Below please find publications from SFB 1361 projects since 2019.


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



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