-55. doi: 10.1038/emboj.2012.240. Epub 2012 Aug 28. PMID: 23032186 

von Muhlinen N, Akutsu M, Ravenhill BJ, Foeglein Á, Bloor S, Rutherford TJ, Freund SM, Komander D, Randow F. LC3C, bound selectively by a noncanonical LIR motif in NDP52, is required for antibacterial autophagy. Mol Cell. 2012 Nov 9;48(3):329-42. doi: 10.1016/j.molcel.2012.08.024. Epub 2012 Sep 27. PMID: 23022382 

Wagner SA, Beli P, Weinert BT, Schölz C, Kelstrup CD, Young C, Nielsen ML, Olsen JV, Brakebusch C, Choudhary C. Proteomic analyses reveal divergent ubiquitylation site patterns in murine tissues. Mol Cell Proteomics. 2012 Dec;11(12):1578-85. doi: 10.1074/mcp.M112.017905. Epub 2012 Jul 11. PMID: 22790023 

Walczak H, Iwai K, Dikic I. Generation and physiological roles of linear ubiquitin chains. BMC Biol. 2012 Mar 15;10:23. doi: 10.1186/1741-7007-10-23. Review. PMID: 22420778 

Xolalpa W, Perez-Galan P, Rodríguez MS, Roue G. Targeting the Ubiquitin Proteasome System: beyond proteasome inhibition. Curr Pharm Des. 2012 Nov 23. [Epub ahead of print] PMID: 23181575 

Ye Y, Blaser G, Horrocks MH, Ruedas-Rama MJ, Ibrahim S, Zhukov AA, Orte A, Klenerman D, Jackson SE, Komander D. Ubiquitin chain conformation regulates recognition and activity of interacting proteins. Nature. 2012 Dec 13;492(7428):266-70. doi: 10.1038/nature11722. Epub 2012 Dec 2. PMID: 23201676 

Yin Y, Seifert A, Chua JS, Maure JF, Golebiowski F, Hay RT. SUMO-targeted ubiquitin E3 ligase RNF4 is required for the response of human cells to DNA damage. Genes Dev. 2012 Jun 1;26(11):1196-208. doi: 10.1101/gad.189274.112. PMID: 22661230 

Zhang G, Kelstrup CD, Hu XW, Kaas Hansen MJ, Singleton MR, Olsen JV, Nilsson J. The Ndc80 internal loop is required for recruitment of the Ska complex to establish end-on microtubule attachment to kinetochores. J Cell Sci. 2012 Jul 1;125(Pt 13):3243-53. doi: 10.1242/jcs.104208. Epub 2012 Mar 27. PMID: 22454517 

Zhang L, Huang H, Zhou F, Schimmel J, Pardo CG, Zhang T, Barakat TS, Sheppard KA, Mickanin C, Porter JA, Vertegaal AC, van Dam H, Gribnau J, Lu CX, ten Dijke P. RNF12 controls embryonic stem cell fate and morphogenesis in zebrafish embryos by targeting Smad7 for degradation. Mol Cell. 2012 Jun 8;46(5):650-61. doi: 10.1016/j.molcel.2012.04.003. Epub 2012 May 3. Erratum in: Mol Cell. 2012 Jul 27;47(2):330. PMID: 22560923 

Zhou W, Hannoun Z, Jaffray E, Medine CN, Black JR, Greenhough S, Zhu L, Ross JA, Forbes S, Wilmut I, Iredale JP, Hay RT, Hay DC. SUMOylation of HNF4α regulates protein stability and hepatocyte function. J Cell Sci. 2012 Aug 1;125(Pt 15):3630-5. Epub 2012 Apr 14. PMID: 22505616