Selected publications

Frank S, Ahuja G, Bartsch D, Russ N, Yao W, Kuo JC, Derks JP, Akhade VS, Kargapolova Y, Georgomanolis T, Messling JE, Gramm M, Brant L, Rehimi R, Vargas NE, Kuroczik A, Yang TP, Sahito RGA, Franzen J, Hescheler J, Sachinidis A, Peifer M, Rada-Iglesias A, Kanduri M, Costa IG, Kanduri C, Papantonis A, Kurian L (2019) yylncT defines a class of divergently transcribed lncRNAs and safeguards the T-mediated mesodermal commitment of human PSCs. Cell Stem Cell 24: 318-327


Rada-Iglesias A*, Grosveld FG, Papantonis A*. Forces driving the three-dimensional folding of eukaryotic genomes. Mol Syst Biol 14: e8214 (*co-corresponding authors)


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


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


Michieletto D, Chiang M, Colì D, Papantonis A, Orlandini E, Cook PR, Marenduzzo D (2018) Shaping epigenetic memory via genomic bookmarking. Nucleic Acids Res 46: 83-93


Franzen J, Zirkel A, Blake J, Rath B, Benes V, Papantonis A, Wagner W (2017) Senescence-associated DNA methylation is stochastically acquired in subpopulations of mesenchymal stem cells. Aging Cell 16: 183-91


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 (*corresponding author)


Nikolic M, Papantonis A, Rada-Iglesias A (2016) GARLiC: A bioinformatic toolkit for etiologically connecting diseases and cell type-specific regulatory maps. Hum Mol Genet doi: 10.1093/hmg/ddw423


Kolovos P*, Georgomanolis T, Koeferle A, Larkin JD, Brant L, Nikolic M, Gusmao EG, Zirkel A, Knoch TA, van Ijcken W, Cook PR, Costa IG, Grosveld FG, Papantonis A* (2016) Binding of nuclear factor kappaB to noncanonical consensus sites reveals its bimodal role during the early proinflammatory response. Genome Res 26: 1478-89 (*corresponding author)


Melnik S, Caudron-Herger M, Brant L, Rippe K, Cook PR, Papantonis A* (2015) Isolation of the protein and RNA content of the active site of transcription in mammalian cells. Nat Protocols 11: 553-65 (*corresponding author)


Caudron-Herger M, Cook PR, Rippe K, Papantonis A* (2015) Dissecting the nascent human transcriptome by analyzing the RNA content of transcription factories. Nucleic Acids Res 43: e95 (*corresponding author)


Kelly S, Georgomanolis T, Zirkel A, Diermeier S, O’Reilly D, Murphy S, Laengst G, Cook PR, Papantonis A* (2015) Splicing of many human genes involves sites embedded within introns. Nucleic Acids Res 43: 4721-32 (*corresponding author)


Kelly S, Greenman C, Cook PR, Papantonis A* (2015) Exon skipping is correlated with exon circularization. J Mol Biol 427: 2414-7 (*corresponding author)


Diermeier S, Kolovos P, Heizinger L, Schwartz U, Georgomanolis T, Zirkel A, Wedemann G, Grosveld F, Knock TA, Merckl R, Cook PR, Laengst G*, Papantonis A* (2014) TNFα signaling primes chromatin for NF-κB binding and induces rapid and widespread nucleosome repositioning. Genome Biol 15: 536 (*co-corresponding authors)


Papantonis A, Cook PR (2013) Transcription factories: genome organization and gene regulation. Chem Rev doi:10.1021/ cr300513p


Larkin JD, Cook PR, Papantonis A* (2012) Dynamic configurations of long human genes during a transcription cycle. Mol Cell Biol 32: 2738-2747 (*corresponding author)



For a complete list of publications by our group, please visit: https://www.ncbi.nlm.nih.gov/pubmed/?term=papantonis+a