Publications acknowledging Media Lab Core Facility

2024

Lee CY, Hubrich D, Varga JK, Schäfer C, Welzel M, Schumbera E, Djokic M, Strom JM, Schönfeld J, Geist JL, Polat F, Gibson TJ, Keller Valsecchi CI, Kumar M, Schueler-Furman O and Luck K (2024) Systematic discovery of protein interaction interfaces using AlphaFold and experimental validation. Mol Syst Biol, 20:75-97 Link  

2023

Braun H*, Xu Z*, Chang F, Viceconte N, Rane G, Levin M, Lototska L, Roth F, Hillairet A, Fradera-Sola A, Khanchandani V, Sin ZW, Yong WK, Dreesen O, Yang Y, Shi Y, Li F, Butter F and Kappei D (2023) ZNF524 directly interacts with telomeric DNA and supports telomere integrity. Nat Commun, 14:8252 (*indicates joint contribution) Link

Fradera-Sola A, Nischwitz E, Bayer ME, Luck K and Butter F (2023) RNA-dependent interactome allows network-based assignment of RNA-binding protein function. Nucleic Acids Res, 51:5162-5176 Link

Kong KE*, Shankar S*, Rühle F and Khmelinskii A (2023) Orphan quality control by an SCF ubiquitin ligase directed to pervasive C-degrons. Nat Commun, 14:8363 (*indicates joint contribution) Link

Nischwitz E, Schoonenberg VAC, Fradera-Sola A, Dejung M, Vydzhak O, Levin M, Luke B, Butter F and Scheibe M (2023) DNA damage repair proteins across the Tree of Life. iScience, 26:106778 Link

Pires VB, Lohner N, Wagner T, Wagner CB, Wilkens M, Hajikazemi M, Paeschke K, Butter F and Luke B (2023) RNA-DNA hybrids prevent resection at dysfunctional telomeres. Cell Rep, 42:112077 Link

Schindler N, Tonn M, Kellner V, Fung JJ, Lockhart A, Vydzhak O, Juretschke T, Möckel S, Beli P, Khmelinskii A and Luke B (2023) Genetic requirements for repair of lesions caused by single genomic ribonucleotides in S phase. Nat Commun, 14:1227 Link

Vu HH, Behrmann H, Hanić M, Jeyasankar G, Krishnan S, Dannecker D, Hammer C, Gunkel M, Solov'yov IA, Wolf E and Behrmann E (2023) A marine cryptochrome with an inverse photo-oligomerization mechanism. Nat Commun, 14:6918 Link

2022

Marnik EA, Almeida MV, Cipriani PG, Chung G, Caspani E, Karaulanov E, Gan HH, Zinno J, Isolehto IJ, Kielisch F, Butter F, Sharp CS, Flanagan RM, Bonnet FX, Piano F, Ketting RF, Gunsalus KC and Updike DL (2022) The Caenorhabditis elegans TDRD5/7-like protein, LOTR-1, interacts with the helicase ZNFX-1 to balance epigenetic signals in the germline. PLoS Genet, 18:e1010245 Link

Misino S, Busch A, Wagner CB, Bento F and Luke B (2022) TERRA increases at short telomeres in yeast survivors and regulates survivor associated senescence (SAS). Nucleic Acids Res, 50:12829-12843 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

Poehn B, Krishnan S, Zurl M, Coric A, Rokvic D, Häfker NS, Jaenicke E, Arboleda E, Orel L, Raible F, Wolf E and Tessmar-Raible K (2022) A Cryptochrome adopts distinct moon- and sunlight states and functions as sun- versus moonlight interpreter in monthly oscillator entrainment. Nat Commun, 13:5220 

Schreier J, Dietz S, Boermel M, Oorschot V, Seistrup AS, de Jesus Domingues AM, Bronkhorst AW, Nguyen DAH, Phillis S, Gleason EJ, L'Hernault SW, Phillips CM, Butter FK and Ketting RF (2022) Membrane-associated cytoplasmic granules carrying the Argonaute protein WAGO-3 enable paternal epigenetic inheritance in Caenorhabditis elegans. Nat Cell Biol, 24:217-229 Link  

Wegmann S, Meister C, Renz C, Yakoub G, Wollscheid HP, Takahashi DT, Mikicic I, Beli P and Ulrich HD (2022) Linkage reprogramming by tailor-made E3s reveals polyubiquitin chain requirements in DNA-damage bypass. Mol Cell, 82:1589-1602.e5

2021

Dietz S, Almeida MV, Nischwitz E, Schreier J, Viceconte N, Fradera-Sola A, Renz C, Ceron-Noriega A, Ulrich HD, Kappei D, Ketting RF and Butter F (2021) The double-stranded DNA-binding proteins TEBP-1 and TEBP-2 form a telomeric complex with POT-1. Nat Commun, 12:2668 Link 

Kong KYE*, Fischer B*, Meurer M*, Kats I, Li Z, Rühle F, Barry JD, Kirrmaier D, Chevyreva V, San Luis BJ, Costanzo M, Huber W, Andrews BJ, Boone C, Knop M# and Khmelinskii A# (2021) Timer-based proteomic profiling of the ubiquitin-proteasome system reveals a substrate receptor of the GID ubiquitin ligase. Mol Cell, 81:2460-2476.e11 (*indicates joint contribution, #indicates joint correspondence) Link

Perez-Borrajero C, Podvalnaya N*, Holleis K*, Lichtenberger R, Karaulanov E, Simon B, Basquin J, Hennig J#, Ketting RF# and Falk S# (2021) Structural basis of PETISCO complex assembly during piRNA biogenesis in C. elegans. Genes Dev, 35:1304-1323 (*indicates joint contribution, #indicates joint correspondence) Link

Placentino M, Jesus Domingues AM, Schreier J, Dietz S, Hellmann S, Albuquerque BF, Butter F and Ketting RF (2021) Intrinsically disordered protein PID‐2 modulates Z granules and is required for heritable piRNA‐induced silencing in the Caenorhabditis elegans embryo. EMBO J, 40:e105280 Link

Redl S, de Jesus Domingues AM, Caspani E, Möckel S, Salvenmoser W, Mendez-Lago M and Ketting RF (2021) Extensive nuclear gyration and pervasive non-genic transcription during primordial germ cell development in zebrafish. Development, 148:dev193060 Link

Wagner T, Pérez-Martínez L, Schellhaas R, Barrientos-Moreno M, Öztürk M, Prado F, Butter F and Luke B (2021) Chromatin modifiers and recombination factors promote a telomere fold-back structure, that is lost during replicative senescence. PLOS Genet, 16:e1008603 Link

2020

Casas-Vila N, Sayols S, Pérez-Martínez L, Scheibe M and Butter F (2020) The RNA fold interactome of evolutionary conserved RNA structures in S. cerevisiae. Nat Commun, 11:2789 Link

Redl S*, de Jesus Domingues AM*, Caspani E, Möckel S, Salvenmoser W, Mendez-Lago M and Ketting RF (2021) Extensive nuclear gyration and pervasive non-genic transcription during primordial germ cell development in zebrafish. Development, 148:dev193060 (*indicates joint contribution) Link

Vydzhak O*, Bender K*, Klermund J, Busch A, Reimann S and Luke B (2020) Checkpoint adaptation in recombination-deficient cells drives aneuploidy and resistance to genotoxic agents. DNA Repair, 95:102939 (*indicates joint contribution) Link

Wong RP, García-Rodríguez N, Zilio N, Hanulová M, Ulrich HD (2020) Processing of DNA polymerase-blocking lesions during genome replication is spatially and temporally segregated from replication forks. Mol Cell, 77:3-16.e4 Link

2019

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

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 TRF2. Nucleic 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 viability. Genes Dev, 2019 33:857-870 Link

Lockhart A, Pires VB, Bento F, Kellner V, Luke-Glaser S, Yakoub G, Ulrich HD and Luke B (2019) RNase H1 and H2 are differentially regulated to process RNA-DNA hybrids. Cell Rep, 29:2890–2900.e5 Link

Wong RP, García-Rodríguez N, Zilio N, Hanulová M and Ulrich HD (2020) Processing of DNA polymerase-blocking lesions during genome replication is spatially and temporally segregated from replication forks. Mol Cell, 77:3–16.e4 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 elegans. EMBO J, 37:e99325 Link

García-Rodríguez N, Morawska M, Wong RP, Daigaku Y and Ulrich HD (2018) Spatial separation between replisome- and template-induced replication stress signaling. EMBO J, 37:e98369 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 (*indicates joint contribution) Link

2017

Graf M, Bonetti D, Lockhart A, Serhal K, Kellner V, Maicher A, Jolivet P, Teixeira MT and Luke B (2017) Telomere length determines TERRA and R-Loop regulation through the cell cycle. Cell, 170:72-85.e14 Link

Wilhelm T, Byrne J, Medina R, Kolundžić E, Geisinger J, Hajduskova M, Tursun B and Richly H. (2017). Neuronal inhibition of the autophagy nucleation complex extends life span in post-reproductive C. elegans. Genes Dev, 31: 1561–1572 Link

2015

de Albuquerque BF, Placentino M and Ketting RF. (2015). Maternal piRNAs are essential for germline development following de-novo establishment of endo-siRNAs in Caenorhabditis elegans. Dev Cell, 34: 448-56 Link