Selected Publications


  • Xie T, Danieli-Mackay A, Buccarelli M, Barbieri M, Papadionysiou I, D’Alessandris QG, Übelmesser N, Vinchure OS, Lauretti L, Fotia G, Wang X, Ricci-Vitiani L, Gopalakrishnan J, Pallini R, Papantonis A* (2023) Extreme structural heterogeneity rewires glioblastoma chromosomes to sustain patient-specific transcriptional programs. bioRxiv doi:10.1101/2023.04.20.537702.
  • Platania A, Erb C, Barbieri M, Molcrette B, Grandgirard E, de Kort MAC, Meaburn K, Taylor T, Shchuka VM, Kocanova S, Oliveira GM, Mitchell JA, Soutoglou E, Lenstra TL, Molina N, Papantonis A, Bystricky K, Sexton T (2023) Competition between transcription and loop extrusion modulates promoter and enhancer dynamics. bioRxiv doi:10.1101/2023.04.25.538222.
  • Duman ET, Sitte M, Conrads K, Mackay A, Ludewig F, Stroebel P, Ellenrieder V, Hessmann E, Papantonis A*, Salinas G* (2023) A single-cell strategy for the identification of intronic variants related to mis-splicing in pancreatic cancer. bioRxiv doi:10.1101/2023.05.08.539836.


  • Zhang S, Übelmesser N, Barbieri M, Papantonis A* (2023) Enhancer-promoter contact formation requires RNAPII and antagonizes loop extrusion. Nat Genet doi:10.1038/s41588-023-01364-4. [Highlighted in Nat Genetics] PDF
  • Debès C, Papadakis A, Grönke S, Karalay Ö, Tain L, Mizi A, Nakamura S, Hahn O, Weigelt C, Josipovic N, Zirkel A, Brusius I, Sofiadis K, Lamprousi M, Lu YX, Huang W, Esmaillie R, Kubacki T, Späth MR, Schermer B, Benzing T, Müller RU, Antebi A*, Partridge L*, Papantonis A*, Beyer A* (2023) Aging-associated changes in transcriptional elongation influence metazoan longevity. Nature doi:10.1038/s41586-023-05922-y. [Highlighted by AAAS EurekaAlert!] PDF
  • Zampetidis CP, Galanos P, Angelopoulou A, Zhu Y, Karamitros T, Polyzou A, Karamitros T, Kotsinas A, Lagopati N, Mourkioti I, Mirzazadeh R, Polyzos A, Garnerone S, Mizi A, Gusmao EG, Sofiadis K, Gal Z, Larsen DH, Pefani DE, Demaria M, Tsirigos A, Crosetto N, Maya-Mendoza A, Papaspyropoulos A, Evangelou K, Bartek J*, Papantonis A*, Gorgoulis VG* (2021) A recurrent chromosomal inversion suffices for driving escape from oncogene-induced senescence via subTAD reorganization. Mol Cell 81:4907-4923. [Highlighted by Cancer Research] PDF
  • Zhang S, Übelmesser N, Josipovic N, Forte G, Slotman JA, Chiang M, Gothe H, Gusmao EG, Becker C, Altmüller J, Houtsmuller AB, Roukos V, Wendt KS, Marenduzzo D, Papantonis A* (2021) RNA polymerase II is required for spatial chromatin reorganization following exit from mitosis. Sci Adv 7: eabg8205. PDF
  • Sofiadis K, Josipovic N, Nikolic M, Kargapolova Y, Übelmesser N, Varamogianni I, Zirkel A, Papadionysiou I, Loughran G, Keanes J, Michel A, Gusmao EG, Becker C, Altmüller J, Georgomanolis T, Mizi A, Papantonis A* (2021) HMGB1 coordinates SASP-related chromatin folding and RNA homeostasis on the path to senescence. Mol Syst Biol 17:e9760. [Featured on the issue’s cover] PDF
  • Kargapolova Y*, Rehimi R, Kayserili H, Brühl J, Zirkel A, Li Y, Yigit G, Hoischen A, Frank S, Russ N, Trautwein J, Laugsch M, Gusmao EG, Josipovic N, Altmüller J, Nürnberg P, Längst G, Kaiser FJ, Watrin E, Brunner H, Rada-Iglesias A, Kurian L, Wollnik B, Bouazoune K*, Papantonis A* (2021) Overarching control of autophagy and DNA damage response by CHD6 revealed by modeling a rare human pathology. Nat Commun 12:3014. PDF
  • Casa V, Gines MM, Gusmao EG, Slotman JA, Zirkel A, Josipovic N, Oole E, van Ijcken WFJ, Houtsmuller AB, Papantonis A*, Wendt KS* (2020) Redundant and specific roles of cohesin STAG subunits in chromatin looping and transcription control. Genome Res 30:515-527. PDF
  • Weiterer SS, Meier-Soelch J, Georgomanolis T, Mizi A, Beyerlein A, Weiser H, Brant L, Mayr-Buro C, Jurida L, Beuerlein K, Müller H, Weber A, Tenekeci U, Dittrich-Breiholz O, Bartkuhn M, Nist A, Stiewe T, van IJcken WF, Riedlinger T, Schmitz ML, Papantonis A*, Kracht M* (2020) Distinct IL-1α-responsive enhancers promote acute and coordinated changes in chromatin topology in a hierarchical manner. EMBO J 39:e101533. [Featured in the German Press] PDF
  • Zirkel A, Nikolic M, Sofiadis K, Mallm JP, Brackley CA, Gothe H, Drechsel O, Becker C, Altmüller J, Josipovic N, Georgomanolis T, Brant L, Franzen J, Koker M, Gusmao EG, Costa IG, Ullrich RT, Wagner W, Roukos V, Nürnberg P, Marenduzzo D, Rippe K, Papantonis A* (2018) HMGB2 loss upon senescence entry disrupts genomic organization and induces CTCF clustering across cell types. Mol Cell 70: 730-744. [Featured in F1000] PDF
  • Brant L, Georgomanolis T, Nikolic M, Brackley CA, Kolovos P, van Ijcken W, Grosveld FG, Marenduzzo D, Papantonis A* (2016) Exploiting native forces to capture chromosome conformation in mammalian cell nuclei. Mol Syst Biol 12: 891. [Highlight of the issue and featured in Nature Methods] PDF
  • Kolovos P, Georgomanolis T, Koeferle A, Larkin JD, Brant L, Nikolić M, Gusmao EG, Zirkel A, Knoch TA, van Ijcken WF, Cook PR, Costa IG, Grosveld FG, Papantonis A* (2016) Binding of nuclear factor κB to noncanonical consensus sites reveals its multimodal role during the early inflammatory response. Genome Res 26:1478-1489. PDF
  • Diermeier S, Kolovos P, Heizinger L, Schwartz U, Georgomanolis T, Zirkel A, Wedemann G, Grosveld F, Knoch TA, Merkl R, Cook PR, Längst G*, Papantonis A* (2014) TNFα signaling primes chromatin for NF-κB binding and induces rapid and widespread nucleosome repositioning. Genome Biol 15:536. [Highlighted in BMC Editors’ picks] PDF


  • Rippe K*, Papantonis A* (2022) Functional organization of RNA polymerase II in nuclear subcompartments. Curr Opin Cell Biol 74:88-96. PDF
  • Papantonis A* (2021) HMGs as rheostats of chromosomal structure and cell proliferation. Trends Genet 37:986-994. PDF
  • Papantonis A*, Rippe K* (2021) RNA polymerase II transcription compartments: from multivalent chromatin binding to liquid droplet formation? Nat Rev Mol Cell Biol 22:645-646. PDF
  • Mizi A, Zhang S, Papantonis A* (2020) Genome folding and refolding in differentiation and cellular senescence. Curr Opin Cell Biol 67:56-63. PDF
  • Danieli A, Papantonis A* (2020) Spatial genome architecture and the emergence of malignancy. Hum Mol Genet 29:R197-R204. PDF
  • Rada-Iglesias A*, Grosveld FG, Papantonis A* (2018) Forces driving the three-dimensional folding of eukaryotic genomes. Mol Syst Biol 14: e8214. PDF
  • Papantonis A, Cook PR* (2013) Transcription factories: genome organization and gene regulation. Chem Rev 113:8683-8705. PDF
  • Kolovos P, Knoch TA, Grosveld FG, Cook PR, Papantonis A* (2012) Enhancers and silencers: an integrated and simple model for their function. Epigenetics Chromatin 5:1. PDF

For a complete list of publications by our group, please visit NCBI PubMed here.