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Guided nuclear exploration increases CTCF target search efficiency.

Hansen AS, Amitai A, Cattoglio C, Tjian R, Darzacq X.

Nat Chem Biol. 2019 Dec 2. doi: 10.1038/s41589-019-0422-3. [Epub ahead of print]


Evaluating phase separation in live cells: diagnosis, caveats, and functional consequences.

McSwiggen DT, Mir M, Darzacq X, Tjian R.

Genes Dev. 2019 Dec 1;33(23-24):1619-1634. doi: 10.1101/gad.331520.119. Epub 2019 Oct 8. Review.


A new class of disordered elements controls DNA replication through initiator self-assembly.

Parker MW, Bell M, Mir M, Kao JA, Darzacq X, Botchan MR, Berger JM.

Elife. 2019 Sep 27;8. pii: e48562. doi: 10.7554/eLife.48562.


Distinct Classes of Chromatin Loops Revealed by Deletion of an RNA-Binding Region in CTCF.

Hansen AS, Hsieh TS, Cattoglio C, Pustova I, Saldaña-Meyer R, Reinberg D, Darzacq X, Tjian R.

Mol Cell. 2019 Nov 7;76(3):395-411.e13. doi: 10.1016/j.molcel.2019.07.039. Epub 2019 Sep 12.


Determining cellular CTCF and cohesin abundances to constrain 3D genome models.

Cattoglio C, Pustova I, Walther N, Ho JJ, Hantsche-Grininger M, Inouye CJ, Hossain MJ, Dailey GM, Ellenberg J, Darzacq X, Tjian R, Hansen AS.

Elife. 2019 Jun 17;8. pii: e40164. doi: 10.7554/eLife.40164.


Evidence for DNA-mediated nuclear compartmentalization distinct from phase separation.

McSwiggen DT, Hansen AS, Teves SS, Marie-Nelly H, Hao Y, Heckert AB, Umemoto KK, Dugast-Darzacq C, Tjian R, Darzacq X.

Elife. 2019 May 7;8. pii: e47098. doi: 10.7554/eLife.47098.


Evidence for an Integrated Gene Repression Mechanism Based on mRNA Isoform Toggling in Human Cells.

Hollerer I, Barker JC, Jorgensen V, Tresenrider A, Dugast-Darzacq C, Chan LY, Darzacq X, Tjian R, Ünal E, Brar GA.

G3 (Bethesda). 2019 Apr 9;9(4):1045-1053. doi: 10.1534/g3.118.200802.


CTCF sites display cell cycle-dependent dynamics in factor binding and nucleosome positioning.

Oomen ME, Hansen AS, Liu Y, Darzacq X, Dekker J.

Genome Res. 2019 Feb;29(2):236-249. doi: 10.1101/gr.241547.118. Epub 2019 Jan 17.


Dynamic multifactor hubs interact transiently with sites of active transcription in Drosophila embryos.

Mir M, Stadler MR, Ortiz SA, Hannon CE, Harrison MM, Darzacq X, Eisen MB.

Elife. 2018 Dec 27;7. pii: e40497. doi: 10.7554/eLife.40497.


[Chromatin mobility upon DNA damage: a multi-scale story].

Miné-Hattab J, Darzacq X.

Med Sci (Paris). 2018 Oct;34(10):778-781. doi: 10.1051/medsci/2018214. Epub 2018 Nov 19. French. No abstract available.


RNA polymerase II clustering through carboxy-terminal domain phase separation.

Boehning M, Dugast-Darzacq C, Rankovic M, Hansen AS, Yu T, Marie-Nelly H, McSwiggen DT, Kokic G, Dailey GM, Cramer P, Darzacq X, Zweckstetter M.

Nat Struct Mol Biol. 2018 Sep;25(9):833-840. doi: 10.1038/s41594-018-0112-y. Epub 2018 Aug 20.


Protein motion in the nucleus: from anomalous diffusion to weak interactions.

Woringer M, Darzacq X.

Biochem Soc Trans. 2018 Aug 20;46(4):945-956. doi: 10.1042/BST20170310. Epub 2018 Jul 31. Review.


Single Molecule Imaging in Live Embryos Using Lattice Light-Sheet Microscopy.

Mir M, Reimer A, Stadler M, Tangara A, Hansen AS, Hockemeyer D, Eisen MB, Garcia H, Darzacq X.

Methods Mol Biol. 2018;1814:541-559. doi: 10.1007/978-1-4939-8591-3_32.


A stable mode of bookmarking by TBP recruits RNA polymerase II to mitotic chromosomes.

Teves SS, An L, Bhargava-Shah A, Xie L, Darzacq X, Tjian R.

Elife. 2018 Jun 25;7. pii: e35621. doi: 10.7554/eLife.35621.


Imaging dynamic and selective low-complexity domain interactions that control gene transcription.

Chong S, Dugast-Darzacq C, Liu Z, Dong P, Dailey GM, Cattoglio C, Heckert A, Banala S, Lavis L, Darzacq X, Tjian R.

Science. 2018 Jul 27;361(6400). pii: eaar2555. doi: 10.1126/science.aar2555. Epub 2018 Jun 21.


Selective Activation of Alternative MYC Core Promoters by Wnt-Responsive Enhancers.

Bardales JA, Wieser E, Kawaji H, Murakawa Y, Darzacq X.

Genes (Basel). 2018 May 23;9(6). pii: E270. doi: 10.3390/genes9060270.


Phase-separation mechanism for C-terminal hyperphosphorylation of RNA polymerase II.

Lu H, Yu D, Hansen AS, Ganguly S, Liu R, Heckert A, Darzacq X, Zhou Q.

Nature. 2018 Jun;558(7709):318-323. doi: 10.1038/s41586-018-0174-3. Epub 2018 May 30.


Robust model-based analysis of single-particle tracking experiments with Spot-On.

Hansen AS, Woringer M, Grimm JB, Lavis LD, Tjian R, Darzacq X.

Elife. 2018 Jan 4;7. pii: e33125. doi: 10.7554/eLife.33125.


Recent evidence that TADs and chromatin loops are dynamic structures.

Hansen AS, Cattoglio C, Darzacq X, Tjian R.

Nucleus. 2018 Jan 1;9(1):20-32. doi: 10.1080/19491034.2017.1389365. Epub 2017 Dec 14. Review.


A dynamic interplay of enhancer elements regulates Klf4 expression in naïve pluripotency.

Xie L, Torigoe SE, Xiao J, Mai DH, Li L, Davis FP, Dong P, Marie-Nelly H, Grimm J, Lavis L, Darzacq X, Cattoglio C, Liu Z, Tjian R.

Genes Dev. 2017 Sep 1;31(17):1795-1808. doi: 10.1101/gad.303321.117.


Dense Bicoid hubs accentuate binding along the morphogen gradient.

Mir M, Reimer A, Haines JE, Li XY, Stadler M, Garcia H, Eisen MB, Darzacq X.

Genes Dev. 2017 Sep 1;31(17):1784-1794. doi: 10.1101/gad.305078.117.


Mutations in the promoter of the telomerase gene TERT contribute to tumorigenesis by a two-step mechanism.

Chiba K, Lorbeer FK, Shain AH, McSwiggen DT, Schruf E, Oh A, Ryu J, Darzacq X, Bastian BC, Hockemeyer D.

Science. 2017 Sep 29;357(6358):1416-1420. doi: 10.1126/science.aao0535. Epub 2017 Aug 17.


Switch-like Arp2/3 activation upon WASP and WIP recruitment to an apparent threshold level by multivalent linker proteins in vivo.

Sun Y, Leong NT, Jiang T, Tangara A, Darzacq X, Drubin DG.

Elife. 2017 Aug 16;6. pii: e29140. doi: 10.7554/eLife.29140.


Multi-scale tracking reveals scale-dependent chromatin dynamics after DNA damage.

Miné-Hattab J, Recamier V, Izeddin I, Rothstein R, Darzacq X.

Mol Biol Cell. 2017 Aug 9. pii: mbc.E17-05-0317. doi: 10.1091/mbc.E17-05-0317. [Epub ahead of print]


Faster and less phototoxic 3D fluorescence microscopy using a versatile compressed sensing scheme.

Woringer M, Darzacq X, Zimmer C, Mir M.

Opt Express. 2017 Jun 12;25(12):13668-13683. doi: 10.1364/OE.25.013668.


Phase separation drives heterochromatin domain formation.

Strom AR, Emelyanov AV, Mir M, Fyodorov DV, Darzacq X, Karpen GH.

Nature. 2017 Jul 13;547(7662):241-245. doi: 10.1038/nature22989. Epub 2017 Jun 21.


Covalent Protein Labeling and Improved Single-Molecule Optical Properties of Aqueous CdSe/CdS Quantum Dots.

Wichner SM, Mann VR, Powers AS, Segal MA, Mir M, Bandaria JN, DeWitt MA, Darzacq X, Yildiz A, Cohen BE.

ACS Nano. 2017 Jul 25;11(7):6773-6781. doi: 10.1021/acsnano.7b01470. Epub 2017 Jun 21.


CTCF and cohesin regulate chromatin loop stability with distinct dynamics.

Hansen AS, Pustova I, Cattoglio C, Tjian R, Darzacq X.

Elife. 2017 May 3;6. pii: e25776. doi: 10.7554/eLife.25776.


Live cell imaging of low- and non-repetitive chromosome loci using CRISPR-Cas9.

Qin P, Parlak M, Kuscu C, Bandaria J, Mir M, Szlachta K, Singh R, Darzacq X, Yildiz A, Adli M.

Nat Commun. 2017 Mar 14;8:14725. doi: 10.1038/ncomms14725.


A dynamic mode of mitotic bookmarking by transcription factors.

Teves SS, An L, Hansen AS, Xie L, Darzacq X, Tjian R.

Elife. 2016 Nov 19;5. pii: e22280. doi: 10.7554/eLife.22280.


A single-molecule view of transcription reveals convoys of RNA polymerases and multi-scale bursting.

Tantale K, Mueller F, Kozulic-Pirher A, Lesne A, Victor JM, Robert MC, Capozi S, Chouaib R, Bäcker V, Mateos-Langerak J, Darzacq X, Zimmer C, Basyuk E, Bertrand E.

Nat Commun. 2016 Jul 27;7:12248. doi: 10.1038/ncomms12248.


Multifocus microscopy with precise color multi-phase diffractive optics applied in functional neuronal imaging.

Abrahamsson S, Ilic R, Wisniewski J, Mehl B, Yu L, Chen L, Davanco M, Oudjedi L, Fiche JB, Hajj B, Jin X, Pulupa J, Cho C, Mir M, El Beheiry M, Darzacq X, Nollmann M, Dahan M, Wu C, Lionnet T, Liddle JA, Bargmann CI.

Biomed Opt Express. 2016 Feb 16;7(3):855-69. doi: 10.1364/BOE.7.000855. eCollection 2016 Mar 1.


Imaging Transcription: Past, Present, and Future.

Coleman RA, Liu Z, Darzacq X, Tjian R, Singer RH, Lionnet T.

Cold Spring Harb Symp Quant Biol. 2015;80:1-8. doi: 10.1101/sqb.2015.80.027201. Epub 2016 Jan 13. Review.


Master regulators in primary skin fibroblast fate reprogramming in a human ex vivo model of chronic wounds.

Noizet M, Lagoutte E, Gratigny M, Bouschbacher M, Lazareth I, Roest Crollius H, Darzacq X, Dugast-Darzacq C.

Wound Repair Regen. 2016 Mar;24(2):247-62. doi: 10.1111/wrr.12392. Epub 2016 Jan 28.


Probing the target search of DNA-binding proteins in mammalian cells using TetR as model searcher.

Normanno D, Boudarène L, Dugast-Darzacq C, Chen J, Richter C, Proux F, Bénichou O, Voituriez R, Darzacq X, Dahan M.

Nat Commun. 2015 Jul 7;6:7357. doi: 10.1038/ncomms8357.


Role of the DHH1 gene in the regulation of monocarboxylic acids transporters expression in Saccharomyces cerevisiae.

Mota S, Vieira N, Barbosa S, Delaveau T, Torchet C, Le Saux A, Garcia M, Pereira A, Lemoine S, Coulpier F, Darzacq X, Benard L, Casal M, Devaux F, Paiva S.

PLoS One. 2014 Nov 3;9(11):e111589. doi: 10.1371/journal.pone.0111589. eCollection 2014.


Transcription factors modulate c-Fos transcriptional bursts.

Senecal A, Munsky B, Proux F, Ly N, Braye FE, Zimmer C, Mueller F, Darzacq X.

Cell Rep. 2014 Jul 10;8(1):75-83. doi: 10.1016/j.celrep.2014.05.053. Epub 2014 Jun 26.


Geometry of the nucleus: a perspective on gene expression regulation.

Woringer M, Darzacq X, Izeddin I.

Curr Opin Chem Biol. 2014 Jun;20:112-9. doi: 10.1016/j.cbpa.2014.05.009. Epub 2014 Jun 27. Review.


Single-molecule tracking in live cells reveals distinct target-search strategies of transcription factors in the nucleus.

Izeddin I, Récamier V, Bosanac L, Cissé II, Boudarene L, Dugast-Darzacq C, Proux F, Bénichou O, Voituriez R, Bensaude O, Dahan M, Darzacq X.

Elife. 2014 Jun 12;3. doi: 10.7554/eLife.02230.


Accessing the third dimension in localization-based super-resolution microscopy.

Hajj B, El Beheiry M, Izeddin I, Darzacq X, Dahan M.

Phys Chem Chem Phys. 2014 Aug 21;16(31):16340-8. doi: 10.1039/c4cp01380h. Review.


The SNARE Sec22b has a non-fusogenic function in plasma membrane expansion.

Petkovic M, Jemaiel A, Daste F, Specht CG, Izeddin I, Vorkel D, Verbavatz JM, Darzacq X, Triller A, Pfenninger KH, Tareste D, Jackson CL, Galli T.

Nat Cell Biol. 2014 May;16(5):434-44. doi: 10.1038/ncb2937. Epub 2014 Apr 6.


Single cell correlation fractal dimension of chromatin: a framework to interpret 3D single molecule super-resolution.

Récamier V, Izeddin I, Bosanac L, Dahan M, Proux F, Darzacq X.

Nucleus. 2014 Jan-Feb;5(1):75-84. doi: 10.4161/nucl.28227. Epub 2014 Feb 19.


Stable assembly of HIV-1 export complexes occurs cotranscriptionally.

Nawroth I, Mueller F, Basyuk E, Beerens N, Rahbek UL, Darzacq X, Bertrand E, Kjems J, Schmidt U.

RNA. 2014 Jan;20(1):1-8. doi: 10.1261/rna.038182.113. Epub 2013 Nov 19.


High-frequency promoter firing links THO complex function to heavy chromatin formation.

Mouaikel J, Causse SZ, Rougemaille M, Daubenton-Carafa Y, Blugeon C, Lemoine S, Devaux F, Darzacq X, Libri D.

Cell Rep. 2013 Nov 27;5(4):1082-94. doi: 10.1016/j.celrep.2013.10.013. Epub 2013 Nov 7.


Quantitative nanoscopy of inhibitory synapses: counting gephyrin molecules and receptor binding sites.

Specht CG, Izeddin I, Rodriguez PC, El Beheiry M, Rostaing P, Darzacq X, Dahan M, Triller A.

Neuron. 2013 Jul 24;79(2):308-21. doi: 10.1016/j.neuron.2013.05.013.


Real-time dynamics of RNA polymerase II clustering in live human cells.

Cisse II, Izeddin I, Causse SZ, Boudarene L, Senecal A, Muresan L, Dugast-Darzacq C, Hajj B, Dahan M, Darzacq X.

Science. 2013 Aug 9;341(6146):664-7. doi: 10.1126/science.1239053. Epub 2013 Jul 4.


Gene expression is circular: factors for mRNA degradation also foster mRNA synthesis.

Haimovich G, Medina DA, Causse SZ, Garber M, Millán-Zambrano G, Barkai O, Chávez S, Pérez-Ortín JE, Darzacq X, Choder M.

Cell. 2013 May 23;153(5):1000-11. doi: 10.1016/j.cell.2013.05.012.


FISH-quant: automatic counting of transcripts in 3D FISH images.

Mueller F, Senecal A, Tantale K, Marie-Nelly H, Ly N, Collin O, Basyuk E, Bertrand E, Darzacq X, Zimmer C.

Nat Methods. 2013 Apr;10(4):277-8. doi: 10.1038/nmeth.2406. No abstract available.


Fast multicolor 3D imaging using aberration-corrected multifocus microscopy.

Abrahamsson S, Chen J, Hajj B, Stallinga S, Katsov AY, Wisniewski J, Mizuguchi G, Soule P, Mueller F, Dugast Darzacq C, Darzacq X, Wu C, Bargmann CI, Agard DA, Dahan M, Gustafsson MG.

Nat Methods. 2013 Jan;10(1):60-3. doi: 10.1038/nmeth.2277. Epub 2012 Dec 9.


PSF shaping using adaptive optics for three-dimensional single-molecule super-resolution imaging and tracking.

Izeddin I, El Beheiry M, Andilla J, Ciepielewski D, Darzacq X, Dahan M.

Opt Express. 2012 Feb 27;20(5):4957-67. doi: 10.1364/OE.20.004957.


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