Chunaram Choudhary

Summary

Publications

  1. pmc A proteome-wide, quantitative survey of in vivo ubiquitylation sites reveals widespread regulatory roles
    Sebastian A Wagner
    Department of Proteomics, The NNF Center for Protein Research, Faculty of Health Sciences, University of Copenhagen, Blegdamsvej 3b, DK 2200 Copenhagen, Denmark
    Mol Cell Proteomics 10:M111.013284. 2011
  2. pmc A phospho-proteomic screen identifies substrates of the checkpoint kinase Chk1
    Melanie Blasius
    The Gurdon Institute and Department of Biochemistry, University of Cambridge, Cambridge CB2 1QN, UK
    Genome Biol 12:R78. 2011
  3. doi request reprint Decoding signalling networks by mass spectrometry-based proteomics
    Chunaram Choudhary
    The Novo Nordisk Foundation Center for Protein Research, Faculty of Health Sciences, University of Copenhagen, 2200 Copenhagen, Denmark
    Nat Rev Mol Cell Biol 11:427-39. 2010
  4. doi request reprint Lysine succinylation is a frequently occurring modification in prokaryotes and eukaryotes and extensively overlaps with acetylation
    Brian T Weinert
    The NNF Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Blegdamsvej 3b, 2200 Copenhagen, Denmark
    Cell Rep 4:842-51. 2013
  5. pmc Proteomic analyses reveal divergent ubiquitylation site patterns in murine tissues
    Sebastian A Wagner
    Department of Proteomics, The NNF Center for Protein Research, Faculty of Health Sciences, University of Copenhagen, Blegdamsvej 3b, DK 2200 Copenhagen, Denmark
    Mol Cell Proteomics 11:1578-85. 2012
  6. pmc A new cellular stress response that triggers centriolar satellite reorganization and ciliogenesis
    Bine H Villumsen
    Ubiquitin Signaling Group, Department of Disease Biology, The Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, Copenhagen, Denmark
    EMBO J 32:3029-40. 2013
  7. pmc RNF111/Arkadia is a SUMO-targeted ubiquitin ligase that facilitates the DNA damage response
    Sara L Poulsen
    Ubiquitin Signaling Group, Department of Disease Biology, The Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, DK 2200 Copenhagen, Denmark
    J Cell Biol 201:797-807. 2013
  8. doi request reprint Systems-wide analysis of ubiquitylation dynamics reveals a key role for PAF15 ubiquitylation in DNA-damage bypass
    Lou K Povlsen
    Ubiquitin Signaling Group, Department of Disease Biology, The Novo Nordisk Foundation Center for Protein Research, Faculty of Health Sciences, University of Copenhagen, Blegdamsvej 3b, DK 2200 Copenhagen, Denmark
    Nat Cell Biol 14:1089-98. 2012
  9. pmc Proteome-wide analysis of lysine acetylation suggests its broad regulatory scope in Saccharomyces cerevisiae
    Peter Henriksen
    Department of Proteomics, The Novo Nordisk Foundation Center for Protein Research, Faculty of Health Sciences, University of Copenhagen, Blegdamsvej 3, DK 2200 Copenhagen, Denmark
    Mol Cell Proteomics 11:1510-22. 2012
  10. doi request reprint Proteome-wide mapping of the Drosophila acetylome demonstrates a high degree of conservation of lysine acetylation
    Brian T Weinert
    Department of Proteomics, The Novo Nordisk Foundation Center for Protein Research, Faculty of Health Sciences, University of Copenhagen, Blegdamsvej 3, 2200 Copenhagen, Denmark
    Sci Signal 4:ra48. 2011

Collaborators

Detail Information

Publications31

  1. pmc A proteome-wide, quantitative survey of in vivo ubiquitylation sites reveals widespread regulatory roles
    Sebastian A Wagner
    Department of Proteomics, The NNF Center for Protein Research, Faculty of Health Sciences, University of Copenhagen, Blegdamsvej 3b, DK 2200 Copenhagen, Denmark
    Mol Cell Proteomics 10:M111.013284. 2011
    ..Taken together, we report the largest site-specific ubiquitylation dataset in human cells, and for the first time demonstrate proteome-wide, site-specific quantification of endogenous putative ubiquitylation sites...
  2. pmc A phospho-proteomic screen identifies substrates of the checkpoint kinase Chk1
    Melanie Blasius
    The Gurdon Institute and Department of Biochemistry, University of Cambridge, Cambridge CB2 1QN, UK
    Genome Biol 12:R78. 2011
    ..Despite its paramount importance, how Chk1 controls these functions remains unclear, mainly because very few Chk1 substrates have hitherto been identified...
  3. doi request reprint Decoding signalling networks by mass spectrometry-based proteomics
    Chunaram Choudhary
    The Novo Nordisk Foundation Center for Protein Research, Faculty of Health Sciences, University of Copenhagen, 2200 Copenhagen, Denmark
    Nat Rev Mol Cell Biol 11:427-39. 2010
    ..Large-scale proteomics-based signalling research will fundamentally change our understanding of signalling networks...
  4. doi request reprint Lysine succinylation is a frequently occurring modification in prokaryotes and eukaryotes and extensively overlaps with acetylation
    Brian T Weinert
    The NNF Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Blegdamsvej 3b, 2200 Copenhagen, Denmark
    Cell Rep 4:842-51. 2013
    ..These data provide a systems-wide view of succinylation and its dynamic regulation and show its extensive overlap with acetylation. ..
  5. pmc Proteomic analyses reveal divergent ubiquitylation site patterns in murine tissues
    Sebastian A Wagner
    Department of Proteomics, The NNF Center for Protein Research, Faculty of Health Sciences, University of Copenhagen, Blegdamsvej 3b, DK 2200 Copenhagen, Denmark
    Mol Cell Proteomics 11:1578-85. 2012
    ....
  6. pmc A new cellular stress response that triggers centriolar satellite reorganization and ciliogenesis
    Bine H Villumsen
    Ubiquitin Signaling Group, Department of Disease Biology, The Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, Copenhagen, Denmark
    EMBO J 32:3029-40. 2013
    ....
  7. pmc RNF111/Arkadia is a SUMO-targeted ubiquitin ligase that facilitates the DNA damage response
    Sara L Poulsen
    Ubiquitin Signaling Group, Department of Disease Biology, The Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, DK 2200 Copenhagen, Denmark
    J Cell Biol 201:797-807. 2013
    ..Our findings establish RNF111 as a new STUbL that directly links nonproteolytic ubiquitylation and SUMOylation in the DNA damage response...
  8. doi request reprint Systems-wide analysis of ubiquitylation dynamics reveals a key role for PAF15 ubiquitylation in DNA-damage bypass
    Lou K Povlsen
    Ubiquitin Signaling Group, Department of Disease Biology, The Novo Nordisk Foundation Center for Protein Research, Faculty of Health Sciences, University of Copenhagen, Blegdamsvej 3b, DK 2200 Copenhagen, Denmark
    Nat Cell Biol 14:1089-98. 2012
    ..Our findings demonstrate widespread involvement of ubiquitin signalling in genotoxic-stress responses and identify a critical function for dynamic PAF15 ubiquitylation in safeguarding genome integrity when DNA replication is challenged...
  9. pmc Proteome-wide analysis of lysine acetylation suggests its broad regulatory scope in Saccharomyces cerevisiae
    Peter Henriksen
    Department of Proteomics, The Novo Nordisk Foundation Center for Protein Research, Faculty of Health Sciences, University of Copenhagen, Blegdamsvej 3, DK 2200 Copenhagen, Denmark
    Mol Cell Proteomics 11:1510-22. 2012
    ..The provided dataset may serve as an important resource for the functional analysis of lysine acetylation in eukaryotes...
  10. doi request reprint Proteome-wide mapping of the Drosophila acetylome demonstrates a high degree of conservation of lysine acetylation
    Brian T Weinert
    Department of Proteomics, The Novo Nordisk Foundation Center for Protein Research, Faculty of Health Sciences, University of Copenhagen, Blegdamsvej 3, 2200 Copenhagen, Denmark
    Sci Signal 4:ra48. 2011
    ..This systems-level analysis of comparative posttranslational modification showed that acetylation is an anciently conserved modification and suggests that phosphorylation sites may have evolved faster than acetylation sites...
  11. doi request reprint Acetyl-phosphate is a critical determinant of lysine acetylation in E. coli
    Brian T Weinert
    The NNF Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Blegdamsvej 3b, DK 2200 Copenhagen, Denmark
    Mol Cell 51:265-72. 2013
    ..These results uncover a critical role for AcP in bacterial acetylation and indicate that most acetylation in E. coli occurs at a low level and is dynamically affected by metabolism and cell proliferation in a global, uniform manner...
  12. pmc Ubiquitin-SUMO circuitry controls activated fanconi anemia ID complex dosage in response to DNA damage
    Ian Gibbs-Seymour
    Ubiquitin Signaling Group, The Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, 2200 Copenhagen, Denmark
    Mol Cell 57:150-64. 2015
    ..Our results uncover a regulatory role for SUMOylation in the FA pathway, and we propose that ubiquitin-SUMO signaling circuitry is a mechanism that contributes to the balance of activated ID complex dosage at sites of DNA damage...
  13. pmc Proteomic investigations reveal a role for RNA processing factor THRAP3 in the DNA damage response
    Petra Beli
    The NNF Center for Protein Research, University of Copenhagen, Blegdamsvej 3b, DK 2200 Copenhagen, Denmark
    Mol Cell 46:212-25. 2012
    ..Moreover, THRAP3 depletion causes cellular hypersensitivity to DNA-damaging agents. Collectively, these data broaden our knowledge of DNA damage signaling networks and highlight an important link between RNA metabolism and DNA repair...
  14. pmc Proteomic investigations of lysine acetylation identify diverse substrates of mitochondrial deacetylase sirt3
    Eri Maria Sol
    Department of Proteomics, The Novo Nordisk Foundation Center for Protein Research, Faculty of Health Sciences, University of Copenhagen, Copenhagen, Denmark
    PLoS ONE 7:e50545. 2012
    ..The experimental strategy described here is generic and can be applied to identify endogenous substrates of other lysine deacetylases...
  15. pmc Proteomic analysis of lysine acetylation sites in rat tissues reveals organ specificity and subcellular patterns
    Alicia Lundby
    Novo Nordisk Foundation Center for Protein Research, Department for Proteomics, Faculty of Health Sciences, University of Copenhagen, Denmark
    Cell Rep 2:419-31. 2012
    ..Furthermore, we illustrate that acetylation of fructose-bisphosphate aldolase and glycerol-3-phosphate dehydrogenase serves as a cellular mechanism to switch off enzymatic activity...
  16. pmc Mte1 interacts with Mph1 and promotes crossover recombination and telomere maintenance
    Sonia Silva
    Department of Biology, University of Copenhagen, DK 2200 Copenhagen N, Denmark
    Genes Dev 30:700-17. 2016
    ..Taken together, our data indicate that Mte1 plays a role in regulation of crossover recombination, response to replication stress, and telomere maintenance. ..
  17. doi request reprint Acetylation site specificities of lysine deacetylase inhibitors in human cells
    Christian Scholz
    Department of Proteomics, The Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
    Nat Biotechnol 33:415-23. 2015
    ..Our results offer a systems view of KDACI specificities, providing a framework for studying function of acetylation and deacetylases. ..
  18. doi request reprint Proteome-wide analysis of SUMO2 targets in response to pathological DNA replication stress in human cells
    Sara Bursomanno
    Center for Healthy Aging, Department of Cellular and Molecular Medicine, University of Copenhagen, Panum Institute, DK 2200 Copenhagen, Denmark
    DNA Repair (Amst) 25:84-96. 2015
    ....
  19. pmc Acetylation dynamics and stoichiometry in Saccharomyces cerevisiae
    Brian T Weinert
    The NNF Center for Protein Research Faculty of Health Sciences University of Copenhagen, Copenhagen, Denmark
    Mol Syst Biol 10:716. 2014
    ..These data show that a majority of acetylation occurs at very low levels in exponentially growing yeast and is uniformly affected by exposure to acetyl-CoA. ..
  20. pmc SPATA2 links CYLD to the TNF-α receptor signaling complex and modulates the receptor signaling outcomes
    Sebastian A Wagner
    Department of Proteomics, The Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark Department of Medicine, Hematology Oncology, Goethe University School of Medicine, Frankfurt, Germany German Cancer Consortium DKTK, Heidelberg, Germany German Cancer Research Center dkfz, Heidelberg, Germany
    EMBO J . 2016
    ..Taken together, our study draws a detailed map of TNF-α signaling, identifies SPATA2 as a novel component of TNF-α signaling, and provides a rich resource for further functional investigations...
  21. doi request reprint Specificity and commonality of the phosphoinositide-binding proteome analyzed by quantitative mass spectrometry
    Stephanie Jungmichel
    Department of Proteomics, The Novo Nordisk Foundation Center for Protein Research, Faculty of Health Sciences, University of Copenhagen, Blegdamsvej 3, 2200 Copenhagen, Denmark
    Cell Rep 6:578-91. 2014
    ..The presented PIP-binding proteome and its specificity toward individual PIPs should be a valuable resource for the community...
  22. doi request reprint DVC1 (C1orf124) is a DNA damage-targeting p97 adaptor that promotes ubiquitin-dependent responses to replication blocks
    Anna Mosbech
    Ubiquitin Signaling Group, Department of Disease Biology, Novo Nordisk Foundation Center for Protein Research, Faculty of Health Sciences, University of Copenhagen, Copenhagen, Denmark
    Nat Struct Mol Biol 19:1084-92. 2012
    ..Our findings establish DVC1 as a DNA damage-targeting p97 adaptor that protects cells from deleterious consequences of replication blocks and suggest an important role of p97 in ubiquitin-dependent regulation of TLS...
  23. pmc The Spindle Assembly Checkpoint Is Not Essential for Viability of Human Cells with Genetically Lowered APC/C Activity
    Thomas Wild
    Proteomics Program, The Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Blegdamsvej 3b, 2200 Copenhagen, Denmark
    Cell Rep 14:1829-40. 2016
    ..These results provide insights into the regulation of APC/C activity and demonstrate that the essentiality of the SAC is imposed by the strength of the APC/C. ..
  24. doi request reprint Histone H1 couples initiation and amplification of ubiquitin signalling after DNA damage
    Tina Thorslund
    Ubiquitin Signaling Group, Protein Signaling Program, The Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Blegdamsvej 3b, DK 2200 Copenhagen, Denmark
    Nature 527:389-93. 2015
    ....
  25. doi request reprint The growing landscape of lysine acetylation links metabolism and cell signalling
    Chunaram Choudhary
    The Novo Nordisk Foundation Center for Protein Research, Faculty of Health Sciences, University of Copenhagen, Blegdamsvej 3, 2200 Copenhagen, Denmark
    Nat Rev Mol Cell Biol 15:536-50. 2014
    ..These emerging findings point to new functions for different lysine acylations and deacylating enzymes and also highlight the mechanisms by which acetylation regulates various cellular processes. ..
  26. pmc Convergence of ubiquitylation and phosphorylation signaling in rapamycin-treated yeast cells
    Vytautas Iesmantavicius
    From the Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Blegdamsvej 3, 2200 Copenhagen, Denmark
    Mol Cell Proteomics 13:1979-92. 2014
    ....
  27. doi request reprint FBH1 influences DNA replication fork stability and homologous recombination through ubiquitylation of RAD51
    Wai Kit Chu
    1 Weatherall Institute of Molecular Medicine, University of Oxford, John Radcliffe Hospital, Oxford OX3 9DS, UK 2 Center for Healthy Aging, Department of Cellular and Molecular Medicine, Panum Institute, University of Copenhagen, Blegdamsvej 3b, 2200 Copenhagen N, Denmark
    Nat Commun 6:5931. 2015
    ..These effects are likely to be mediated by the enhanced nuclear matrix association of the ubiquitylation-resistant RAD51. These data are consistent with FBH1 acting as a negative regulator of RAD51 function in human cells. ..
  28. pmc OTULIN restricts Met1-linked ubiquitination to control innate immune signaling
    Berthe Katrine Fiil
    Department of Disease Biology, Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, DK 2200 Copenhagen, Denmark
    Mol Cell 50:818-30. 2013
    ..We propose that OTULIN restricts Met1-Ub formation after immune receptor stimulation to prevent unwarranted proinflammatory signaling. ..
  29. pmc A PTIP-PA1 subcomplex promotes transcription for IgH class switching independently from the associated MLL3/MLL4 methyltransferase complex
    Linda M Starnes
    Chromatin Structure and Function Group, The Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen 2200, Denmark
    Genes Dev 30:149-63. 2016
    ..These results further our understanding of how multifunctional chromatin-modifying complexes are organized by subcomplexes that harbor unique and distinct activities. ..
  30. pmc Systems-wide analysis of BCR signalosomes and downstream phosphorylation and ubiquitylation
    Shankha Satpathy
    Department of Proteomics, The Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
    Mol Syst Biol 11:810. 2015
    ..Our results offer a global and integrated view of BCR signaling, and the provided datasets can serve as a valuable resource for further understanding BCR signaling networks. ..
  31. pmc Cmr1/WDR76 defines a nuclear genotoxic stress body linking genome integrity and protein quality control
    Irene Gallina
    Department of Biology, University of Copenhagen, Room 4 1 07, Copenhagen N DK 2200, Denmark
    Nat Commun 6:6533. 2015
    ..We propose that Cmr1/WDR76 plays a role in the recovery from genotoxic stress through regulation of the turnover of sumoylated and phosphorylated proteins...