Publications co-authored by the Proteomics Core Facility

2018

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 Drosophila. Mol Cell, 72: 661–672.e4. Link

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

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 elegans. EMBO J, 37: e99325. 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 repair. Plant Physiol, 177: 311–327. Link

Dal Magro C, Keller P, Kotter A, Werner S, Duarte V, Marchand V, Ignarski M, Freiwald A, Müller RU, Dieterich C, Motorin Y, Butter F, Atta M and Helm M. (2018). A vastly increased chemical variety of RNA modifications containing a thioacetal structure. Angew Chemie Int Ed, 57: 7893–7897. 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 cells. Arch 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 cells. Arch 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 trypanosomes. Nucleic Acids Res, 46: 2820–2833. Link

Roovers EF, Kaaij LJT, Redl S, Bronkhorst AW, Wiebrands K, de Jesus Domingues AM, Huang HY, Han CT, 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 specification. Dev 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 cells. PLoS 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 melanogaster. Genome 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 brucei. PLoS One, 12: e0181884. Link

Jahn A*, Rane G*, Paszkowski‐Rogacz M, Sayols S, Bluhm A, Han CT, 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 activator. EMBO 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 birds. Proteomics, 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 brucei. PLOS 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 repeats. BMC 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 embryos. Cell 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 characteristics. Mol 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 bodies. Mol 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.