Publications

Below please find publications from SFB 1361 projects since 2019.

Carnie CJ, Jackson SP, Stingele J (2024) Transcription-coupled repair of DNA-protein crosslinks.Trends Cell Biol., doi: 10.1016/j.tcb.2024.11.003 Link

Sahin H, Salehi R, Islam S, Müller M, Giehr P, Carell T (2024) Robust Bisulfite-Free Single-Molecule Real-Time Sequencing of Methyldeoxycytidine Based on a Novel hpTet3 Enzyme.Angew Chem Int Ed Engl., doi: 10.1002/anie.202418500 Link

Halbritter AJ, Gärtner YV, Nabiev J, Hernichel F, Ganazzoli G, Özdemir D, Pappa A, Veth S, Stazzoni S, Müller M, Hornung V, Carell T (2024) A Phosphotriester-Masked Dideoxy-cGAMP Derivative as a Cell-Permeable STING Agonist.Angew Chem Int Ed Engl., doi: 10.1002/anie.202416353 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, Roukos V (2024) Type II topoisomerases shape multi-scale 3D chromatin folding in regions of positive supercoils. Mol Cell., doi: 10.1016/j.molcel.2024.10.007 Link

Ren M, Gut F, Fan Y, Ma J, Shan X, Yikilmazsoy A, Likhodeeva M, Hopfner KP, Zhou C (2024) Structural basis for human OGG1 processing 8-oxodGuo within nucleosome core particles.Nat Commun., doi: 10.1038/s41467-024-53811-3 Link

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, O'Carroll D (2024) Two-factor authentication underpins the precision of the piRNA pathway. Nature, doi: 10.1038/s41586-024-07963-3 Link

Halilovic M, Abdelsalam M, Zabkiewicz J, Lazenby M, Alvares C, Schmidt M, Brenner W, Najafi S, Oehme I, Hieber C, Zeyn Y, Bros M, Sippl W, Krämer OH (2024) Selective degradation of mutant FMS-like tyrosine kinase-3 requires BIM-dependent depletion of heat shock proteins.Leukemia, doi: 10.1038/s41375-024-02405-5 Link

Bejarano Franco M, Boujataoui S, Hadji M, Hammer L, Ulrich H, Reuter M (2024) Analysis of cell cycle stage, replicated DNA, and chromatin-associated proteins using high-throughput flow cytometry. Biological Chemistry, doi: 10.1515/hsz-2024-0058 Link

Arroyo M, Casas-Delucchi CS, Pabba MK, Prorok P, Pradhan SK, Rausch C, Lehmkuhl A, Maiser A, Buschbeck M, Pasque V, Bernstein E, Luck K, Cardoso MC (2024) Histone variant macroH2A1 regulates synchronous firing of replication origins in the inactive X chromosome.Nucleic Acids Res., doi: 10.1093/nar/gkae734 Link

Hieber C, Mustafa AM, Neuroth S, Henninger S, Wollscheid HP, Zabkiewicz J, Lazenby M, Alvares C, Mahboobi S, Butter F, Brenner W, Bros M, Krämer OH (2024) Inhibitors of the tyrosine kinases FMS-like tyrosine kinase-3 and WEE1 induce apoptosis and DNA damage synergistically in acute myeloid leukemia cells.Biomed Pharmacother., doi: 10.1016/j.biopha.2024.117076  Link

Bauer N, Oberist C, Poth M, Stingele J, Popp O, Ausländer S (2024) Genomic barcoding for clonal diversity monitoring and control in cell-based complex antibody production. Sci Rep., doi: 10.1038/s41598-024-65323-7 Link

Weickert P, Dürauer S, Götz MJ, Li HY, Stingele J (2024) Electro-elution-based purification of covalent DNA-protein cross-links.Nat Protoc., doi: 10.1038/s41596-024-01004-z Link

Schmidt A, Allmann S, Schwarzenbach C, Snyder P, Chen J, Nagel G, Schöneis A, Rasenberger B, Beli P, Loewer A, Hofmann T, Tomicic M, Christmann M (2024) The p21CIP1-CDK4-DREAM axis is a master regulator of genotoxic stress-induced cellular senescence.Nucleic Acids Research, doi: 10.1093/nar/gkae426 Link

Carnie C, Götz M, Palma-Chaundler C, Weickert P, Wanders A, Serrano-Benitez A, Li H, Gupta V, Awwad S, Blum C, Sczaniecka-Clift M, Cordes J, Zagnoli-Vieira G, D´Alessandro G, Richards S, Gueorguieva N, Lam S, Beli P, Stingele J, Jackson S (2024) Decitabine cytotoxicity is promoted by dCMP deaminase DCTD and mitigated by SUMO-dependent E3 ligase TOPORS. EMBO J., doi: 10.1038/s44318-024-00108-2 Link

Longo GMC, Sayols S, Kotini AG, Heinen S, Möckel MM, Beli P, 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

Pabba MK, Meyer J, Celikay K, Schermelleh L, Rohr K, Cardoso MC (2024) DNA choreography: correlating mobility and organization of DNA across different resolutions from loops to chromosomes.Histochem Cell Biol., doi: 10.1007/s00418-024-02285-x Link

Fischer MA, Mustafa AM, Hausmann K, Ashry R, Kansy AG, Liebl MC, Brachetti C, Piée-Staffa A, Zessin M, Ibrahim HS, Hofmann TG, Schutkowski M, Sippl W, Krämer OH (2024) Novel hydroxamic acid derivative induces apoptosis and constrains autophagy in leukemic cells. J Adv Res., doi: 10.1016/j.jare.2023.07.005 Link

Zhang N, Harbers L, Simonetti M, Diekmann C, Verron Q, Berrino E, Bellomo SE, Longo GMC, Ratz M, Schultz N, Tarish F, Su P, Han B, Wang W, Onorato S, Grassini D, Ballarino R, Giordano S, Yang Q, Sapino A, Frisén J, Alkass K, Druid H, Roukos V, Helleday T, Marchiò C, Bienko M, Crosetto N (2024) High clonal diversity and spatial genetic admixture in early prostate cancer and surrounding normal tissue. Nat Commun., doi: 10.1038/s41467-024-47664-z Link

Wen T, Zhao S, Stingele J, Ravanat JL, Greenberg MM (2024) Quantification of Intracellular DNA-Protein Cross-Links with N7-Methyl-2'-Deoxyguanosine and Their Contribution to Cytotoxicity. Chem Res Toxicol., doi: 10.1021/acs.chemrestox.4c00076 Link

Carnie CJ, Acampora AC, Bader AS, Erdenebat C, Zhao S, Bitensky E, van den Heuvel D, Parnas A, Gupta V, D´Alessandro G, Sczaniecka-Clift M, Weickert P, Aygenli F, Götz MJ, Cordes J, Esain-Garcia I, Melidis L, Wondergem AP, Lam S, Robles, MS, Balasubramanian S, Adar S, Luijsterburg MS, Jackson SP, Stingele J (2024) Transcription-coupled repair of DNA–protein cross-links depends on CSA and CSB. Nat Cell Biol., doi.org/10.1038/s41556-024-01391-1 Link

Kansy A, Ashry R, Mustafa A, Alfayomy A, Radsak M, Zeyn Y, Bros M, Sippl W, Krämer O (2024)Pharmacological degradation of ATR induces antiproliferative DNA replication stress in leukemic cells. Mol. Oncol., doi:10.1002/1878-0261.13638 Link

Nugyen A, Mustafa A, Leydecker A, Halilovic M, Murr J, Butter F, Krämer O (2024) The protein phosphatase-2A subunit PR130 is involved in the formation of cytotoxic protein aggregates in pancreatic ductal adenocarcinoma cells. Cell Commun Signal, doi:10.1186/s12964-024-01597-8 Link

Węgrzyn E, Mejdrová I, Müller F, Nainytė M, Escobar L and Carell T (2024) RNA‐Templated Peptide Bond Formation Promotes L‐Homochirality. Angew Chemie Int Ed, doi: 10.1002/anie.202319235 Link

Pradhan SK, Lozoya T, Prorok P, Yuan Y, Lehmkuhl A, Zhang P and Cardoso MC (2024) Developmental Changes in Genome Replication Progression in Pluripotent versus Differentiated Human Cells. Genes (Basel), doi.org/10.3390/genes15030305 Link

Prorok P, Wolf E and Cardoso MC (2024) Timeless–Tipin interactions with MCM and RPA mediate DNA replication stress response. Front Cell Dev Biol, doi: 10.3389/fcell.2024.1346534 Link

Alfayomy AM, Ashry R, Kansy AG, Sarnow A-C, Erdmann F, Schmidt M, Krämer OH and Sippl W (2024) Design, synthesis, and biological characterization of proteolysis targeting chimera (PROTACs) for the ataxia telangiectasia and RAD3-related (ATR) kinase.Eur J Med Chem, doi: 10.1016/j.ejmech.2024.116167 Link

Sayols S (2023) rrvgo: a Bioconductor package for interpreting lists of Gene Ontology terms. MicroPubl Biol.,  doi: 10.17912/micropub.biology.000811 Link

D’Alessandro G, Morales-Juarez DA, Richards SL, Nitiss KC, Serrano-Benitez A, Wang J, Thomas JC, Gupta V, Voigt A, Belotserkovskaya R, Goh CG, Bowden AR, Galanty Y, Beli P, Nitiss JL, Zagnoli-Vieira G and Jackson SP (2023) RAD54L2 counters TOP2-DNA adducts to promote genome stability. Sci Adv, doi: 10.1126/sciadv.adl2108 Link

Renz C, Asimaki E, Meister C, Albanèse V, Petriukov K, Krapoth NC, Wegmann S, Wollscheid H-P, Wong RP, Fulzele A, Chen J-X, Léon S and Ulrich HD (2023) Ubiquiton—An inducible, linkage-specific polyubiquitylation tool. Mol Cell, doi: 10.1016/j.molcel.2023.11.016 Link

Zhao S, Cordes J, Caban KM, Götz MJ, Mackens-Kiani T, Veltri AJ, Sinha NK, Weickert P, Kaya S, Hewitt G, Nedialkova DD, Fröhlich T, Beckmann R, Buskirk AR, Green R and Stingele J (2023) RNF14-dependent atypical ubiquitylation promotes translation-coupled resolution of RNA-protein crosslinks. Mol Cell, doi: 10.1016/j.molcel.2023.10.012 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 J-X, 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, doi: 10.1016/j.molcel.2023.10.011 Link

Pabba MK, Ritter C, Chagin VO, Meyer J, Celikay K, Stear JH, Loerke D, Kolobynina K, Prorok P, Schmid AK, Leonhardt H, Rohr K and Cardoso MC (2023) Replisome loading reduces chromatin motion independent of DNA synthesis. Elife, doi: 10.7554/eLife.87572 Link

Gül D, Krämer OH and Reinhardt C (2023) Starving out brain tumors: a reprogrammed lysine catabolism serves as a novel target for glioblastoma treatment. Signal Transduct Target Ther, doi: 10.1038/s41392-023-01616-z Link

Wollscheid H-P and Ulrich HD (2023) Chromatin meets the cytoskeleton: the importance of nuclear actin dynamics and associated motors for genome stability. DNA Repair (Amst), doi: 10.1016/j.dnarep.2023.103571 Link

Zeyn Y, Hausmann K, Halilovic M, Beyer M, Ibrahim HS, Brenner W, Mahboobi S, Bros M, Sippl W and Krämer OH (2023) Histone deacetylase inhibitors modulate hormesis in leukemic cells with mutant FMS-like tyrosine kinase-3. Leukemia, doi: 10.1038/s41375-023-02036-2 Link

Yakoub G, Choi Y-S, 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, doi:10.1126/sciadv.adf3041 Link

Wirth M, Brenner W and Krämer OH (2023) Boosting T cell immunity against cytomegalovirus: a potential strategy combating human aging and age-related diseases. Signal Transduct Target Ther, doi:10.1038/s41392-023-01590-6 Link

Donsbach M, Dürauer S, Grünert F, Nguyen KT, Nigam R, Yaneva D, Weickert P, Bezalel‐Buch R, Semlow DR and Stingele J (2023) A non‐proteolytic release mechanism for HMCES‐DNA‐protein crosslinks. EMBO J, doi: 10.15252/embj.2022113360 Link

Fischer MA, Mustafa AHM, Hausmann K, Ashry R, Kansy AG, Liebl MC, Brachetti C, Piée-Staffa A, Zessin M, Ibrahim HS, Hofmann TG, Schutkowski M, Sippl W and Krämer OH (2023) Novel hydroxamic acid derivative induces apoptosis and constrains autophagy in leukemic cells. J Adv Res, doi: 10.1016/j.jare.2023.07.005 Link 

Ashry R, Mustafa AHM, Hausmann K, Linnebacher M, Strand S, Sippl W, Wirth M and Krämer OH (2023) NOXA Accentuates Apoptosis Induction by a Novel Histone Deacetylase Inhibitor. Cancers (Basel), doi: 10.3390/cancers15143650 Link

Shi J, Hauschulte K, Mikicic I, Maharjan S, Arz V, Heidelberger JB, Schaefer J V, Dreier B, Plückthun A, Beli P, Ulrich HD and Wollscheid H-P (2022) Nuclear myosin VI maintains replication fork stability. Nat Commun, doi: 10.1038/s41467-023-39517-y 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, doi: 10.1016/j.isci.2023.106778 Link

Hopfner K-P (2023) Mre11–Rad50: the DNA end game. Biochem Soc Trans, doi: 10.1042/BST20220754 Link

Singer JN, Müller FM, Węgrzyn E, Hölzl C, Hurmiz H, Liu C, Escobar L and Carell T (2023) Loading of Amino Acids onto RNA in a Putative RNA‐Peptide World. Angew Chemie Int Ed, doi: 10.1002/anie.202302360 Link

Schindler N, Tonn M, Kellner V, Fung JJ, Lockhart A, Vydzhak O, Juretschke T, Möckel S, Beli P, Khmelinskii A and Luke B (2022) Genetic requirements for repair of lesions caused by single genomic ribonucleotides in S phase. Nat Commun, doi: 10.1038/s41467-023-36866-6 Link

Fahrer J and Christmann M (2023) DNA Alkylation Damage by Nitrosamines and Relevant DNA Repair Pathways. Int J Mol Sci, doi: 10.3390/ijms24054684 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, doi: 10.1016/j.celrep.2023.112077 Link

Sigismondo G, Arseni L, Palacio-Escat N, Hofmann TG, Seiffert M and Krijgsveld J (2023) Multi-layered chromatin proteomics identifies cell vulnerabilities in DNA repair. Nucleic Acids Res, doi: 10.1093/nar/gkac1264 Link

Rotheneder M, Stakyte K, van de Logt E, Bartho JD, Lammens K, Fan Y, Alt A, Kessler B, Jung C, Roos WP, Steigenberger B and Hopfner K-P (2023) Cryo-EM structure of the Mre11-Rad50-Nbs1 complex reveals the molecular mechanism of scaffolding functions. Mol Cell, doi: 10.1016/j.molcel.2022.12.003 Link

Mustafa AHM and Krämer OH (2023) Pharmacological Modulation of the Crosstalk between Aberrant Janus Kinase Signaling and Epigenetic Modifiers of the Histone Deacetylase Family to Treat Cancer. Pharmacol Rev, doi: 10.1124/pharmrev.122.000612 Link

Misino S, Busch A, Wagner CB and Luke B (2022) TERRA increases at short telomeres in yeast survivors and regulates survivor associated senescence (SAS). Nucleic Acids Res, doi: 10.1093/nar/gkac1125 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, doi: 10.1126/sciadv.add3189 Link

Oravcová M, Nie M, Zilio N, Maeda S, Jami-Alahmadi Y, Lazzerini-Denchi E, Wohlschlegel JA, Ulrich HD, Otomo T and Boddy MN (2022) The Nse5/6-like SIMC1-SLF2 Complex Localizes SMC5/6 to Viral Replication Centers. Elife, doi: 10.7554/eLife.79676 Link

Pradhan SK and Cardoso MC (2023) Analysis of Cell Cycle and DNA Compaction Dependent Subnuclear Distribution of Histone Marks. Pp 225–239 in: Methods in molecular biology (Clifton, N.J.) vol. 2589, doi: 10.1038/s41467-022-33814-8 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, doi: 10.1038/s41467-022-33731-w Link

Liebl MC and Hofmann TG (2022) Regulating the p53 Tumor Suppressor Network at PML Biomolecular Condensates. Cancers (Basel), doi: 10.3390/cancers14194549 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 , Beli P (2022) PARP1 proximity reveals interaction partners at stressedreplication forksy.Nucleic Acids Re, doi: 10.1093/nar/gkac948 Link

Qin W, Steinek C, Kolobynina K, Cardoso MC and Leonhardt H (2022) Probing protein ubiquitination in live cells. Nucleic Acids Res, doi: 10.1093/nar/gkac805 Link

Gräf JF, Mikicic I, Ping X, Scalera C, Mayr K, Stelzl LS, Beli P and Wagner SA (2022) Substrate spectrum of PPM1D in the cellular response to DNA double-strand breaks. iScience, doi: 10.1016/j.isci.2022.104892 Link

Winkler R, Mägdefrau A-S, Piskor E-M, Kleemann M, Beyer M, Linke K, Hansen L, Schaffer A-M, Hoffmann ME, Poepsel S, Heyd F, Beli P, Möröy T, Mahboobi S, Krämer OH and Kosan C (2022) Targeting the MYC interaction network in B-cell lymphoma via histone deacetylase 6 inhibition. Oncogene, doi: 10.1038/s41388-022-02450-3 Link

Pan L, Tormey D, Bobon N and Baumann P (2022) Rap1 prevents fusions between long telomeres in fission yeast. EMBO J, doi: 10.15252/embj.2021110458 Link

Xu F, Crisp A, Schinkel T, Dubini RCA, Hübner S, Becker S, Schelter F, Rovó P and Carell T (2022) Isoxazole Nucleosides as Building Blocks for a Plausible Proto‐RNA. Angew Chemie Int Ed, doi: 10.1002/anie.202211945 Link

Stazzoni S, Böhmer DFR, Hernichel F, Özdemir D, Pappa A, Drexler D, Bauernfried S, Witte G, Wagner M, Veth S, Hopfner K-P, Hornung V, König LM and Carell T (2022) Novel Poxin Stable cGAMP‐Derivatives Are Remarkable STING Agonists. Angewandte Chemie Int Ed, doi: 10.1002/anie.202207175 Link

Marx C, Sonnemann J, Maddocks ODK, Marx-Blümel L, Beyer M, Hoelzer D, Thierbach R, Maletzki C, Linnebacher M, Heinzel T and Krämer OH (2022) Global metabolic alterations in colorectal cancer cells during irinotecan-induced DNA replication stress. Cancer Metab, doi:10.1186/s40170-022-00286-9 Link

Tsaridou S, Velimezi G, Willenbrock F, Chatzifrangkeskou M, Elsayed W, Panagopoulos A, Karamitros D, Gorgoulis V, Lygerou Z, Roukos V, O’Neill E and Pefani DE (2022) 53BP1 ‐mediated recruitment of RASSF1A to ribosomal DNA breaks promotes local ATM signaling. EMBO Rep, doi: 10.15252/embr.202154483 Link

Al-Hassan MM, Ashry R and Kramer OH (2022) Monitoring Changes in Intracellular Reactive Oxygen Species Levels in Response to Histone Deacetylase Inhibitors.Pp 293–302 in: Methods in molecular biology (Clifton, N.J.) vol. 2589, doi: 10.1007/978-1-0716-2788-4_22 Link

Beyer M and Krämer OH (2022) RNA interference protocol to silence oncogenic drivers in leukemia cell lines. STAR Protoc, doi: 10.1016/j.xpro.2022.101512 Link

Kramer OH, Diehl T and Roos WP (2022) Assessing the Effect of Histone Deacetylase Inhibitors on DNA Double-Strand Break Repair by Non-Homologous End Joining .Pp 293–302 in: Methods in molecular biology (Clifton, N.J.) vol. 2589, doi: 10.1007/978-1-0716-2788-4_19 Link

Pons M, Conradi R, Brenner W and Kramer OH (2022) Human Platelet Lysate as Valid Cell Growth Additive to Assess Protein Acetylation.Pp 87–94 in: Methods in molecular biology (Clifton, N.J.) vol. 2589, doi: 10.1007/978-1-0716-2788-4_6 Link

Kiweler N, Schwarz H, Nguyen A, Matschos S, Mullins C, Piée-Staffa A, Brachetti C, Roos WP, Schneider G, Linnebacher M, Brenner W and Krämer OH (2022) The epigenetic modifier HDAC2 and the checkpoint kinase ATM determine the responses of microsatellite instable colorectal cancer cells to 5-fluorouracil. Cell Biol Toxicol, doi: 10.1007/s10565-022-09731-3 Link

Krämer OH and Schneider G (2022) Single‐cell profiling guided combination therapy of c‐Fos and histone deacetylase inhibitors in diffuse large B‐cell lymphoma. Clin Transl Med, doi: 10.1002/ctm2.858 Link

Mieland AO, Beyer M and Krämer OH (2022) AUTOTACs join the arena for targeted protein degradation. Arch Toxicol, doi: 10.1007/s00204-022-03312-3 Link

Müller F, Escobar L, Xu F, Węgrzyn E, Nainytė M, Amatov T, Chan C, Pichler A and Carell T (2022) A prebiotically plausible scenario of an RNA–peptide world. Nature, doi: 10.1038/s41586-022-04676-3 Link

Kissling V, Reginato G, Bianco E, Kasaciunaite K, Tilma J, Cereghetti G, Lee SS, Guérois R, Seidel R, Cejka P and others (2021) Mre11-Rad50 oligomerization promotes DNA double-strand break repair. Nat Commun, doi: 10.1038/s41467-022-29841-0 Link

Wegmann S, Meister C, Renz C, Yakoub G, Wollscheid H-P, 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, doi: 10.1016/j.molcel.2022.02.016 Link

Traube FR, Brás NF, Roos WP, Sommermann CC, Diehl T, Mayer RJ, Ofial AR, Müller M, Zipse H and Carell T (2022) Epigenetic Anti‐Cancer Treatment With a Stabilized Carbocyclic Decitabine Analogue. Chem – A Eur J, doi: 10.1002/chem.202200640 Link

Schneeweis C, Hassan Z, Ascherl K, Wirth M, Koutsouli S, Orben F, Krauß L, Schneider C, Öllinger R, Krämer OH, Rad R, Reichert M, Robles MS, Saur D and Schneider G (2022) Indirect targeting of MYC sensitizes pancreatic cancer cells to mechanistic target of rapamycin (mTOR) inhibition. Cancer Commun, doi:  10.1002/cac2.12280 Link

Mamberti S, Pabba MK, Rapp A, Cardoso MC and Scholz M (2022) The Chromatin Architectural Protein CTCF Is Critical for Cell Survival upon Irradiation-Induced DNA Damage. Int J Mol Sci, doi: 10.3390/ijms23073896 Link

Páez-Moscoso DJ, Ho D V., Pan L, Hildebrand K, Jensen KL, Levy MJ, Florens L and Baumann P (2022) A putative cap binding protein and the methyl phosphate capping enzyme Bin3/MePCE function in telomerase biogenesis. Nat Commun, doi: 10.1038/s41467-022-28545-9 Link

Doffo J, Bamopoulos SA, Köse H, Orben F, Zang C, Pons M, den Dekker AT, Brouwer RWW, Baluapuri A, Habringer S, Reichert M, Illendula A, Krämer OH, Schick M, Wolf E, van IJcken WFJ, Esposito I, Keller U, Schneider G and Wirth M (2022) NOXA expression drives synthetic lethality to RUNX1 inhibition in pancreatic cancer. Proc Natl Acad Sci, doi: 10.1073/pnas.2105691119 Link

Abu-Libdeh B, Jhujh SS, Dhar S, Sommers JA, Datta A, Longo GMC, Grange LJ, Reynolds JJ, Cooke SL, McNee GS, Hollingworth R, Woodward BL, Ganesh AN, Smerdon SJ, Nicolae CM, Durlacher-Betzer K, Molho-Pessach V, Abu-Libdeh A, Meiner V, Moldovan G-L, Roukos V, Harel T, Brosh Jr. RM and Stewart GS (2022) RECON syndrome is a genome instability disorder caused by mutations in the DNA helicase RECQL1. J Clin Invest, doi: 10.1172/JCI147301 Link

Ibrahim HS, Abdelsalam M, Zeyn Y, Zessin M, Mustafa A-HM, Fischer MA, Zeyen P, Sun P, Bülbül EF, Vecchio A, Erdmann F, Schmidt M, Robaa D, Barinka C, Romier C, Schutkowski M, Krämer OH and Sippl W (2021) Synthesis, Molecular Docking and Biological Characterization of Pyrazine Linked 2-Aminobenzamides as New Class I Selective Histone Deacetylase (HDAC) Inhibitors with Anti-Leukemic Activity. Int J Mol Sci, doi: 10.3390/ijms23010369 Link

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, doi: 10.1038/s41467-021-27530-y Link

Arnold C, Demuth P, Seiwert N, Wittmann S, Boengler K, Rasenberger B, Christmann M, Huber M, Brunner T, Linnebacher M and Fahrer J (2021) The Mitochondrial Disruptor Devimistat (CPI-613) Synergizes with Genotoxic Anticancer Drugs in Colorectal Cancer Therapy in a Bim-Dependent Manner. Mol Cancer Ther, doi: 10.1158/1535-7163.MCT-21-0393 Link

Eisenhuth N, Vellmer T, Rauh ET, Butter F and Janzen CJ (2021) A DOT1B/Ribonuclease H2 Protein Complex Is Involved in R-Loop Processing, Genomic Integrity, and Antigenic Variation in Trypanosoma brucei. MBio, doi: 10.1128/mBio.01352-21 Link

Beyer M, Henninger SJ, Haehnel PS, Mustafa A-HM, Gurdal E, Schubert B, Christmann M, Sellmer A, Mahboobi S, Drube S, Sippl W, Kindler T and Krämer OH (2021) Identification of a highly efficient dual type I/II FMS-like tyrosine kinase inhibitor that disrupts the growth of leukemic cells. Cell Chem Biol, doi: 10.1016/j.chembiol.2021.10.011 Link

Llorens-Agost M, Ensminger M, Le HP, Gawai A, Liu J, Cruz-García A, Bhetawal S, Wood RD, Heyer W-D and Löbrich M (2021) POLθ-mediated end joining is restricted by RAD52 and BRCA2 until the onset of mitosis. Nat Cell Biol, doi: 10.1038/s41556-021-00764-0 Link

Müller N, Ponkkonen E, Carell T and Khobta A (2021) Direct and Base Excision Repair-Mediated Regulation of a GC-Rich cis-Element in Response to 5-Formylcytosine and 5-Carboxycytosine. Int J Mol Sci, doi: 10.3390/ijms222011025 Link

Wachholz V, Mustafa A-HM, Zeyn Y, Henninger SJ, Beyer M, Dzulko M, Piée-Staffa A, Brachetti C, Haehnel PS, Sellmer A, Mahboobi S, Kindler T, Brenner W, Nikolova T and Krämer OH (2021) Inhibitors of class I HDACs and of FLT3 combine synergistically against leukemia cells with mutant FLT3. Arch Toxicol, doi: 10.1007/s00204-021-03174-1 Link

Nguyen A, Dzulko M, Murr J, Yen Y, Schneider G and Krämer OH (2021) Class 1 Histone Deacetylases and Ataxia-Telangiectasia Mutated Kinase Control the Survival of Murine Pancreatic Cancer Cells upon dNTP Depletion. Cells, doi: 10.3390/cells10102520 Link

Zhang S, Übelmesser N, Josipovic N, Forte G, Slotman JA, Chiang M, Gothe HJ, Gusmao EG, Becker C, Altmüller J, Houtsmuller AB, Roukos V, Wendt KS, Marenduzzo D and Papantonis A (2021) RNA polymerase II is required for spatial chromatin reorganization following exit from mitosis. Sci Adv, doi: 10.1126/sciadv.abg8205 Link

Stakyte K, Rotheneder M, Lammens K, Bartho JD, Grädler U, Fuchß T, Pehl U, Alt A, van de Logt E and Hopfner KP (2021) Molecular basis of human ATM kinase inhibition. Nat Struct Mol Biol, doi: 10.1038/s41594-021-00654-x Link

Kamińska E, Korytiaková E, Reichl A, Müller M and Carell T (2021) Intragenomic decarboxylation of 5‐carboxy‐2’‐deoxycytidine. Angew Chemie Int Ed, doi: 10.1002/anie.202109995 Link

Elbakry A and Löbrich M (2021) Homologous Recombination Subpathways: A Tangle to Resolve. Front Genet, doi: 10.3389/fgene.2021.723847 Link

Mustafa A-HM and Krämer OH (2021) Novel insight into mechanisms for ATR activation by chromatin structures. Arch Toxicol, doi: 10.1007/s00204-021-03133-w Link

Marx C, Sonnemann J, Beyer M, Maddocks ODK, Lilla S, Hauzenberger I, Piée‐Staffa A, Siniuk K, Nunna S, Marx‐Blümel L, Westermann M, Wagner T, Meyer FB, Thierbach R, Mullins CS, Kdimati S, Linnebacher M, Neri F, Heinzel T, Wang Z and Krämer OH (2021) Mechanistic insights into p53‐regulated cytotoxicity of combined entinostat and irinotecan against colorectal cancer cells. Mol Oncol, doi: 10.1002/1878-0261.13060 Link

Pons M, Zeyn Y, Zahn S, Mahendrarajah N, Page BDG, Gunning PT, Moriggl R, Brenner W, Butter F and Krämer OH (2021) Oncogenic Kinase Cascades Induce Molecular Mechanisms That Protect Leukemic Cell Models from Lethal Effects of De Novo dNTP Synthesis Inhibition. Cancers (Basel), doi: 10.3390/cancers13143464 Link

Cabello-Lobato MJ, González-Garrido C, Cano-Linares MI, Wong RP, Yáñez-Vílchez A, Morillo-Huesca M, Roldán-Romero JM, Vicioso M, González-Prieto R, Ulrich HD and Prado F (2021) Physical interactions between MCM and Rad51 facilitate replication fork lesion bypass and ssDNA gap filling by non-recombinogenic functions. Cell Rep, doi: 10.1016/j.celrep.2021.109440 Link

Traube FR, Özdemir D, Sahin H, Scheel C, Glück AF, Geserich AS, Oganesian S, Kostidis S, Iwan K, Rahimoff R, Giorgio G, Müller M, Spada F, Biel M, Cox J, Giera M, Michalakis S and Carell T (2021) Redirected nuclear glutamate dehydrogenase supplies Tet3 with α-ketoglutarate in neurons. Nat Commun, doi: 10.1038/s41467-021-24353-9 Link

Runtsch LS, Stadlmeier M, Schön A, Müller M and Carell T (2021) Comparative nucleosomal reactivity of 5‐formyl‐uridine and 5‐formyl‐cytidine. Chem – A Eur J, doi: 10.1002/chem.202102159 Link

Korytiaková E, Kamińska E, Müller M and Carell T (2021) Deformylation of 5‐Formylcytidine in Different Cell Types. Angew Chemie Int Ed, doi: 10.1002/anie.202107089 Link

Wong RP, Petriukov K and Ulrich HD (2021) Daughter-strand gaps in DNA replication – substrates of lesion processing and initiators of distress signalling. DNA Repair (Amst), doi: 10.1016/j.dnarep.2021.103163 Link

Rausch C, Zhang P, Casas-Delucchi CS, Daiß JL, Engel C, Coster G, Hastert FD, Weber P and Cardoso MC (2021) Cytosine base modifications regulate DNA duplex stability and metabolism. Nucleic Acids Res, doi: 10.1093/nar/gkab509 Link

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, doi: 10.1038/s41467-021-22861-2 Link

Gnan S, Flyamer IM, Klein KN, Castelli E, Rapp A, Maiser A, Chen N, Weber P, Enervald E, Cardoso MC, Bickmore WA, Gilbert DM and Buonomo SCB (2021) Nuclear organisation and replication timing are coupled through RIF1–PP1 interaction. Nat Commun, doi: 10.1038/s41467-021-22899-2 Link

Göder A, Ginter T, Heinzel T, Stroh S, Fahrer J, Henke A and Krämer OH (2021) STAT1 N-terminal domain discriminatively controls type I and type II IFN signaling. Cytokine, doi: 10.1016/j.cyto.2021.155552 Link

Müller N and Khobta A (2021) Regulation of GC box activity by 8-oxoguanine. Redox Biol, doi: 10.1016/j.redox.2021.101997 Link

Liebl MC and Hofmann TG (2021) The Role of p53 Signaling in Colorectal Cancer. Cancers (Basel), doi: 10.3390/cancers13092125 Link

Schelter F, Kirchner A, Traube FR, Müller M, Steglich W and Carell T (2021) 5‐Hydroxymethyl‐, 5‐Formyl‐ and 5‐Carboxydeoxycytidines as Oxidative Lesions and Epigenetic Marks. Chem – A Eur J, doi: 10.1002/chem.202100551 Link

Liebl MC, Moehlenbrink J, Becker H, Raddatz G, Abdeen SK, Aqeilan RI, Lyko F and Hofmann TG (2021) DAZAP2 acts as specifier of the p53 response to DNA damage. Nucleic Acids Res, doi: 10.1093/nar/gkab084 Link

Rausch C, Weber P, Prorok P, Hörl D, Maiser A, Lehmkuhl A, Chagin VO, Casas-Delucchi CS, Leonhardt H and Cardoso MC (2020) Developmental differences in genome replication program and origin activation. Nucleic Acids Res, doi: 10.1093/nar/gkaa1124 Link

Jansma M and Hopfner K-P (2020) Structural basis of the (in)activity of the apical DNA damage response kinases ATM, ATR and DNA-PKcs. Prog Biophys Mol Biol, doi: 10.1016/j.pbiomolbio.2020.10.009 Link

Allmann S, Mayer L, Olma J, Kaina B, Hofmann TG, Tomicic MT and Christmann M (2020) Benzo[a]pyrene represses DNA repair through altered E2F1/E2F4 function marking an early event in DNA damage-induced cellular senescence. Nucleic Acids Res, doi: 10.1093/nar/gkaa965 Link

Alberge J-B, Magrangeas F, Wagner M, Denié S, Guérin-Charbonnel C, Campion L, Attal M, Avet-Loiseau H, Carell T, Moreau P, Minvielle S and Sérandour AA (2020) DNA hydroxymethylation is associated with disease severity and persists at enhancers of oncogenic regions in multiple myeloma. Clin Epigenetics, doi: 10.1186/s13148-020-00953-y Link

Bouwman BAM, Agostini F, Garnerone S, Petrosino G, Gothe HJ, Sayols S, Moor AE, Itzkovitz S, Bienko M, Roukos V and Crosetto N (2020) Genome-wide detection of DNA double-strand breaks by in-suspension BLISS. Nat Protoc, doi: 10.1038/s41596-020-0397-3 Link

Dzulko M, Pons M, Henke A, Schneider G and Krämer OH (2020) The PP2A subunit PR130 is a key regulator of cell development and oncogenic transformation. Biochim Biophys Acta - Rev Cancer, doi: 10.1016/j.bbcan.2020.188453 Link

Zilio N and Ulrich HD (2020) Exploring the SSBreakome: genome‐wide mapping of DNA single‐strand breaks by next‐generation sequencing. FEBS J, doi: 10.1111/febs.15568 Link

Volcic M, Sparrer KMJ, Koepke L, Hotter D, Sauter D, Stürzel CM, Scherer M, Stamminger T, Hofmann TG, Arhel NJ, Wiesmüller L and Kirchhoff F (2020) Vpu modulates DNA repair to suppress innate sensing and hyper-integration of HIV-1. Nat Microbiol, doi: 10.1038/s41564-020-0753-6 Link

Petrosino G, Zilio N, Sriramachandran AM and Ulrich HD (2020) Preparation and Analysis of GLOE-Seq Libraries for Genome-Wide Mapping of DNA Replication Patterns, Single-Strand Breaks, and Lesions.  STAR Protocols, doi: 10.1016/j.xpro.2020.100076 Link

Spada F, Schiffers S, Kirchner A, Zhang Y, Arista G, Kosmatchev O, Korytiakova E, Rahimoff R, Ebert C and Carell T (2020) Active turnover of genomic methylcytosine in pluripotent cells. Nat Chem Biol, doi: 10.1038/s41589-020-0621-y Link

Rodriguez-Alvarez M, Kim D and Khobta A (2020) EGFP Reporters for Direct and Sensitive Detection of Mutagenic Bypass of DNA Lesions. Biomolecules, doi: 10.3390/biom10060902 Link

Wolf E and Kramer A (2020) Circadian Regulation: From Molecules to Physiology. J Mol Biol, doi: 10.1016/j.jmb.2020.05.004 Link

Vydzhak O, Luke B and Schindler N (2020) Non-coding RNAs at the eukaryotic rDNA locus: RNA-DNA hybrids and beyond. J Mol Biol, doi: 10.1016/j.jmb.2020.05.011 Link

Sriramachandran AM, Petrosino G, Méndez-Lago M, Schäfer AJ, Batista-Nascimento LS, Zilio N and Ulrich HD (2020) Genome-wide Nucleotide-Resolution Mapping of DNA Replication Patterns, Single-Strand Breaks, and Lesions by GLOE-Seq. Mol Cell, doi: 10.1016/j.molcel.2020.03.027 Link

Maddi K, Sam DK, Bonn F, Prgomet S, Tulowetzke E, Akutsu M, Lopez-Mosqueda J and Dikic I (2020) Wss1 Promotes Replication Stress Tolerance by Degrading Histones. Cell Rep, doi: 10.1016/j.celrep.2020.02.018 Link

Beckwitt EC, Jang S, Carnaval Detweiler I, Kuper J, Sauer F, Simon N, Bretzler J, Watkins SC, Carell T, Kisker C and Van Houten B (2020) Single molecule analysis reveals monomeric XPA bends DNA and undergoes episodic linear diffusion during damage search. Nat Commun, doi: 10.1038/s41467-020-15168-1 Link

Thumbs P, Ensfelder TT, Hillmeier M, Wagner M, Heiss M, Scheel C, Schön A, Müller M, Michalakis S, Kellner S and Carell T (2020) Synthesis of galactosyl‐queuosine and distribution of hypermodified Q‐nucleosides in mouse tissues. Angew Chemie Int Ed, doi: 10.1002/anie.202002295 Link

Ensminger M and Löbrich M (2020) One end to rule them all: Non-homologous end-joining and homologous recombination at DNA double-strand breaks. Br J Radiol, doi: 10.1259/bjr.20191054 Link

Lowe DJ, Herzog M, Mosler T, Cohen H, Felton S, Beli P, Raj K, Galanty Y and Jackson SP (2020) Chronic irradiation of human cells reduces histone levels and deregulates gene expression. Sci Rep, doi: 10.1038/s41598-020-59163-4 Link

Niehrs C and Luke B (2020) Regulatory R-loops as facilitators of gene expression and genome stability. Nat Rev Mol Cell Biol, doi: 10.1038/s41580-019-0206-3 Link

Kiweler N, Wünsch D, Wirth M, Mahendrarajah N, Schneider G, Stauber RH, Brenner W, Butter F and Krämer OH (2020) Histone deacetylase inhibitors dysregulate DNA repair proteins and antagonize metastasis-associated processes. J Cancer Res Clin Oncol, doi: 10.1007/s00432-019-03118-4 Link

Schön A, Kaminska E, Schelter F, Ponkkonen E, Korytiaková E, Schiffers S and Carell T (2020) Analysis of an active deformylation mechanism of 5-formyl-deoxycytidine (fdC) in stem cells. Angew Chemie Int Ed, doi: 10.1002/anie.202000414 Link

Liebl MC and Hofmann TG (2019) Identification of responders to immune checkpoint therapy: which biomarkers have the highest value?J Eur Acad Dermatology Venereol, doi: 10.1111/jdv.15992 Link

Kellner V and Luke B (2019) Molecular and physiological consequences of faulty eukaryotic ribonucleotide excision repair. EMBO J, doi: 10.15252/embj.2019102309 Link

Chagin VO, Reinhart B, Becker A, Mortusewicz O, Jost KL, Rapp A, Leonhardt H and Cardoso MC (2019) Processive DNA synthesis is associated with localized decompaction of constitutive heterochromatin at the sites of DNA replication and repair. Nucleus, doi: 10.1080/19491034.2019.1688932 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, doi: 10.1016/j.celrep.2019.10.108 Link

Greulich W, Wagner M, Gaidt MM, Stafford C, Cheng Y, Linder A, Carell T and Hornung V (2019) TLR8 Is a Sensor of RNase T2 Degradation Products. Cell, doi: 10.1016/j.cell.2019.11.001 Link

Jansma M, Linke-Winnebeck C, Eustermann S, Lammens K, Kostrewa D, Stakyte K, Litz C, Kessler B and Hopfner K-P (2019) Near-Complete Structure and Model of Tel1ATM from Chaetomium thermophilum Reveals a Robust Autoinhibited ATP State. Structure, doi: 10.1016/j.str.2019.10.013 Link

Han D, Schomacher L, Schüle KM, Mallick M, Musheev MU, Karaulanov E, Krebs L, von Seggern A and Niehrs C (2019) NEIL1 and NEIL2 DNA glycosylases protect neural crest development against mitochondrial oxidative stress. Elife, doi: 10.7554/eLife.49044 Link

Liebl MC and Hofmann TG (2019) Cell Fate Regulation upon DNA Damage: p53 Serine 46 Kinases Pave the Cell Death Road. BioEssays, doi: 10.1002/bies.201900127 Link

Beyer M, Romanski A, Mustafa A-HM, Pons M, Büchler I, Vogel A, Pautz A, Sellmer A, Schneider G, Bug G and Krämer OH (2019) HDAC3 Activity is Essential for Human Leukemic Cell Growth and the Expression of β-catenin, MYC, and WT1. Cancers (Basel), doi: 10.3390/cancers11101436 Link

Käshammer L, Saathoff J-H, Lammens K, Gut F, Bartho J, Alt A, Kessler B and Hopfner K-P (2019) Mechanism of DNA End Sensing and Processing by the Mre11-Rad50 Complex. Mol Cell, doi: 10.1016/j.molcel.2019.07.035 Link

Gothe HJ, Bouwman BAM, Gusmao EG, Piccinno R, Petrosino G, Sayols S, Drechsel O, Minneker V, Josipovic N, Mizi A, Nielsen CF, Wagner E-M, Takeda S, Sasanuma H, Hudson DF, Kindler T, Baranello L, Papantonis A, Crosetto N and Roukos V (2019) Spatial Chromosome Folding and Active Transcription Drive DNA Fragility and Formation of Oncogenic MLL Translocations. Mol Cell, doi: 10.1016/j.molcel.2019.05.015 Link

Kitsera N, Rodriguez-Alvarez M, Emmert S, Carell T and Khobta A (2019) Nucleotide excision repair of abasic DNA lesions. Nucleic Acids Res, doi: 10.1093/nar/gkz558 Link

Wildenhof T, Schiffers S, Traube FR, Mayer P and Carell T (2019) Influencing epigenetic information with a hydrolytically stable carbocyclic 5 aza-2’-deoxycytidine. Angew Chemie Int Ed, doi: 10.1002/anie.201904794 Link

Wong RP, García-Rodríguez N, Zilio N, Hanulová M and Ulrich HD (2019) Processing of DNA Polymerase-Blocking Lesions during Genome Replication Is Spatially and Temporally Segregated from Replication Forks. Mol Cell, doi: 10.1016/j.molcel.2019.09.015 Link