Research Group Matic

March 2, 2017 Volume 65 No 5 (Bonfiglio et al.)
March 2, 2017 Volume 65 No 5 (Bonfiglio et al.)

Publications

Immunoprecipitation Using Mono-ADP-Ribosylation-Specific Antibodies

  • Dauben, H.
  • Matic, I.
(2023) Methods Mol Biol, 2609, 135-146

Hypoxia promotes osteogenesis by facilitating acetyl-CoA-mediated mitochondrial-nuclear communication

  • Pouikli, A.
  • Maleszewska, M.
  • Parekh, S.
  • Yang, M.
  • Nikopoulou, C.
  • Bonfiglio, J. J.
  • Mylonas, C.
  • Sandoval, T.
  • Schumacher, A. L.
  • Hinze, Y.
  • Matic, I.
  • Frezza, C.
  • Tessarz, P.
(2022) EMBO J, e111239

The fast-growing business of Serine ADP-ribosylation

  • Longarini, E. J.
  • Matic, I.
(2022) DNA Repair (Amst), 118, 103382

Structural basis for protein glutamylation by the Legionella pseudokinase SidJ

  • Adams, M.
  • Sharma, R.
  • Colby, T.
  • Weis, F.
  • Matic, I.
  • Bhogaraju, S.
(2021) Nat Commun, 12, 1, 6174

ADP-ribosyltransferases, an update on function and nomenclature

  • Luscher, B.
  • Ahel, I.
  • Altmeyer, M.
  • Ashworth, A.
  • Bai, P.
  • Chang, P.
  • Cohen, M.
  • Corda, D.
  • Dantzer, F.
  • Daugherty, M. D.
  • Dawson, T. M.
  • Dawson, V. L.
  • Deindl, S.
  • Fehr, A. R.
  • Feijs, K. L. H.
  • Filippov, D. V.
  • Gagne, J. P.
  • Grimaldi, G.
  • Guettler, S.
  • Hoch, N. C.
  • Hottiger, M. O.
  • Korn, P.
  • Kraus, W. L.
  • Ladurner, A.
  • Lehtio, L.
  • Leung, A. K. L.
  • Lord, C. J.
  • Mangerich, A.
  • Matic, I.
  • Matthews, J.
  • Moldovan, G. L.
  • Moss, J.
  • Natoli, G.
  • Nielsen, M. L.
  • Niepel, M.
  • Nolte, F.
  • Pascal, J.
  • Paschal, B. M.
  • Pawlowski, K.
  • Poirier, G. G.
  • Smith, S.
  • Timinszky, G.
  • Wang, Z. Q.
  • Yelamos, J.
  • Yu, X.
  • Zaja, R.
  • Ziegler, M.
(2021) FEBS J

Serine-ubiquitination regulates Golgi morphology and the secretory pathway upon Legionella infection

  • Liu, Y.
  • Mukherjee, R.
  • Bonn, F.
  • Colby, T.
  • Matic, I.
  • Glogger, M.
  • Heilemann, M.
  • Dikic, I.
(2021) Cell Death Differ, 28, 10, 2957-2969

An HPF1/PARP1-Based Chemical Biology Strategy for Exploring ADP-Ribosylation

  • Bonfiglio, J. J.
  • Leidecker, O.
  • Dauben, H.
  • Longarini, E. J.
  • Colby, T.
  • San Segundo-Acosta, P.
  • Perez, K. A.
  • Matic, I.
(2020) Cell, 183, 4, 1086-1102 e23

Interplay of Histone Marks with Serine ADP-Ribosylation

  • Bartlett, E.
  • Bonfiglio, J. J.
  • Prokhorova, E.
  • Colby, T.
  • Zobel, F.
  • Ahel, I.
  • Matic, I.
(2018) Cell Rep, 24, 13, 3488-3502 e5

Nonlocalized Searching of HCD Data for Fast and Sensitive Identification of ADP-Ribosylated Peptides

  • Colby, T.
  • Bonfiglio, J. J.
  • Matic, I.
(2018) Methods Mol Biol, 1813, 255-269

Serine is the major residue for ADP-ribosylation upon DNA damage

  • Palazzo, L.*
  • Leidecker, O.*
  • Prokhorova, E.*
  • Dauben, H.
  • Matic, I.**
  • Ahel, I.**
(2018) Elife, 7

Specificity of reversible ADP-ribosylation and regulation of cellular processes

  • Crawford, K.
  • Bonfiglio, J. J.
  • Mikoc, A.
  • Matic, I.
  • Ahel, I.
(2018) Crit Rev Biochem Mol Biol, 53, 1, 64-82

Mitotic post-translational modifications of histones promote chromatin compaction in vitro

  • Zhiteneva, A.
  • Bonfiglio, J. J.
  • Makarov, A.
  • Colby, T.
  • Vagnarelli, P.
  • Schirmer, E. C.
  • Matic, I.
  • Earnshaw, W. C.
(2017) Open Biol, 7, 9

Serine ADP-ribosylation reversal by the hydrolase ARH3

  • Fontana, P.*
  • Bonfiglio, J. J.*
  • Palazzo, L.*
  • Bartlett, E.
  • Matic, I.**
  • Ahel, I.**
(2017) Elife, 6

Mass spectrometry for serine ADP-ribosylation? Think o-glycosylation!

  • Bonfiglio, J. J.
  • Colby, T.
  • Matic, I.
(2017) Nucleic Acids Res, 45, 11, 6259-6264

cAMP-dependent cell differentiation triggered by activated CRHR1 in hippocampal neuronal cells

  • Inda, C.
  • Bonfiglio, J. J.
  • Dos Santos Claro, P. A.
  • Senin, S. A.
  • Armando, N. G.
  • Deussing, J. M.
  • Silberstein, S.
(2017) Sci Rep, 7(1): 1944

Serine ADP-Ribosylation Depends on HPF1

  • Bonfiglio, J. J.
  • Fontana, P.
  • Zhang, Q.
  • Colby, T.
  • Gibbs-Seymour, I.
  • Atanassov, I.
  • Bartlett, E.
  • Zaja, R.
  • Ahel, I.**
  • Matic, I.**
(2017) Mol Cell, 65, 5, 932-940 e6

Phosphoribosylation of Ubiquitin Promotes Serine Ubiquitination and Impairs Conventional Ubiquitination

  • Bhogaraju, S.
  • Kalayil, S.
  • Liu, Y.
  • Bonn, F.
  • Colby, T.
  • Matic, I.
  • Dikic, I.
(2016) Cell, 167, 6, 1636-1649 e13

Serine is a new target residue for endogenous ADP-ribosylation on histones

  • Leidecker, O.*
  • Bonfiglio, J. J.*
  • Colby, T.
  • Zhang, Q.
  • Atanassov, I.
  • Zaja, R.
  • Palazzo, L.
  • Stockum, A.
  • Ahel, I.
  • Matic, I.
(2016) Nat Chem Biol, 12, 12, 998-1000

Disruption of Macrodomain Protein SCO6735 Increases Antibiotic Production in Streptomyces coelicolor

  • Lalić, J.
  • Posavec Marjanović, M.
  • Palazzo, L.
  • Perina, D.
  • Sabljić, I.
  • Žaja, R.
  • Colby, T.
  • Pleše, B.
  • Halasz, M.
  • Jankevicius, G.
  • Bucca, G.
  • Ahel, M.
  • Matić, I.
  • Ćetković, H.
  • Luić, M.
  • Mikoč, A.
  • Ahel, I.
(2016) J Biol Chem, 291(44): 23175-23187

Proteome-wide identification of SUMO modification sites by mass spectrometry

  • Tammsalu, T.*
  • Matic, I.*
  • Jaffray, E. G.
  • Ibrahim, A. F.
  • Tatham, M. H.
  • Hay, R. T.
(2015) Nat Protoc, 10, 9, 1374-88

Identification of a Class of Protein ADP-Ribosylating Sirtuins in Microbial Pathogens

  • Rack, J. G.
  • Morra, R.
  • Barkauskaite, E.
  • Kraehenbuehl, R.
  • Ariza, A.
  • Qu, Y.
  • Ortmayer, M.
  • Leidecker, O.
  • Cameron, D. R.
  • Matic, I.
  • Peleg, A. Y.
  • Leys, D.
  • Traven, A.
  • Ahel, I.
(2015) Mol Cell, 59, 2, 309-20

Processing of protein ADP-ribosylation by Nudix hydrolases

  • Palazzo, L.
  • Thomas, B.
  • Jemth, A. S.
  • Colby, T.
  • Leidecker, O.
  • Feijs, K. L.
  • Zaja, R.
  • Loseva, O.
  • Puigvert, J. C.
  • Matic, I.
  • Helleday, T.
  • Ahel, I.
(2015) Biochem J, 468, 2, 293-301

Family-wide analysis of poly(ADP-ribose) polymerase activity

  • Vyas, S.*
  • Matic, I.*
  • Uchima, L.
  • Rood, J.
  • Zaja, R.
  • Hay, R. T.
  • Ahel, I.
  • Chang, P.
(2014) Nat Commun, 5, 4426

Proteome-wide identification of SUMO2 modification sites

  • Tammsalu, T.*
  • Matic, I.*
  • Jaffray, E. G.
  • Ibrahim, A. F.
  • Tatham, M. H.
  • Hay, R. T.
(2014) Sci Signal, 7, 323, rs2

Deficiency of terminal ADP-ribose protein glycohydrolase TARG1/C6orf130 in neurodegenerative disease

  • Sharifi, R.
  • Morra, R.
  • Appel, C. D.
  • Tallis, M.
  • Chioza, B.
  • Jankevicius, G.
  • Simpson, M. A.
  • Matic, I.
  • Ozkan, E.
  • Golia, B.
  • Schellenberg, M. J.
  • Weston, R.
  • Williams, J. G.
  • Rossi, M. N.
  • Galehdari, H.
  • Krahn, J.
  • Wan, A.
  • Trembath, R. C.
  • Crosby, A. H.
  • Ahel, D.
  • Hay, R.
  • Ladurner, A. G.
  • Timinszky, G.
  • Williams, R. S.
  • Ahel, I.
(2013) EMBO J, 32, 9, 1225-37

Mediator phosphorylation prevents stress response transcription during non-stress conditions

  • Miller, C.*
  • Matic, I.*
  • Maier, K. C.*
  • Schwalb, B.
  • Roether, S.
  • Strasser, K.
  • Tresch, A.
  • Mann, M.
  • Cramer, P.
(2012) J Biol Chem, 287, 53, 44017-26

Reanalysis of phosphoproteomics data uncovers ADP-ribosylation sites

  • Matic, I.**
  • Ahel, I.
  • Hay, R. T.
(2012) Nat Methods, 9, 8, 771-2

The ubiquitin E1 enzyme Ube1 mediates NEDD8 activation under diverse stress conditions

  • Leidecker, O.
  • Matic, I.
  • Mahata, B.
  • Pion, E.
  • Xirodimas, D. P.
(2012) Cell Cycle, 11, 6, 1142-50

Detection and quantitation of SUMO chains by mass spectrometry

  • Matic, I.**
  • Hay, R. T.
(2012) Methods Mol Biol, 832, 239-47

Absolute SILAC-compatible expression strain allows Sumo-2 copy number determination in clinical samples

  • Matic, I.
  • Jaffray, E. G.
  • Oxenham, S. K.
  • Groves, M. J.
  • Barratt, C. L.
  • Tauro, S.
  • Stanley-Wall, N. R.
  • Hay, R. T.
(2011) J Proteome Res, 10, 10, 4869-75

Comparative proteomic analysis identifies a role for SUMO in protein quality control

  • Tatham, M. H.
  • Matic, I.
  • Mann, M.
  • Hay, R. T.
(2011) Sci Signal, 4, 178, rs4

Purification and identification of endogenous polySUMO conjugates

  • Bruderer, R.
  • Tatham, M. H.
  • Plechanovova, A.
  • Matic, I.
  • Garg, A. K.
  • Hay, R. T.
(2011) EMBO Rep, 12, 2, 142-8

Defining the transcriptome and proteome in three functionally different human cell lines

  • Lundberg, E.
  • Fagerberg, L.
  • Klevebring, D.
  • Matic, I.
  • Geiger, T.
  • Cox, J.
  • Algenas, C.
  • Lundeberg, J.
  • Mann, M.
  • Uhlen, M.
(2010) Mol Syst Biol, 6, 450

Site-specific identification of SUMO-2 targets in cells reveals an inverted SUMOylation motif and a hydrophobic cluster SUMOylation motif

  • Matic, I.*
  • Schimmel, J.*
  • Hendriks, I. A.*
  • van Santen, M. A.*
  • van de Rijke, F.
  • van Dam, H.
  • Gnad, F.
  • Mann, M.
  • Vertegaal, A. C.
(2010) Mol Cell, 39, 4, 641-52

Regulation of translesion synthesis DNA polymerase eta by monoubiquitination

  • Bienko, M.
  • Green, C. M.
  • Sabbioneda, S.
  • Crosetto, N.
  • Matic, I.
  • Hibbert, R. G.
  • Begovic, T.
  • Niimi, A.
  • Mann, M.
  • Lehmann, A. R.
  • Dikic, I.
(2010) Mol Cell, 37, 3, 396-407

System-wide changes to SUMO modifications in response to heat shock

  • Golebiowski, F.*
  • Matic, I.*
  • Tatham, M. H.*
  • Cole, C.
  • Yin, Y.
  • Nakamura, A.
  • Cox, J.
  • Barton, G. J.
  • Mann, M.
  • Hay, R. T.
(2009) Sci Signal, 2, 72, ra24

A practical guide to the MaxQuant computational platform for SILAC-based quantitative proteomics

  • Cox, J.
  • Matic, I.
  • Hilger, M.
  • Nagaraj, N.
  • Selbach, M.
  • Olsen, J. V.
  • Mann, M.
(2009) Nat Protoc, 4, 5, 698-705

Identification of SUMO target proteins by quantitative proteomics

  • Andersen, J. S.
  • Matic, I.
  • Vertegaal, A. C.
(2009) Methods Mol Biol, 497, 19-31

The ubiquitin-proteasome system is a key component of the SUMO-2/3 cycle

  • Schimmel, J.*
  • Larsen, K. M.*
  • Matic, I.*
  • van Hagen, M.
  • Cox, J.
  • Mann, M.
  • Andersen, J. S.
  • Vertegaal, A. C.
(2008) Mol Cell Proteomics, 7, 11, 2107-22

Phosphorylation of SUMO-1 occurs in vivo and is conserved through evolution

  • Matic, I.
  • Macek, B.
  • Hilger, M.
  • Walther, T. C.
  • Mann, M.
(2008) J Proteome Res, 7, 9, 4050-7

In vivo identification of human small ubiquitin-like modifier polymerization sites by high accuracy mass spectrometry and an in vitro to in vivo strategy

  • Matic, I.
  • van Hagen, M.
  • Schimmel, J.
  • Macek, B.
  • Ogg, S. C.
  • Tatham, M. H.
  • Hay, R. T.
  • Lamond, A. I.
  • Mann, M.
  • Vertegaal, A. C.
(2008) Mol Cell Proteomics, 7, 1, 132-44

Proteomic-based analysis of nuclear signaling: PLCbeta1 affects the expression of the splicing factor SRp20 in Friend erythroleukemia cells

  • Bavelloni, A.
  • Faenza, I.
  • Cioffi, G.
  • Piazzi, M.
  • Parisi, D.
  • Matic, I.
  • Maraldi, N. M.
  • Cocco, L.
(2006) Proteomics, 6, 21, 5725-34

*equal contribution; **corresponding author