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Items: 37


Forces driving the three-dimensional folding of eukaryotic genomes.

Rada-Iglesias A, Grosveld FG, Papantonis A.

Mol Syst Biol. 2018 Jun 1;14(6):e8214. doi: 10.15252/msb.20188214. Review.


HMGB2 Loss upon Senescence Entry Disrupts Genomic Organization and Induces CTCF Clustering across Cell Types.

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.

Mol Cell. 2018 May 17;70(4):730-744.e6. doi: 10.1016/j.molcel.2018.03.030. Epub 2018 Apr 26.


Detecting Circular RNAs by RNA Fluorescence In Situ Hybridization.

Zirkel A, Papantonis A.

Methods Mol Biol. 2018;1724:69-75. doi: 10.1007/978-1-4939-7562-4_6.


Shaping epigenetic memory via genomic bookmarking.

Michieletto D, Chiang M, Colì D, Papantonis A, Orlandini E, Cook PR, Marenduzzo D.

Nucleic Acids Res. 2018 Jan 9;46(1):83-93. doi: 10.1093/nar/gkx1200.


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 LM, Goranci-Buzhala G, Krut O, Peters F, Nikolic M, Kuivanen S, Korhonen E, Smura T, Vapalahti O, Papantonis A, Schmidt-Chanasit J, Riparbelli M, Callaini G, Krönke M, Utermöhlen O, Gopalakrishnan J.

Cell Stem Cell. 2017 Mar 2;20(3):397-406.e5. doi: 10.1016/j.stem.2016.12.005. Epub 2017 Jan 26.


GARLIC: a bioinformatic toolkit for aetiologically connecting diseases and cell type-specific regulatory maps.

Nikolic M, Papantonis A, Rada-Iglesias A.

Hum Mol Genet. 2017 Feb 15;26(4):742-752. doi: 10.1093/hmg/ddw423.


Cutting a Long Intron Short: Recursive Splicing and Its Implications.

Georgomanolis T, Sofiadis K, Papantonis A.

Front Physiol. 2016 Nov 29;7:598. eCollection 2016.


Exploiting native forces to capture chromosome conformation in mammalian cell nuclei.

Brant L, Georgomanolis T, Nikolic M, Brackley CA, Kolovos P, van Ijcken W, Grosveld FG, Marenduzzo D, Papantonis A.

Mol Syst Biol. 2016 Dec 9;12(12):891. doi: 10.15252/msb.20167311.


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 JD, Brant L, Nikolicć M, Gusmao EG, Zirkel A, Knoch TA, van Ijcken WF, Cook PR, Costa IG, Grosveld FG, Papantonis A.

Genome Res. 2016 Nov;26(11):1478-1489. Epub 2016 Sep 15.


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.

Aging Cell. 2017 Feb;16(1):183-191. doi: 10.1111/acel.12544. Epub 2016 Oct 26.


Isolation of the protein and RNA content of active sites of transcription from mammalian cells.

Melnik S, Caudron-Herger M, Brant L, Carr IM, Rippe K, Cook PR, Papantonis A.

Nat Protoc. 2016 Mar;11(3):553-65. doi: 10.1038/nprot.2016.032. Epub 2016 Feb 25.


Dissecting the nascent human transcriptome by analysing the RNA content of transcription factories.

Caudron-Herger M, Cook PR, Rippe K, Papantonis A.

Nucleic Acids Res. 2015 Aug 18;43(14):e95. doi: 10.1093/nar/gkv390. Epub 2015 Apr 20.


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, Cook PR, Papantonis A.

Nucleic Acids Res. 2015 May 19;43(9):4721-32. doi: 10.1093/nar/gkv386. Epub 2015 Apr 20.


Exon Skipping Is Correlated with Exon Circularization.

Kelly S, Greenman C, Cook PR, Papantonis A.

J Mol Biol. 2015 Jul 31;427(15):2414-2417. doi: 10.1016/j.jmb.2015.02.018. Epub 2015 Feb 26.


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, Grosveld F, Knoch TA, Merkl R, Cook PR, Längst G, Papantonis A.

Genome Biol. 2014 Dec 3;15(12):536. doi: 10.1186/s13059-014-0536-6.


Chorion genes: a landscape of their evolution, structure, and regulation.

Papantonis A, Swevers L, Iatrou K.

Annu Rev Entomol. 2015 Jan 7;60:177-94. doi: 10.1146/annurev-ento-010814-020810. Epub 2014 Oct 17. Review.


Transcription as a force partitioning the eukaryotic genome.

Zirkel A, Papantonis A.

Biol Chem. 2014 Nov 1;395(11):1301-5. doi: 10.1515/hsz-2014-0196. Review.


Nonspecific bridging-induced attraction drives clustering of DNA-binding proteins and genome organization.

Brackley CA, Taylor S, Papantonis A, Cook PR, Marenduzzo D.

Proc Natl Acad Sci U S A. 2013 Sep 17;110(38):E3605-11. doi: 10.1073/pnas.1302950110. Epub 2013 Sep 3.


Transcription factories: genome organization and gene regulation.

Papantonis A, Cook PR.

Chem Rev. 2013 Nov 13;113(11):8683-705. doi: 10.1021/cr300513p. Epub 2013 Apr 18. Review. No abstract available.


Promoter type influences transcriptional topography by targeting genes to distinct nucleoplasmic sites.

Larkin JD, Papantonis A, Cook PR.

J Cell Sci. 2013 May 1;126(Pt 9):2052-9. doi: 10.1242/jcs.123653. Epub 2013 Feb 26.


Space exploration by the promoter of a long human gene during one transcription cycle.

Larkin JD, Papantonis A, Cook PR, Marenduzzo D.

Nucleic Acids Res. 2013 Feb 1;41(4):2216-27. doi: 10.1093/nar/gks1441. Epub 2013 Jan 8.


TNFα signals through specialized factories where responsive coding and miRNA genes are transcribed.

Papantonis A, Kohro T, Baboo S, Larkin JD, Deng B, Short P, Tsutsumi S, Taylor S, Kanki Y, Kobayashi M, Li G, Poh HM, Ruan X, Aburatani H, Ruan Y, Kodama T, Wada Y, Cook PR.

EMBO J. 2012 Nov 28;31(23):4404-14. doi: 10.1038/emboj.2012.288. Epub 2012 Oct 26.


Dynamic reconfiguration of long human genes during one transcription cycle.

Larkin JD, Cook PR, Papantonis A.

Mol Cell Biol. 2012 Jul;32(14):2738-47. doi: 10.1128/MCB.00179-12. Epub 2012 May 14.


Enhancers and silencers: an integrated and simple model for their function.

Kolovos P, Knoch TA, Grosveld FG, Cook PR, Papantonis A.

Epigenetics Chromatin. 2012 Jan 9;5(1):1. doi: 10.1186/1756-8935-5-1.


The proteomes of transcription factories containing RNA polymerases I, II or III.

Melnik S, Deng B, Papantonis A, Baboo S, Carr IM, Cook PR.

Nat Methods. 2011 Sep 25;8(11):963-8. doi: 10.1038/nmeth.1705.


Fixing the model for transcription: the DNA moves, not the polymerase.

Papantonis A, Cook PR.

Transcription. 2011 Jan-Feb;2(1):41-4. doi: 10.4161/trns.2.1.14275. Review.


Active RNA polymerases: mobile or immobile molecular machines?

Papantonis A, Larkin JD, Wada Y, Ohta Y, Ihara S, Kodama T, Cook PR.

PLoS Biol. 2010 Jul 13;8(7):e1000419. doi: 10.1371/journal.pbio.1000419.


Modeling bidirectional transcription using silkmoth chorion gene promoters.

Lecanidou R, Papantonis A.

Organogenesis. 2010 Jan-Mar;6(1):54-8. Review.


Genome architecture and the role of transcription.

Papantonis A, Cook PR.

Curr Opin Cell Biol. 2010 Jun;22(3):271-6. doi: 10.1016/ Epub 2010 Mar 29.


Silkmoth chorion gene regulation revisited: promoter architecture as a key player.

Lecanidou R, Papantonis A.

Insect Mol Biol. 2010 Apr;19(2):141-51. doi: 10.1111/j.1365-2583.2009.00969.x. Epub 2009 Dec 7. Review.


A wave of nascent transcription on activated human genes.

Wada Y, Ohta Y, Xu M, Tsutsumi S, Minami T, Inoue K, Komura D, Kitakami J, Oshida N, Papantonis A, Izumi A, Kobayashi M, Meguro H, Kanki Y, Mimura I, Yamamoto K, Mataki C, Hamakubo T, Shirahige K, Aburatani H, Kimura H, Kodama T, Cook PR, Ihara S.

Proc Natl Acad Sci U S A. 2009 Oct 27;106(43):18357-61. doi: 10.1073/pnas.0902573106. Epub 2009 Oct 13.


CHD1 assumes a central role during follicle development.

Papantonis A, Tsatsarounos S, Vanden Broeck J, Lecanidou R.

J Mol Biol. 2008 Nov 28;383(5):957-69. doi: 10.1016/j.jmb.2008.09.011. Epub 2008 Sep 16.


Architectural factor HMGA induces promoter bending and recruits C/EBP and GATA during silkmoth chorion gene regulation.

Papantonis A, Vanden Broeck J, Lecanidou R.

Biochem J. 2008 Nov 15;416(1):85-97. doi: 10.1042/BJ20081012.


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.

Mol Biol Rep. 2009 Apr;36(4):733-6. doi: 10.1007/s11033-008-9236-1. Epub 2008 Mar 27.


Chorion gene activation and repression is dependent on BmC/EBP expression and binding to cognate cis-elements.

Papantonis A, Sourmeli S, Lecanidou R.

Biochem Biophys Res Commun. 2008 May 9;369(3):905-9. doi: 10.1016/j.bbrc.2008.02.113. Epub 2008 Mar 4.


BmCbZ, an insect-specific factor featuring a composite DNA-binding domain, interacts with BmC/EBPgamma.

Sourmeli S, Papantonis A, Lecanidou R.

Biochem Biophys Res Commun. 2005 Dec 30;338(4):1957-65. Epub 2005 Nov 10.


A novel role for the Bombyx Slbo homologue, BmC/EBP, in insect choriogenesis.

Sourmeli S, Papantonis A, Lecanidou R.

Biochem Biophys Res Commun. 2005 Nov 18;337(2):713-9. Epub 2005 Sep 26.


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