Prof. Dr. Argyris Papantonis

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  • 2023 | Journal Article
    ​ ​Decoding of translation‐regulating entities reveals heterogeneous translation deficiency patterns in cellular senescence​
    Papaspyropoulos, A.; Hazapis, O.; Altulea, A.; Polyzou, A.; Verginis, P.; Evangelou, K. & Fousteri, M. et al.​ (2023) 
    Aging Cell, art. e13893​.​ DOI: https://doi.org/10.1111/acel.13893 
    ​Details  DOI 
  • 2023 | Journal Article
    ​ ​mRNA translational specialization by RBPMS presets the competence for cardiac commitment in hESCs​
    Bartsch, D.; Kalamkar, K.; Ahuja, G.; Lackmann, J.-W.; Hescheler, J.; Weber, T. & Bazzi, H. et al.​ (2023) 
    Science Advances, 9(13) art. eade1792​.​ DOI: https://doi.org/10.1126/sciadv.ade1792 
    ​Details  DOI 
  • 2023 | Journal Article
    ​ ​Enhancer–promoter contact formation requires RNAPII and antagonizes loop extrusion​
    Zhang, S.; Übelmesser, N.; Barbieri, M. & Papantonis, A. ​ (2023) 
    Nature Genetics,.​ DOI: https://doi.org/10.1038/s41588-023-01364-4 
    ​Details  DOI 
  • 2022 | Journal Article
    ​ ​circRAB3IP modulates cell proliferation by reorganizing gene expression and mRNA processing in a paracrine manner​
    Josipovic, N.; Ebbesen, K. K; Zirkel, A.; Mackay-Danieli, A.; Dieterich, C.; Kurian, L. & Hansen, T. B et al.​ (2022) 
    RNA, art. rna.079195.122​.​ DOI: https://doi.org/10.1261/rna.079195.122 
    ​Details  DOI 
  • 2022 | Journal Article
    ​ ​Functional organization of RNA polymerase II in nuclear subcompartments​
    Rippe, K. & Papantonis, A. ​ (2022) 
    Current Opinion in Cell Biology, 74 pp. 88​-96​.​ DOI: https://doi.org/10.1016/j.ceb.2022.01.005 
    ​Details  DOI 
  • 2021 | Journal Article
    ​ ​Cohesin puts a break on distal homology hunt​
    Papantonis, A.   & Roukos, V.​ (2021) 
    Nature Cell Biology, 23(11) pp. 1112​-1114​.​ DOI: https://doi.org/10.1038/s41556-021-00791-x 
    ​Details  DOI  PMID  PMC 
  • 2021 | Journal Article | Research Paper | 
    ​ ​Overarching control of autophagy and DNA damage response by CHD6 revealed by modeling a rare human pathology​
    Kargapolova, Y.; Rehimi, R.; Kayserili, H.; Brühl, J.; Sofiadis, K.; Zirkel, A. & Palikyras, S. et al.​ (2021) 
    Nature Communications, 12(1) art. 3014​.​ DOI: https://doi.org/10.1038/s41467-021-23327-1 
    ​Details  DOI  PMID  PMC 
  • 2021 | Journal Article
    ​ ​RNA polymerase II transcription compartments: from multivalent chromatin binding to liquid droplet formation?​
    Rippe, K. & Papantonis, A. ​ (2021) 
    Nature Reviews. Molecular Cell Biology,.​ DOI: https://doi.org/10.1038/s41580-021-00401-6 
    ​Details  DOI 
  • 2021 | Journal Article
    ​ ​Isolation methodology is essential to the evaluation of the extracellular vesicle component of the senescence‐associated secretory phenotype​
    Wallis, R.; Josipovic, N.; Mizen, H.; Robles‐Tenorio, A.; Tyler, E. J.; Papantonis, A.   & Bishop, C. L.​ (2021) 
    Journal of Extracellular Vesicles, 10(4).​ DOI: https://doi.org/10.1002/jev2.12041 
    ​Details  DOI 
  • 2021 | Journal Article
    ​ ​HMGs as rheostats of chromosomal structure and cell proliferation​
    Papantonis, A. ​ (2021) 
    Trends in Genetics,.​ DOI: https://doi.org/10.1016/j.tig.2021.07.004 
    ​Details  DOI 
  • 2021 | Journal Article | Research Paper | 
    ​ ​HMGB1 coordinates SASP‐related chromatin folding and RNA homeostasis on the path to senescence​
    Sofiadis, K.; Josipovic, N.; Nikolic, M.; Kargapolova, Y.; Übelmesser, N.; Varamogianni‐Mamatsi, V. & Zirkel, A. et al.​ (2021) 
    Molecular Systems Biology, 17(6).​ DOI: https://doi.org/10.15252/msb.20209760 
    ​Details  DOI 
  • 2021 | Journal Article
    ​ ​RNA polymerase II is required for spatial chromatin reorganization following exit from mitosis​
    Zhang, S.; Übelmesser, N.; Josipovic, N.; Forte, G.; Slotman, J. A.; Chiang, M. & Gothe, H. J. et al.​ (2021) 
    Science Advances, 7(43).​ DOI: https://doi.org/10.1126/sciadv.abg8205 
    ​Details  DOI 
  • 2020 | Journal Article
    ​ ​Genome folding and refolding in differentiation and cellular senescence​
    Mizi, A.; Zhang, S. & Papantonis, A. ​ (2020) 
    Current Opinion in Cell Biology, 67 pp. 56​-63​.​ DOI: https://doi.org/10.1016/j.ceb.2020.08.002 
    ​Details  DOI 
  • 2020 | Journal Article
    ​ ​Redundant and specific roles of cohesin STAG subunits in chromatin looping and transcriptional control​
    Casa, V.; Moronta Gines, M.; Gade Gusmao, E.; Slotman, J. A.; Zirkel, A.; Josipovic, N. & Oole, E. et al.​ (2020) 
    Genome Research, 30(4) pp. 515​-527​.​ DOI: https://doi.org/10.1101/gr.253211.119 
    ​Details  DOI 
  • 2020 | Journal Article
    ​ ​Spatial genome architecture and the emergence of malignancy​
    Danieli, A. & Papantonis, A. ​ (2020) 
    Human Molecular Genetics, 29(R2) pp. R197​-R204​.​ DOI: https://doi.org/10.1093/hmg/ddaa128 
    ​Details  DOI 
  • 2020 | Journal Article
    ​ ​iHi-C 2.0: A simple approach for mapping native spatial chromatin organisation from low cell numbers​
    Mizi, A.; Gade Gusmao, E. & Papantonis, A. ​ (2020) 
    Methods, 170 pp. 33​-37​.​ DOI: https://doi.org/10.1016/j.ymeth.2019.07.003 
    ​Details  DOI 
  • 2019 | Journal Article
    ​ ​GemC1 is a critical switch for neural stem cell generation in the postnatal brain​
    Lalioti, M.; Kaplani, K.; Lokka, G.; Georgomanolis, T.; Kyrousi, C.; Dong, W. & Dunbar, A. et al.​ (2019) 
    Glia, 67(12) pp. 2360​-2373​.​ DOI: https://doi.org/10.1002/glia.23690 
    ​Details  DOI 
  • 2019 | Journal Article
    ​ ​yylncT Defines a Class of Divergently Transcribed lncRNAs and Safeguards the T-mediated Mesodermal Commitment of Human PSCs​
    Frank, S.; Ahuja, G.; Bartsch, D.; Russ, N.; Yao, W.; Kuo, J. C. Kuo, Joseph Chao-Chung & Derks, J.-P. et al.​ (2019) 
    Cell Stem Cell, 24(2) pp. 318​-327.e8​.​ DOI: https://doi.org/10.1016/j.stem.2018.11.005 
    ​Details  DOI 
  • 2019 | Journal Article
    ​ ​Technologies to study spatial genome organization: beyond 3C​
    Übelmesser, N. & Papantonis, A. ​ (2019) 
    Briefings in Functional Genomics,.​ DOI: https://doi.org/10.1093/bfgp/elz019 
    ​Details  DOI 
  • 2019 | Journal Article
    ​ ​GemC1 governs multiciliogenesis through direct interaction with and transcriptional regulation of p73​
    Lalioti, M.-E.; Arbi, M.; Loukas, I.; Kaplani, K.; Kalogeropoulou, A.; Lokka, G. & Kyrousi, C. et al.​ (2019) 
    Journal of Cell Science, 132(11) pp. jcs228684​.​ DOI: https://doi.org/10.1242/jcs.228684 
    ​Details  DOI 
  • 2019 | Journal Article
    ​ ​Loss of genomic integrity induced by lysosphingolipid imbalance drives ageing in the heart​
    Ahuja, G.; Bartsch, D.; Yao, W.; Geissen, S.; Frank, S.; Aguirre, A. & Russ, N. et al.​ (2019) 
    EMBO reports, 20(4).​ DOI: https://doi.org/10.15252/embr.201847407 
    ​Details  DOI 
  • 2019 | Journal Article
    ​ ​Spatial Chromosome Folding and Active Transcription Drive DNA Fragility and Formation of Oncogenic MLL Translocations​
    Gothe, H. J.; Bouwman, B. A. M.; Gusmao, E. G.; Piccinno, R.; Petrosino, G.; Sayols, S. & Drechsel, O. et al.​ (2019) 
    Molecular Cell, 75(2) pp. 267​-283.e12​.​ DOI: https://doi.org/10.1016/j.molcel.2019.05.015 
    ​Details  DOI 
  • 2019 | Journal Article | 
    ​ ​Modes of phase separation affecting chromatin regulation​
    Palikyras, S. & Papantonis, A. ​ (2019) 
    Open Biology, 9(10) pp. 190167​.​ DOI: https://doi.org/10.1098/rsob.190167 
    ​Details  DOI 
  • 2019 | Journal Article | 
    ​ ​ARID1A facilitates KRAS signaling-regulated enhancer activity in an AP1-dependent manner in colorectal cancer cells​
    Sen, M. ; Wang, X.; Hamdan, F. H. ; Rapp, J.; Eggert, J.; Kosinsky, R. L.   & Wegwitz, F.  et al.​ (2019) 
    Clinical Epigenetics, 11(1).​ DOI: https://doi.org/10.1186/s13148-019-0690-5 
    ​Details  DOI 
  • 2018 | Journal Article
    ​ ​Shaping epigenetic memory via genomic bookmarking​
    Michieletto, D.; Chiang, M.; Colì, D.; Papantonis, A. ; Orlandini, E.; Cook, P. R. & Marenduzzo, D.​ (2018) 
    Nucleic Acids Research, 46(1) pp. 83​-93​.​ DOI: https://doi.org/10.1093/nar/gkx1200 
    ​Details  DOI  PMID  PMC  arXiv 
  • 2018 | Journal Article
    ​ ​Forces driving the three-dimensional folding of eukaryotic genomes​
    Rada-Iglesias, A.; Grosveld, F. G. & Papantonis, A. ​ (2018) 
    Molecular Systems Biology, 14(6) art. e8214​.​ DOI: https://doi.org/10.15252/msb.20188214 
    ​Details  DOI  PMID  PMC 
  • 2017 | Journal Article
    ​ ​Recent Zika Virus Isolates Induce Premature Differentiation of Neural Progenitors in Human Brain Organoids​
    Gabriel, E.; Ramani, A.; Karow, U.; Gottardo, M.; Natarajan, K.; Gooi, L. M. & Goranci-Buzhala, G. et al.​ (2017) 
    Cell Stem Cell, 20(3) pp. 397​-406.e5​.​ DOI: https://doi.org/10.1016/j.stem.2016.12.005 
    ​Details  DOI  PMID  PMC 
  • 2017 | Journal Article
    ​ ​GARLIC: a bioinformatic toolkit for aetiologically connecting diseases and cell type-specific regulatory maps​
    Nikolic, M.; Papantonis, A.   & Rada-Iglesias, A.​ (2017) 
    Human Molecular Genetics, 26(4) pp. 742​-752​.​ DOI: https://doi.org/10.1093/hmg/ddw423 
    ​Details  DOI  PMID  PMC 
  • 2017 | Journal Article
    ​ ​Senescence-associated DNA methylation is stochastically acquired in subpopulations of mesenchymal stem cells​
    Franzen, J.; Zirkel, A.; Blake, J.; Rath, B.; Benes, V.; Papantonis, A.   & Wagner, W.​ (2017) 
    Aging Cell, 16(1) pp. 183​-191​.​ DOI: https://doi.org/10.1111/acel.12544 
    ​Details  DOI  PMID  PMC 
  • 2016 | Journal Article
    ​ ​Exploiting native forces to capture chromosome conformation in mammalian cell nuclei​
    Brant, L.; Georgomanolis, T.; Nikolic, M.; Brackley, C. A.; Kolovos, P.; van Ijcken, W. & Grosveld, F. G. et al.​ (2016) 
    Molecular Systems Biology, 12(12) pp. 891​.​ DOI: https://doi.org/10.15252/msb.20167311 
    ​Details  DOI  PMID  PMC 
  • 2016 | Journal Article
    ​ ​Binding of nuclear factor κB to noncanonical consensus sites reveals its multimodal role during the early inflammatory response​
    Kolovos, P.; Georgomanolis, T.; Koeferle, A.; Larkin, J. D.; Brant, L.; Nikolicć, M. & Gusmao, E. G. et al.​ (2016) 
    Genome Research, 26(11) pp. 1478​-1489​.​ DOI: https://doi.org/10.1101/gr.210005.116 
    ​Details  DOI  PMID  PMC 
  • 2016 | Journal Article
    ​ ​Isolation of the protein and RNA content of active sites of transcription from mammalian cells​
    Melnik, S.; Caudron-Herger, M.; Brant, L.; Carr, I. M.; Rippe, K.; Cook, P. R. & Papantonis, A. ​ (2016) 
    Nature Protocols, 11(3) pp. 553​-565​.​ DOI: https://doi.org/10.1038/nprot.2016.032 
    ​Details  DOI  PMID  PMC 
  • 2016 | Journal Article
    ​ ​Cutting a Long Intron Short: Recursive Splicing and Its Implications​
    Georgomanolis, T.; Sofiadis, K. & Papantonis, A. ​ (2016) 
    Frontiers in Physiology, 7 pp. 598​.​ DOI: https://doi.org/10.3389/fphys.2016.00598 
    ​Details  DOI  PMID  PMC 
  • 2015 | Journal Article
    ​ ​Dissecting the nascent human transcriptome by analysing the RNA content of transcription factories​
    Caudron-Herger, M.; Cook, P. R.; Rippe, K. & Papantonis, A. ​ (2015) 
    Nucleic Acids Research, 43(14) pp. e95​-e95​.​ DOI: https://doi.org/10.1093/nar/gkv390 
    ​Details  DOI  PMID  PMC 
  • 2015 | Journal Article
    ​ ​Exon Skipping Is Correlated with Exon Circularization​
    Kelly, S.; Greenman, C.; Cook, P. R. & Papantonis, A. ​ (2015) 
    Journal of Molecular Biology, 427(15) pp. 2414​-2417​.​ DOI: https://doi.org/10.1016/j.jmb.2015.02.018 
    ​Details  DOI  PMID  PMC 
  • 2015 | Journal Article
    ​ ​Splicing of many human genes involves sites embedded within introns​
    Kelly, S.; Georgomanolis, T.; Zirkel, A.; Diermeier, S.; O'Reilly, D.; Murphy, S. & Längst, G. et al.​ (2015) 
    Nucleic Acids Research, 43(9) pp. 4721​-4732​.​ DOI: https://doi.org/10.1093/nar/gkv386 
    ​Details  DOI  PMID  PMC 
  • 2015 | Journal Article
    ​ ​Chorion genes: a landscape of their evolution, structure, and regulation​
    Papantonis, A. ; Swevers, L. & Iatrou, K.​ (2015) 
    Annual Review of Entomology, 60(1) pp. 177​-194​.​ DOI: https://doi.org/10.1146/annurev-ento-010814-020810 
    ​Details  DOI  PMID  PMC 
  • 2014 | Journal Article
    ​ ​TNFα signalling primes chromatin for NF-κB binding and induces rapid and widespread nucleosome repositioning​
    Diermeier, S.; Kolovos, P.; Heizinger, L.; Schwartz, U.; Georgomanolis, T.; Zirkel, A. & Wedemann, G. et al.​ (2014) 
    Genome Biology, 15(12) pp. 536​.​ DOI: https://doi.org/10.1186/s13059-014-0536-6 
    ​Details  DOI  PMID  PMC 
  • 2014 | Journal Article
    ​ ​Transcription as a force partitioning the eukaryotic genome​
    Zirkel, A. & Papantonis, A. ​ (2014) 
    Biological Chemistry, 395(11) pp. 1301​-1305​.​ DOI: https://doi.org/10.1515/hsz-2014-0196 
    ​Details  DOI  PMID  PMC 
  • 2013 | Journal Article
    ​ ​Nonspecific bridging-induced attraction drives clustering of DNA-binding proteins and genome organization​
    Brackley, C. A.; Taylor, S.; Papantonis, A. ; Cook, P. R. & Marenduzzo, D.​ (2013) 
    Proceedings of the National Academy of Sciences of the United States of America, 110(38) pp. E3605​-E3611​.​ DOI: https://doi.org/10.1073/pnas.1302950110 
    ​Details  DOI  PMID  PMC 
  • 2013 | Journal Article
    ​ ​Promoter type influences transcriptional topography by targeting genes to distinct nucleoplasmic sites​
    Larkin, J. D.; Papantonis, A.   & Cook, P. R.​ (2013) 
    Journal of Cell Science, 126(9) pp. 2052​-2059​.​ DOI: https://doi.org/10.1242/jcs.123653 
    ​Details  DOI  PMID  PMC 
  • 2013 | Journal Article
    ​ ​Space exploration by the promoter of a long human gene during one transcription cycle​
    Larkin, J. D.; Papantonis, A. ; Cook, P. R. & Marenduzzo, D.​ (2013) 
    Nucleic Acids Research, 41(4) pp. 2216​-2227​.​ DOI: https://doi.org/10.1093/nar/gks1441 
    ​Details  DOI  PMID  PMC 
  • 2012 | Journal Article
    ​ ​TNFα signals through specialized factories where responsive coding and miRNA genes are transcribed​
    Papantonis, A. ; Kohro, T.; Baboo, S.; Larkin, J. D.; Deng, B.; Short, P. & Tsutsumi, S. et al.​ (2012) 
    The EMBO Journal, 31(23) pp. 4404​-4414​.​ DOI: https://doi.org/10.1038/emboj.2012.288 
    ​Details  DOI  PMID  PMC 
  • 2012 | Journal Article
    ​ ​Dynamic reconfiguration of long human genes during one transcription cycle​
    Larkin, J. D.; Cook, P. R. & Papantonis, A. ​ (2012) 
    Molecular and Cellular Biology, 32(14) pp. 2738​-2747​.​ DOI: https://doi.org/10.1128/MCB.00179-12 
    ​Details  DOI  PMID  PMC 
  • 2012 | Journal Article
    ​ ​Enhancers and silencers: an integrated and simple model for their function​
    Kolovos, P.; Knoch, T. A.; Grosveld, F. G.; Cook, P. R. & Papantonis, A. ​ (2012) 
    Epigenetics & Chromatin, 5(1) pp. 1​.​ DOI: https://doi.org/10.1186/1756-8935-5-1 
    ​Details  DOI  PMID  PMC 
  • 2011 | Journal Article
    ​ ​The proteomes of transcription factories containing RNA polymerases I, II or III​
    Melnik, S.; Deng, B.; Papantonis, A. ; Baboo, S.; Carr, I. M. & Cook, P. R.​ (2011) 
    Nature Methods, 8(11) pp. 963​-968​.​ DOI: https://doi.org/10.1038/nmeth.1705 
    ​Details  DOI  PMID  PMC 
  • 2010 | Journal Article
    ​ ​Active RNA polymerases: mobile or immobile molecular machines?​
    Papantonis, A. ; Larkin, J. D.; Wada, Y.; Ohta, Y.; Ihara, S.; Kodama, T. & Cook, P. R.​ (2010) 
    PLoS Biology, 8(7) art. e1000419​.​ DOI: https://doi.org/10.1371/journal.pbio.1000419 
    ​Details  DOI  PMID  PMC 
  • 2010 | Journal Article
    ​ ​Genome architecture and the role of transcription​
    Papantonis, A.   & Cook, P. R.​ (2010) 
    Current Opinion in Cell Biology, 22(3) pp. 271​-276​.​ DOI: https://doi.org/10.1016/j.ceb.2010.03.004 
    ​Details  DOI  PMID  PMC 
  • 2010 | Journal Article
    ​ ​Silkmoth chorion gene regulation revisited: promoter architecture as a key player​
    Lecanidou, R. & Papantonis, A. ​ (2010) 
    Insect Molecular Biology, 19(2) pp. 141​-151​.​ DOI: https://doi.org/10.1111/j.1365-2583.2009.00969.x 
    ​Details  DOI  PMID  PMC 
  • 2010 | Journal Article
    ​ ​Modeling bidirectional transcription using silkmoth chorion gene promoters​
    Lecanidou, R. & Papantonis, A. ​ (2010) 
    Organogenesis, 6(1) pp. 54​-58​.​ DOI: https://doi.org/10.4161/org.6.1.10696 
    ​Details  DOI  PMID  PMC 
  • 2009 | Journal Article
    ​ ​A wave of nascent transcription on activated human genes​
    Wada, Y.; Ohta, Y.; Xu, M.; Tsutsumi, S.; Minami, T.; Inoue, K. & Komura, D. et al.​ (2009) 
    Proceedings of the National Academy of Sciences of the United States of America, 106(43) pp. 18357​-18361​.​ DOI: https://doi.org/10.1073/pnas.0902573106 
    ​Details  DOI  PMID  PMC 
  • 2009 | Journal Article
    ​ ​A modified chromatin-immunoprecipitation protocol for silkmoth ovarian follicular cells reveals C/EBP and GATA binding modes on an early chorion gene promoter​
    Papantonis, A.   & Lecanidou, R.​ (2009) 
    Molecular Biology Reports, 36(4) pp. 733​-736​.​ DOI: https://doi.org/10.1007/s11033-008-9236-1 
    ​Details  DOI  PMID  PMC 
  • 2008 | Journal Article
    ​ ​CHD1 assumes a central role during follicle development​
    Papantonis, A. ; Tsatsarounos, S.; Vanden Broeck, J. & Lecanidou, R.​ (2008) 
    Journal of Molecular Biology, 383(5) pp. 957​-969​.​ DOI: https://doi.org/10.1016/j.jmb.2008.09.011 
    ​Details  DOI  PMID  PMC 
  • 2008 | Journal Article
    ​ ​Architectural factor HMGA induces promoter bending and recruits C/EBP and GATA during silkmoth chorion gene regulation​
    Papantonis, A. ; Vanden Broeck, J. & Lecanidou, R.​ (2008) 
    Biochemical Journal, 416(1) pp. 85​-97​.​ DOI: https://doi.org/10.1042/BJ20081012 
    ​Details  DOI  PMID  PMC 
  • 2008 | Journal Article
    ​ ​Chorion gene activation and repression is dependent on BmC/EBP expression and binding to cognate cis-elements​
    Papantonis, A. ; Sourmeli, S. & Lecanidou, R.​ (2008) 
    Biochemical and Biophysical Research Communications, 369(3) pp. 905​-909​.​ DOI: https://doi.org/10.1016/j.bbrc.2008.02.113 
    ​Details  DOI  PMID  PMC 
  • 2005 | Journal Article
    ​ ​BmCbZ, an insect-specific factor featuring a composite DNA-binding domain, interacts with BmC/EBPgamma​
    Sourmeli, S.; Papantonis, A.   & Lecanidou, R.​ (2005) 
    Biochemical and Biophysical Research Communications, 338(4) pp. 1957​-1965​.​ DOI: https://doi.org/10.1016/j.bbrc.2005.10.174 
    ​Details  DOI  PMID  PMC 
  • 2005 | Journal Article
    ​ ​A novel role for the Bombyx Slbo homologue, BmC/EBP, in insect choriogenesis​
    Sourmeli, S.; Papantonis, A.   & Lecanidou, R.​ (2005) 
    Biochemical and Biophysical Research Communications, 337(2) pp. 713​-719​.​ DOI: https://doi.org/10.1016/j.bbrc.2005.09.103 
    ​Details  DOI  PMID  PMC 

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