Protein Production Core Facility
Overview Head of the Core Facility Core Facility Members PublicationsPublications co-authored by the Protein Production Core Facility
2024
Longo GMC*, Sayols S*, Kotini AG, Heinen S, Möckel MM, Beli P and Roukos V (2024) Linking CRISPR-Cas9 double-strand break profiles to gene editing precision with BreakTag. Nat Biotechnol, doi: 10.1038/s41587-024-02238-8 Link
2023
Bronkhorst AW, Lee CY, Möckel MM, Ruegenberg S, de Jesus Domingues AM, Sadouki S, Piccinno R, Sumiyoshi T, Siomi MC, Stelzl L, Luck K and Ketting RF (2023) An extended Tudor domain within Vreteno interconnects Gtsf1L and Ago3 for piRNA biogenesis in Bombyx mori. EMBO J, 42:e114072 Link
Ebersberger S*, Hipp C*, Mulorz MM*, Buchbender A, Hubrich D, Kang HS, Martínez-Lumbreras S, Kristofori P, Sutandy FXR, Llacsahuanga Allcca L, Schönfeld J, Bakisoglu C, Busch A, Hänel H, Tretow K, Welzel M, Di Liddo A, Möckel MM, Zarnack K, Ebersberger I, Legewie S, Luck K#, Sattler M# and König J# (2023) FUBP1 is a general splicing factor facilitating 3' splice site recognition and splicing of long introns. Mol Cell, 83:2653-2672.e15 (*indicates joint contribution, #indicates joint correspondence) Link
Kalita AI, Marois E*, Kozielska M, Weissing FJ, Jaouen E, Möckel MM, Rühle F, Butter F, Basilicata MF* and Keller Valsecchi CI* (2023) The sex-specific factor SOA controls dosage compensation in Anopheles mosquitoes. Nature, 623:175-182 (*indicates joint contribution) Link
Suryo Rahmanto A, 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
2021
Mosler T, Conte F, Longo GMC, Mikicic I, Kreim N, Möckel MM, Petrosino G, Flach J, Barau J, Luke B, Roukos V and Beli P (2021) R-loop proximity proteomics identifies a role of DDX41 in transcription-associated genomic instability. Nat Commun, 12:7314 Link
Worpenberg L, Paolantoni C, Longhi S, Mulorz MM, Lence T, Wessels HH, Dassi E, Aiello G, Sutandy FXR, Scheibe M, Edupuganti RR, Busch A, Möckel MM, Vermeulen M, Butter F, König J, Notarangelo M, Ohler U, Dieterich C, Quattrone A#, Soldano A# and Roignant JY# (2021) Ythdf is a N6-methyladenosine reader that modulates Fmr1 target mRNA selection and restricts axonal growth in Drosophila. EMBO J, 40:e104975 Link
2019
Hildebrandt A, Brüggemann M, Rücklé C, Boerner S, Heidelberger JB, Busch A, Hänel H, Voigt A, Möckel MM, Ebersberger S, Scholz A, Dold A, Schmid T, Ebersberger I, Roignant J-Y, Zarnack K#, König J# and Beli P# (2019) The RNA-binding ubiquitin ligase MKRN1 functions in ribosome-associated quality control of poly(A) translation. Genome Biol, 20:216 (#indicates joint correspondence) Link
Publications acknowledging the Protein production core facility
2025
Gameiro E, Juárez-Núñez KA, Fung JJ, Shankar S, Luke B and Khmelinskii A (2025) Genome-wide conditional degron libraries for functional genomics. J Cell Biol, 224:e202409007 Link
2024
Dias Mirandela M, Zoch A, Leismann J, Webb S, Berrens RV, Valsakumar D, Kabayama Y, Auchynnikava T, Schito M, Chowdhury T, MacLeod D, Xiang X, Zou J, Rappsilber J, Allshire RC, Voigt P, Cook AG, Barau J and O'Carroll D (2024) Two-factor authentication underpins the precision of the piRNA pathway. Nature, 634:979-985 Link
Longo GMC, Sayols S, Stefanova ME, Xie T, Elsayed W, Panagi A, Stavridou AI, Petrosino G, Ing-Simmons E, Melo US, Gothe HJ, Vaquerizas JM, Kotini AG, Papantonis A, Mundlos S and Roukos V (2024) Type II topoisomerases shape multi-scale 3D chromatin folding in regions of positive supercoils. Mol Cell, 84:4267-4281.e8 Link
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
Parasyraki E, Mallick M, Hatch V, Vastolo V, Musheev MU, Karaulanov E, Gopanenko A, Moxon S, Méndez-Lago M, Han D, Schomacher L, Mukherjee D and Niehrs C (2024) 5-Formylcytosine is an activating epigenetic mark for RNA Pol III during zygotic reprogramming. Cell, 187:6088-6103.e18 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 (2024) Ubiquiton-An inducible, linkage-specific polyubiquitylation tool. Mol Cell, 84:386-400.e11 Link
Zhou Y, Ćorović M, Hoch-Kraft P, Meiser N, Mesitov M, Körtel N, Back H, Naarmann-de Vries IS, Katti K, Obrdlík A, Busch A, Dieterich C, Vaňáčová Š, Hengesbach M, Zarnack K and König J (2024) m6A sites in the coding region trigger translation-dependent mRNA decay. Mol Cell, 84:4576-4593.e12 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 Link
Kong KYE, 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 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
Podvalnaya N*, Bronkhorst AW*, Lichtenberger R, Hellmann S, Nischwitz E, Falk T, Karaulanov E, Butter F, Falk S# and Ketting RF# (2023) piRNA processing by a trimeric Schlafen-domain nuclease. Nature, 622:402-409 (*indicates joint contribution, #indicates joint correspondence) 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
Shi J, Hauschulte K, Mikicic I, Maharjan S, Arz V, Strauch T, Heidelberger JB, Schaefer JV, Dreier B, Plückthun A, Beli P, Ulrich HD and Wollscheid HP (2023) Nuclear myosin VI maintains replication fork stability. Nat Commun, 14:3787 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 (*indicates joint contribution)
Yakoub G, Choi YS, Wong RP, Strauch T, Ann KJ, Cohen RE and Ulrich HD (2023) Avidity-based biosensors for ubiquitylated PCNA reveal choreography of DNA damage bypass. Sci Adv, 9:eadf3041 Link
Yu M*, Heidari M*, Mikhaleva S*, Tan PS*, Mingu S, Ruan H, Reinkemeier CD, Obarska-Kosinska A, Siggel M, Beck M, Hummer G and Lemke EA (2023) Visualizing the disordered nuclear transport machinery in situ. Nature, 617:162-169 (*indicates joint contribution) Link
2022
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
Mosler T, Baymaz HI, Gräf JF, Mikicic I, Blattner G, Bartlett E, Ostermaier M, Piccinno R, Yang J, Voigt A, Gatti M, Pellegrino S, Altmeyer M, Luck K, Ahel I, Roukos V and Beli P (2022) PARP1 proximity proteomics reveals interaction partners at stressed replication forks. Nucleic Acids Res, 50:11600-11618 Link
Musheev MU, Schomacher L, Basu A, Han D, Krebs L, Scholz C and Niehrs C (2022) Mammalian N1-adenosine PARylation is a reversible DNA modification. Nat Commun, 13:6138 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
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
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
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
Vydzhak O, Luke B and Schindler N (2020) Non-coding RNAs at the eukaryotic rDNA locus: RNA–DNA hybrids and beyond. J Mol Biol, 432:4287–4304 Link
2019
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