Translational Epigenetics Laboratory

AG Papantonis

Our research focuses on dissecting the structure-to-function relationship of the human genome at the molecular level. We wish to understand how chromatin integrates the various signaling stimuli of its environment to control transitions between homeostatic and deregulated functional programs. We particularly ask how changes along the linear DNA fiber translate into dynamic higher-order regulatory networks. Ultimately, by deciphering the general rules governing transcriptional and chromatin homeostasis, we will be able to compile a parsimonious set of rules that allows prediction of how a cell might respond during development, in ageing or upon malignancy.

What we do (for the non-scientific audience)

The efforts of the Human Genome Project have revealed the sequence of the billions of bases in our chromosomes. However, how these very long molecules fold in 3D space, and how this folding allows our genes to be expressed at the right time and place, still eludes us. We are currently trying to generate 3D maps of the human genome to identify gene neighborhoods. This should allow us to understand the rules that govern gene function, and to predict how a cell might respond in disease or ageing.

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

Lab members

Argyris Papantonis (b. 1978, Athens, Greece) studied Biology at the National and Kapodistrian University of Athens, where he also undertook his PhD studies under the supervision of Prof. Rena Lecanidou. In 2008 he moved to Oxford for his post-doctoral work with Prof. Peter Cook at the Sir William Dunn School of Pathology. In 2013 he was appointed as a Junior Research Group Leader for Chromatin Systems Biology at the CMMC, and in 2018 he was recruited to the Medical Faculty of the Georg-August University of Göttingen where he is currently a W2-Professor for Translational Epigenetics. When he is not doing research he reads, writes, or translates literary texts.

E-mail: argyris.papantonis [at] med.uni-goettingen.de / Twitter: @apapant


Current lab members:

Dr. Athanasia Mizi (Senior postdoc) studied Biology at the National and Kapodistrian University of Athens, where she also undertook her PhD studies under the supervision of Prof. George Rodakis on the molecular evolution of molluscan mtDNA. Before joining our lab, Athanasia did her first post-doctoral work with Dr. Paul Brinkkoetter on the role of the key mitochondrial factor, TFAM, in kidney function. Currently Athanasia is working on miRNA-centered 3D networks; she is funded by the UMG.

E-mail: athanasia.mizi [at] med.uni-goettingen.de


Dr. Eduardo Gade Gusmao (Bioinformatician) initially studied Computer Sciences in Pernambuco, Brazil, before undertaking his PhD work with Ivan Costa at the RWTH University of Aachen, Germany, and developing an interest in transcription factor binding properties on chromatin. Eduardo joined our laboratory in February 2018 and is interested in deep learning and in new tools that further exploit native Hi-C data; he is funded via the SPP 2202 Priority Program.

E-mail: eduardo.gusmao [at] med.uni-goettingen.de


Natasa Josipovic (PhD student) studied Biology at the University of Belgrade, where she also undertook his MSc studies. Her placement as a PhD student started in 2016, and she has been working on single-nulceotide resolution and single-cell nascent RNA-seq to understand fundamental differences in the temporal deployment of TNF- versus TGF-driven transcriptional responses; she is funded by a DFG grant.

E-mail: natasa.josipovic [at] med.uni-goettingen.de


Konstantinos Sofiadis (PhD student) studied Biology at the University of Crete, Greece, where he also undertook his MSc studies. His placement as a PhD student started in 2015, and he has been working on the molecular basis of recursive splicing; he is funded via the SPP 1935 Priority Program.

E-mail: konstantinos.sofiadis [at] med.uni-goettingen.de


Nadine Übelmesser (PhD student) studied Biology in Erlagen, where she also undertook her MSc studies on Cellular and Molecular Biology. Her placement as a PhD student started in 2015, and she is working on cell cycle progression and its link to chromosomal folding in cancer; she is funded via TRR81/SFB program.

E-mail: nadine.uebelmesser [at] med.uni-goettingen.de


Shu Zhang (PhD student) studied Agricultural Sciences in China, where she also did an MSc specialized in bioinformatics. Her placement as a PhD student started in late 2018, and she is working on genome reogranziation upon aging; she is supported by a full CAAS scholarship.

E-mail: shu.zhang [at] med.uni-goettingen.de


Spiros Palikyras (PhD student) studied Biology in Greece and received his MSc degree at the University of Heidelberg. His placement as a PhD student started in 2019, and he is working on phase-separated CTCF clustering in cellular senescence; he is funded via TRR81/SFB program.

E-mail: spyridon.palikyras [at] med.uni-goettingen.de


Shu Zhang (PhD student) studied Agricultural Sciences in China, where she also did an MSc specialized in bioinformatics. Her placement as a PhD student started in late 2018, and she is working on genome reogranziation upon aging; she is supported by a full CAAS scholarship.

E-mail: shu.zhang [at] med.uni-goettingen.de


Adi Danieli (MSc student) studied Applied Biology in Bonn, and she is currently undertaking her MSc Molecular Biology thesis in our lab working on probing genome reorganization via ligation-/crosslinking-free methods in live cells.

E-mail: adi.danieli [at] stud.uni-goettingen.de


Helene Kabbech (MSc student) studied Biology in Paris, where she currently is an MSc Bioinformatics student at Paris-Diderot University; she is undertaking her MSc thesis in our lab working on a deep learning approach to analyse and integrate Hi-C data.

E-mail: helene.kabbech [at] gmail.com


Alumni:
  • Dr. Anne Zirkel (former postdoc), currently holding a managerial position in the private healthcare sector.
  • Dr. Lilija Brant (former PhD student), currently holding a consultant in the private sector.
  • Dr. Milos Nikolic (former PhD student), currently a postdoc with the Peifer lab in Cologne
  • Ms. Michaela Bozukova (former MSc student), currently a PhD student with the Tessarz lab in Cologne.

Contact

How to find us? We are currently located on the 2nd floor of the main UMG building (Room 2.E1.216).

Postal address:

AG Papantonis: Translational Epigenetics
Institute of Pathology, University Medical Center,
Georg-August University of Göttingen,
Robert-Koch-Str. 40, 37075 Göttingen, Germany
Tel.: +49 551 39 65734

Group leader

Prof. Dr. Argyris Papantonis

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