Publications co-authored by the Proteomics Core Facility

2023

Greither T#, Dejung M, Behre HM, Butter F and Herlyn H# (2023) The human sperm proteome — toward a panel for male fertility testing. Andrology, 11:1418–1436 (#indicates joint correspondence) Link

Maus H, Gellert A, Englert OR, Chen JX, Schirmeister T and Barthels F (2023) Designing photoaffinity tool compounds for the investigation of the DENV NS2B-NS3 protease allosteric binding pocket. RSC Med Chem, 14:2365-2379 Link

Penner I, Dejung M, Freiwald A, Butter F, Chen JX and Plachter B (2023) Proteome changes of fibroblasts and endothelial cells upon incubation with human cytomegalovirus subviral Dense Bodies. Sci Data, 10:517 Link

Rahmanto AS, Blum CJ, Scalera C, Heidelberger JB, Mesitov M, Horn-Ghetko D, Gräf JF, Mikicic I, Hobrecht R, Orekhova A, Ostermaier M, Ebersberger S, Möckel MM, Krapoth N, Da Silva Fernandes N, Mizi A, Zhu Y, Chen JX, Choudhary C, Papantonis A, Ulrich HD, Schulman BA, König J and Beli P (2023) K6-linked ubiquitylation marks formaldehyde-induced RNA-protein crosslinks for resolution. Mol Cell, 83:4272-4289.e10 Link

Renz C, Asimaki E, Meister C, Albanèse V, Petriukov K, Krapoth NC, Wegmann S, Wollscheid HP, Wong RP, Fulzele A, Chen JX, Léon S and Ulrich HD (2023) Ubiquiton-An inducible, linkage-specific polyubiquitylation tool. Mol Cell, S1097-2765:00961-9 Link

2022

Hanisch D, Krumm A, Diehl T, Stork CM, Dejung M, Butter F, Kim E, Brenner W, Fritz G, Hofmann TG and Roos WP (2022) Class I HDAC overexpression promotes temozolomide resistance in glioma cells by regulating RAD18 expression. Cell Death Dis, 13:293 Link

Kong G, Zhou L, Freiwald A, Shkura K and Di Giovanni S (2022) Purification of mouse axoplasmic proteins from dorsal root ganglia nerves for proteomics analysis. STAR Protoc, 3:101166 Link

Krauter S, Büscher N, Bräuchle E, Ortega Iannazzo S, Penner I, Krämer N, Gogesch P, Thomas S, Kreutz M, Dejung M, Freiwald A, Butter F, Waibler Z and Plachter B (2022) An attenuated strain of human cytomegalovirus for the establishment of a subviral particle vaccine. Vaccines, 10:1326 Link

Kunert F, Metzner FJ, Jung J, Höpfler M, Woike S, Schall K, Kostrewa D, Moldt M, Chen JX, Bantele S, Pfander B, Eustermann S and Hopfner KP (2022) Structural mechanism of extranucleosomal DNA readout by the INO80 complex. Sci Adv, 8:eadd3189 Link

Öztürk M, Freiwald A, Cartano J, Schmitt R, Dejung M, Luck K, Al-Sady B, Braun S, Levin M and Butter F (2022) Proteome effects of genome-wide single gene perturbations. Nat Commun, 13:6153 Link

Penner I, Büscher N, Dejung M, Freiwald A, Butter F and Plachter B (2022) Subviral dense bodies of human cytomegalovirus induce an antiviral type I Interferon response. Cells, 11:4028 Link

Prieto Huarcaya S, Drobny A, Marques ARA, Di Spiezio A, Dobert JP, Balta D, Werner C, Rizo T, Gallwitz L, Bub S, Stojkovska I, Belur NR, Fogh J, Mazzulli JR, Xiang W, Fulzele A, Dejung M, Sauer M, Winner B, Rose-John S, Arnold P, Saftig P and Zunke F (2022) Recombinant pro-CTSD (cathepsin D) enhances SNCA/α-Synuclein degradation in α-Synucleinopathy models. Autophagy, 18:1127-1151 Link

2021

Zhang X, Harding BW, Aggad D, Courtine D, Chen JX, Pujol N and Ewbank JJ (2021) Antagonistic fungal enterotoxins intersect at multiple levels with host innate immune defences. PLoS Genet, 17:e1009600 Link 

Zimmermann C, Krämer N, Krauter S, Strand D, Sehn E, Wolfrum U, Freiwald A, Butter F and Plachter B (2021) Autophagy interferes with human cytomegalovirus genome replication, morphogenesis, and progeny release. Autophagy, 17:779-795 Link  

2020

Greither T, Schumacher J, Dejung M, Behre HM, Zischler H, Butter F and Herlyn H (2020) Fertility relevance probability analysis shortlists genetic markers for male fertility impairment. Cytogenet Genome Res, 160:506-522 Link

Kong G*, Zhou L*, Serger E, Palmisano I, De Virgiliis F, Hutson TH, Mclachlan E, Freiwald A, La Montanara P, Shkura K, Puttagunta R and Di Giovanni S (2020) AMPK controls the axonal regenerative ability of dorsal root ganglia sensory neurons after spinal cord injuryNat Metab, 2:918–933 (*indicates joint contribution) Link

2019

Bluhm A, Viceconte N, Li F, Rane G, Ritz S, Wang S, Levin M, Shi Y, Kappei D and Butter F (2019) ZBTB10 binds the telomeric variant repeat TTGGGG and interacts with TRF2Nucleic Acids Res, 47:1896–1907 Link

Cordeiro Rodrigues RJ, de Jesus Domingues AM, Hellmann S, Dietz S, de Albuquerque BFM, Renz C, Ulrich HD, Sarkies P, Butter F and Ketting RF (2019) PETISCO is a novel protein complex required for 21U RNA biogenesis and embryonic viabilityGenes Dev, 33:857–870 Link

Goos C, Dejung M, Wehman AM, M-Natus E, Schmidt J, Sunter J, Engstler M, Butter F# and Kramer S# (2019) Trypanosomes can initiate nuclear export co-transcriptionallyNucleic Acids Res, 47:266–282 (#indicates joint correspondence) Link

Pons M, Nagel G, Zeyn Y, Beyer M, Laguna T, Brachetti T, Sellmer A, Mahboobi S, Conradi R, Butter F and Kramer OH (2019) Human platelet lysate as validated replacement for animal serum to assess chemosensitivityALTEX, 36:277–288 Link

Warncke JD, Passecker A, Kipfer E, Brand F, Pérez-Martínez L, Proellochs NI, Kooij TWA, Butter F, Voss TS# and Beck HP# (2019) The PHIST protein GEXP02 targets the host cytoskeleton during sexual development of Plasmodium falciparumCell Microbiol, 22:e13123 (#indicates joint correspondence) Link 

Wohlfahrt T, Rauber S, Uebe S, Luber M, Soare A, Ekici A, Weber S, Matei A-E, Chen C-W, Maier C, Karouzakis E, Kiener HP, Pachera E, Dees C, Beyer C, Daniel C, Gelse K, Kremer AE, Naschberger E, Stürzl M, Butter F, Sticherling M, Finotto S, Kreuter A, Kaplan MH, Jüngel A, Gay S, Nutt SL, Boykin DW, Poon GMK, Distler O, Schett G, Distler JHW and Ramming A (2019) PU.1 controls fibroblast polarization and tissue fibrosisNature, 566:344–349 Link

2018

Almeida MV, Dietz S, Redl S, Karaulanov E, Hildebrandt A, Renz C, Ulrich HD, König J, Butter F and Ketting RF (2018) GTSF‐1 is required for formation of a functional RNA‐dependent RNA Polymerase complex in Caenorhabditis elegansEMBO J, 37:e99325 Link

Baldi S, Jain DS, Harpprecht L, Zabel A, Scheibe M, Butter F, Straub T and Becker PB (2018) Genome-wide rules of nucleosome phasing in DrosophilaMol Cell, 72:661–672.e4 Link

Becker K, Bluhm A*, Casas-Vila N*, Dinges N*, Dejung M, Sayols S, Kreutz C, Roignant J-Y, Butter F# and Legewie S# (2018) Quantifying post-transcriptional regulation in the development of Drosophila melanogasterNat Commun, 9:4970 (*indicates joint contribution, #indicates joint correspondence) Link

Charbonnel C, Rymarenko O, Da Ines O, Benyahya F, White CI, Butter F and Amiard S (2018) The linker histone GH1-HMGA1 is involved in telomere stability and DNA damage repairPlant Physiol, 177:311–327 Link

Dal Magro C, Keller P, Kotter A, Werner S, Duarte V, Marchand V, Ignarski M, Freiwald A, Müller R-U, Dieterich C, Motorin Y, Butter F, Atta M and Helm M (2018) A vastly increased chemical variety of RNA modifications containing a thioacetal structureAngew Chemie Int Ed, 57:7893–7897 Link

Harris CJ*, Scheibe M*, Wongpalee SP, Liu W, Cornett EM, Vaughan RM, Li X, Chen W, Xue Y, Zhong Z, Yen L, Barshop WD, Rayatpisheh S, Gallego-Bartolome J, Groth M, Wang Z, Wohlschlegel JA, Du J, Rothbart SB, Butter F# and Jacobsen SE# (2018) A DNA methylation reader complex that enhances gene transcriptionScience, 362:1182–1186 (*indicates joint contribution, #indicates joint correspondence) Link

Kiweler N, Brill B, Wirth M, Breuksch I, Laguna T, Dietrich C, Strand S, Schneider G, Groner B, Butter F, Heinzel T, Brenner W and Krämer OH (2018) The histone deacetylases HDAC1 and HDAC2 are required for the growth and survival of renal carcinoma cellsArch Toxicol, 92:2227–2243 Link

Pons M, Reichardt CM, Hennig D, Nathan A, Kiweler N, Stocking C, Wichmann C, Christmann M, Butter F, Reichardt S, Schneider G, Heinzel T, Englert C, Hartkamp J, Krämer OH and Mahendrarajah N (2018) Loss of Wilms tumor 1 protein is a marker for apoptosis in response to replicative stress in leukemic cellsArch Toxicol, 92:2119–2135 Link

Reis H, Schwebs M, Dietz S, Janzen CJ and Butter F (2018) TelAP1 links telomere complexes with developmental expression site silencing in African trypanosomesNucleic Acids Res, 46:2820–2833 Link

Roovers EF, Kaaij LJT, Redl S, Bronkhorst AW, Wiebrands K, de Jesus Domingues AM, Huang H-Y, Han C-T, Riemer S, Dosch R, Salvenmoser W, Grün D, Butter F, van Oudenaarden A and Ketting RF (2018) Tdrd6a regulates the aggregation of Buc into functional subcellular compartments that drive germ cell specificationDev Cell, 46:285–301.e9 Link

Winzi M, Casas Vila N, Paszkowski-Rogacz M, Ding L, Noack S, Theis M, Butter F and Buchholz F (2018) The long noncoding RNA lncR492 inhibits neural differentiation of murine embryonic stem cellsPLOS One, 13:e0191682 Link

2017

Casas-Vila N*, Bluhm A*, Sayols S*, Dinges N, Dejung M, Altenhein T, Kappei D, Altenhein B, Roignant JY and Butter F (2017) The developmental proteome of Drosophila melanogasterGenome Res, 27:1273–1285 (*indicates joint contribution) Link

Goos C, Dejung M, Janzen CJ, Butter F and Kramer S (2017) The nuclear proteome of Trypanosoma bruceiPLOS One, 12:e0181884 Link

Jahn A*, Rane G*, Paszkowski‐Rogacz M, Sayols S, Bluhm A, Han C, Draškovič I, Londoño‐Vallejo JA, Kumar AP, Buchholz F#, Butter F# and Kappei D# (2017) ZBTB48 is both a vertebrate telomere‐binding protein and a transcriptional activatorEMBO Rep, 18:929–946 (*indicates joint contribution, #indicates joint correspondence) Link

Lebedeva S, de Jesus Domingues AM, Butter F and Ketting RF (2017) Characterization of genetic loss-of-function of Fus in zebrafish. RNA Biol, 14:29–35 Link

2016

Bluhm A, Casas-Vila N, Scheibe M and Butter F (2016) Reader interactome of epigenetic histone marks in birdsProteomics, 16:427–436 Link

Cicova Z, Dejung M, Skalicky T, Eisenhuth N, Hanselmann S, Morriswood B, Figueiredo LM, Butter F# and Janzen CJ# (2016) Two flagellar BAR domain proteins in Trypanosoma brucei with stage-specific regulation. Sci Rep, 6:35826 (#indicates joint correspondence) Link

Dejung M, Subota I, Bucerius F, Dindar G, Freiwald A, Engstler M, Boshart M, Butter F# and Janzen CJ# (2016) Quantitative proteomics uncovers novel factors involved in developmental differentiation of trypanosoma bruceiPLOS Pathog, 12:e1005439 (#indicates joint correspondence) Link

Klassen R, Ciftci A, Funk J, Bruch A, Butter F and Schaffrath R (2016) tRNA anticodon loop modifications ensure protein homeostasis and cell morphogenesis in yeast. Nucleic Acids Res, 44:10946–10959 Link

Wagner SA, Oehler H, Voigt A, Dalic D, Freiwald A, Serve H and Beli P (2016) ATR inhibition rewires cellular signaling networks induced by replication stress. Proteomics, 16:402–416 Link

2015

Casas-Vila N, Scheibe M, Freiwald A, Kappei D and Butter F (2015) Identification of TTAGGG-binding proteins in Neurospora crassa, a fungus with vertebrate-like telomere repeatsBMC Genomics, 16:965 Link

Roovers EF, Rosenkranz D, Mahdipour M, Han CT, He N, Chuva de Sousa Lopes SM, van der Westerlaken LAJ, Zischler H, Butter F, Roelen BAJ and Ketting RF (2015) Piwi proteins and piRNAs in mammalian oocytes and early embryosCell Rep, 10:2069–2082 Link

2014

Hornburg D, Drepper C, Butter F, Meissner F, Sendtner M and Mann M (2014) Deep proteomic evaluation of primary and cell line motoneuron disease models delineates major differences in neuronal characteristicsMol Cell Proteomics, 13:3410–3420 Link

Machyna M, Kehr S, Straube K, Kappei D, Buchholz F, Butter F, Ule J, Hertel J, Stadler PF and Neugebauer KM (2014) The coilin interactome identifies hundreds of small noncoding RNAs that traffic through cajal bodiesMol Cell, 56:389–399 Link


Publications acknowledging the Proteomics Core Facility

2018

Borisova ME, Voigt A, Tollenaere MAX, Sahu SK, Juretschke T, Kreim N, Mailand N, Choudhary C, Bekker-Jensen S, Akutsu M, Wagner SA and Beli P (2018) p38-MK2 signaling axis regulates RNA metabolism after UV-light-induced DNA damageNat Commun, 9: 1017

Heidelberger JB, Voigt A, Borisova ME, Petrosino G, Ruf S, Wagner SA and Beli P (2018) Proteomic profiling of VCP substrates links VCP to K6‐linked ubiquitylation and c‐Myc functionEMBO Rep, pii: e44754

Knuckles P, Lence T, Haussmann IU, Jacob D, Kreim N, Carl SH, Masiello I, Hares T, Villaseñor R, Hess D, Andrade-Navarro MA, Biggiogera M, Helm M, Soller M, Bühler M and Roignant JY (2018) Zc3h13/Flacc is required for adenosine methylation by bridging the mRNA-binding factor Rbm15/Spenito to the m6A machinery component Wtap/Fl(2)dGenes Dev, 32: 415–429

2017

Chitale S and Richly H (2017) Nuclear organization of nucleotide excision repair is mediated by RING1B dependent H2A-ubiquitylationOncotarget, 8: 30870-30887

Lebedeva S, de Jesus Domingues AM, Butter F and Ketting RF (2017) Characterization of genetic loss-of-function of Fus in zebrafishRNA Biol, 14: 29-35

2016

Thakurela S, Garding A, Jung RB, Müller C, Goebbels S, White R, Werner HB and Tiwari VK (2016) The transcriptome of mouse central nervous system myelinSci Rep, 6: 25828