Publications Roukos & Zarnack

Longo GMC, Sayols S, Roukos V (2025) Multilevel characterization of genome editor nuclease activity with BreakTag. Nat Protoc, 21:2043-2082 Link

van Schaik T, Magnitov M, de Haas M, Breda J, de Wit E, Manjon AG, Medema RH, Gothe HJ, Roukos V, Buckle AJ, Naughton C, Gilbert N, van Steensel B, Manzo SG (2025) Coordinated control of genome-nuclear lamina interactions by topoisomerase 2B and lamin B receptor. Nucleic Acids Res, 53:gkaf964 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, 84:4267-4281.e8 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, 43:608-622 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, 15:3475 Link

Lewinski M, Steffen A, Kachariya N, Elgner M, Schmal C, Messini N, Köster T, Reichel M, Sattler M, Zarnack K, Staiger D (2023) Arabidopsis thaliana GLYCINE RICH RNA-BINDING PROTEIN 7 interaction with its iCLIP target LHCB1.1 correlates with changes in RNA stability and circadian oscillation. Plant J, 118:203-224 Link

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:EMBJ2023114072 Link

Zarnack K, Eyras E (2023) ‘Artificial intelligence and machine learning in RNA biology’. Brief Bioinform, 24:bbad415 Link

Glaser SF, Brezski A, Baumgarten N, Klangwart M, Heumüller AW, Maji RK, Leisegang MS, Guenther S, Zehendner CM, John D, Schulz MH, Zarnack K, Dimmeler S (2023) Circular RNA circPLOD2 regulates pericyte function by targeting the transcription factor KLF4. Cell Rep, 42:112824 Link

Sankaranarayanan S, Haag C, Petzsch P, Köhrer K, Matuszyńska A, Zarnack K and Feldbrügge M (2023) The mRNA stability factor Khd4 defines a specific mRNA regulon for membrane trafficking in the pathogen Ustilago maydis. Proc Natl Acad Sci, 120:e2301731120 Link

Ebersberger S, Hipp C, Mulorz MM, Buchbender A, Merzhakupova D, Kang H-S, Martínez-Lumbreras S, Kristoferi P, Sutandy R, Llacsahuanga L, Schönfeld J, Bakisoglu C, Busch A, Hänel H, Welzel M, di Liddo A, Möckel M, Zarnack K, Ebersberger I, Legewie S, Luck K, Sattler M, 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 Link

Bauer R, Meyer SP, Raue R, Palmer MA, Guerrero Ruiz VM, Cardamone G, Rösser S, Heffels M, Roesmann F, Wilhelm A, Lütjohann D, Zarnack K, Fuhrmann DC, Widera M, Schmid T, Brüne B (2023) Hypoxia-altered cholesterol homeostasis enhances the expression of interferon-stimulated genes upon SARS-CoV-2 infections in monocytes. Front Immunol, 14:1121864 Link

Rücklé C, Körtel N, Basilicata MF, Busch A, Zhou Y, Hoch-Kraft P, Tretow K, Kielisch F, Bertin M, Pradhan M, Musheev M, Schweiger S, Niehrs C, Rausch O, Zarnack K, Keller Valsecchi CI, König J (2023) RNA stability controlled by m6A methylation contributes to X-to-autosome dosage compensation in mammals.  Nat Struct Mol Biol, 30:1607 Link

Acera Mateos P, Zhou Y, Zarnack K, Eyras E (2023) Concepts and methods for transcriptome-wide prediction of chemical messenger RNA modifications with machine learning. Brief Bioinform, 24:bbad163 Link

Molitor L, Klostermann M, Bacher S, Merl-Pham J, Spranger N, Burczyk S, Ketteler C, Rusha E, Tews D, Pertek A, Proske M, Busch A, Reschke S, Feederle R, Hauck SM, Blum H, Drukker M, Fischer-Posovszky P, König J, Zarnack K, Niessing D (2023) Depletion of the RNA-binding protein PURA triggers changes in posttranscriptional gene regulation and loss of P-bodies. Nucleic Acids Res, 51:1297-1316 Link

Keil P, Wulf A, Kachariya N, Reuscher S, Hühn K, Silbern I, Altmüller J, Keller M, Stehle R, Zarnack K, Sattler M, Urlaub H, Sträßer K (2023) Npl3 functions in mRNP assembly by recruitment of mRNP components to the transcription site and their transfer onto the mRNA. Nucleic Acids Res, 51:831-851 Link

de Oliveira Freitas Machado C, Schafranek M, Brüggemann M, Hernández Cañás MC, Keller M, Di Liddo A, Brezski A, Blümel N, Arnold B, Bremm A, Wittig I, Jaé N, McNicoll F, Dimmeler S, Zarnack K and Müller-McNicoll M (2023) Poison cassette exon splicing of SRSF6 regulates nuclear speckle dispersal and the response to hypoxia. Nucleic Acids Res, 51:870-890 Link 

Petropoulos M, Champeris Tsaniras S, Nikou S, Maxouri S, Dionellis VS, Kalogeropoulou A, Karamichali A, Ioannidis K, Danalatos I-R, Obst M, Naumann R, Delinasios GJ, Gorgoulis VG, Roukos V, Anastassiadis K, Halazonetis TD, Bravou V, Lygerou Z and Taraviras S (2022) Cdt1 overexpression drives colorectal carcinogenesis through origin overlicensing and DNA damage.J Pathol, 259:10-20 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 Res, 50:11600–11618Link

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, 23:EMBR202154483 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

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

Papantonis A and Roukos V (2021) Cohesin puts a break on distal homology hunt. Nat Cell Biol, 23:1112-1114 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, 7:eabg8205 Link

Longo GMC and Roukos V (2021) Territories or spaghetti? Chromosome organization exposed. Nat Rev Mol Cell Biol, doi: 10.1038/s41580-021-00372-8 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, 15:3894-3941 Link

Lucic B, Chen HC, Kuzman M, Zorita E, Wegner J, Minneker V, Wang W, Fronza R, Laufs S, Schmidt M, Stadhouders R, Roukos V, Vlahovicek K, Filion GJ and Lusic M (2019) Spatially clustered loci with multiple enhancers are frequent targets of HIV-1 integration.  Nat Commun, 10:4059 Link

Gothe HJ, Bouwman BAM, Gusmao EG, Piccinno R, Petrosino G, Sayols S, Drechsel O, Minneker V, Josipovic N, Mizi A, Nielsen CF, Wagner EM, 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, 75:267-283.e12 Link

Piccinno R, Minneker V and Roukos V (2019) 53BP1—DNA repair enters a new liquid phase. EMBO J, 38:EMBJ2019102871 Link