Publications

Publications


2018

Bardales, J, E Weiser, H Kawaji, Y Murakawa, and X Darzacq. 2018. "Selective Activation of Alternative MYC Core Promoters by Wnt-Responsive Enhancers ." Genes, 9 (6): 270.

Boehning, M, C Dugast Darzacq, M Rankovic, A Hansen, T Yu, H Marie Nelly, D McSwiggen, G Kokic, G Dailey, P Cramer, X Darzacq, and M Zweckstetter. 2018. "RNA polymerase II clustering through CTD phase separation." Nature Structural & Molecular Biology.

Cattoglio, C, I Pustova, J Ho, C Inouye, G Dailey, X Darzacq, R Tjian, and A Hansen. 2018. "Architectural Features of 3D Genome Organization Revealed by Counting CTCF and Cohesin Molecules ." bioRxiv, 370650.

Chong, S, C Dugast Darzacq, Z Liu, P Dong, G Dailey, C Cattoglio, A Heckert, S Banala, L Lavis, X Darzacq, and R Tjian. 2018. "Imaging dynamic and selective low-complexity domain interactions that control gene transcription." Science, 361 (6400): 2018 Jul 27.

Hansen, A, M Woringer, J Grimm, L Lavis, R Tjian, and X Darzacq. 2018. "Robust model-based analysis of single-particle tracking experiments with Spot-On." eLife.

Hollerer, I, J Barker, V Jorgensen, A Tresenrider, C D Darzacq, X Darzacq, L Chan, R Tjian, E Unal, and G Brar. 2018. "Evidence for an Integrated Gene Repression Mechanism based on mRNA Isoform Switching in Human Cells." BioRxiv, 264721.

Lu, H, D Yu, A Hansen, S Ganguly, R Liu, A Heckert, X Darzacq, and Q Zhou. 2018. "Phase-separation mechanism for C-terminal hyperphosphorylation of RNA polymerase II ." Nature, 558 (7709): 318-323.

McSwiggen, D, A Hansen, H Marie Nelly, S Teves, A Heckert, C Dugast Darzacq, Y Hao, K Umemoto, R Tjian, and X Darzacq. 2018. "Transient DNA Binding Induces RNA Polymerase II Compartmentalization During Herpesviral Infection Distinct From Phase Separation." bioRxiv, 375071.

Mir, M, M Stadler, S Ortiz, M Harrison, X Darzacq, and M Eisen. 2018. "Dynamic multifactor hubs interact transiently with sites of active transcription in Drosophila embryos." bioRxiv, 377812.

Mir, M, A Reimer, M Stadler, A Tangara, A Hansen, D Hockemeyer, M Eisen, H Garcia, and X Darzacq. 2018. "Single Molecule Imaging in Live Embryos Using Lattice Light-Sheet Microscopy." Methods Mol Biol., 2018 (1814): 541-559.

Oomen, M, A Hansen, Y Liu, X Darzacq, and J Dekker. 2018. "CTCF sites display cell cycle dependent dynamics in factor binding and nucleosome positioning." bioRxiv, 365866.

Teves, S, L An, A Bhargava Shah, L Xie, X Darzacq, and R Tjian. 2018. "A stable mode of bookmarking by TBP recruits RNA Polymerase II to mitotic chromosomes." eLife (7): 2018 Jun 25.

Tsui, C, C Inouye, M Levy, A Lu, L Florens, M Washburn, and R Tjian. 2018. "dCas9-targeted locus-specific protein isolation method identifies histone gene regulators." Proceedings of the National Academy of Sciences, 115 (12): 2018 Mar 20.

Woringer, M and X Darzacq. 2018. "Protein motion in the nucleus: from anomalous diffusion to weak interactions." Biochemical Society Transactions.

2017

Hansen, A, I Pustova, C Cattloglio, R Tjian, and X Darzacq. 2017. "CTCF and cohesin regulate chromatin loop stability with distinct dynamics." Elife, eLife 2017;6:e25776.

Hansen, A, C Cattoglio, X Darzacq, and R Tjian. 2017. "Recent evidence that TADs and chromatin loops are dynamic structures." Nucleus, 1-18.

Ho, J, C Cattoglio, D McSwiggen, R Tjian, and Y Fong. 2017. "Regulation of DNA demethylation by the XPC DNA repair complex in somatic and pluripotent stem cells." Genes Dev, 31 (8): 830-844.

Mir, M, A Reimer, J Haines, X Li, M Stadler, H Garcia, M Eisen, and X Darzacq. 2017. "Dense Bicoid hubs accentuate binding along the morphogen gradient." Genes Dev, 31 (17): 1784.

Qin, P, M Parlak, C Kuscu, J Bandaria, M Mir, K Szlachta, R Singh, X Darzacq, A Yildiz, and M Adli. 2017. "Live cell imaging of low- and non-repetitive chromosome loci using CRISPR-Cas9." Nature Communications, 8.

Strom, A, A Emelyanov, M Mir, D Fyodorov, X Darzacq, and G Karpen. 2017. "Phase separation drives heterochromatin domain formation." Nature, 547 (13 July 2017): 241-245.

Wichner, S, V Mann, A Powers, M Segal, M Mir, J Bandaria, M DeWitt, X Darzacq, A Yildiz, and B Cohen. 2017. "Covalent Protein Labeling and Improved Single-Molecule Optical Properties of Aqueous CdSe/CdS Quantum Dots." ACS Nano, 11 (7): 6773-6781.

Worringer, M, X Darzacq, C Zimmer, and M Mir. 2017. "Faster and less phototoxic 3D fluorescence microscopy using a versatile compressed sensing scheme." Opt. Express, 25 (12): 13668-13683.

Xie, L, S Torigoe, J Xiao, D Mai, L Li, F Davis, P Dong, H Marie-Nelly, J Grimm, L Lavis, X Darzacq, C Cattoglio, Z Liu, and R Tjian. 2017. "A dynamic interplay of enhancer elements regulates Klf4 expression in naïve pluripotency ." Genes Dev, 31 (17): 1795.

2016

Abrahamsson, S, R Ilic, J Wisniewski, B Mehl, L Yu, L Chen, M Davanco, L Oudjedi, J Fiche, B Hajj, X Jin, J Pulupa, C Cho, M Mir, M El Beheiry, X Darzacq, M Nollmann, M Dahan, C Wu, T Lionnet, J Liddle, and C Bargmann. 2016. "Multifocus microscopy with precise color multi-phase diffractive optics applied in functional neuronal imaging." Biomed Opt Express, 7 (3): 855-869.

East-Saletsky, A, M O\'Connell, S Knight, D Burstein, J Cate, R Tjian, and J Doudna. 2016. "Two distinct RNase activities of CRISPR-C2c2 enable guide-RNA processing and RNA detection." Nature, 538 (7624): 270-273.

He, Y, C Yan, J Fang, C Inouye, R Tjian, I Ivanov, and E Nogales. 2016. "Near-atomic resolution visualization of human transcription promoter opening." Nature, 533 (7603): 359-365.

Horlbeck, M, L Witkowsky, B Guglielmi, J Replogle, L Gilbert, J Villalta, S Torigoe, R Tjian, and J Weissman. 2016. " Nucleosomes impede Cas9 access to DNA in vivo and in vitro." Elife.

Kong, N, M Davis, L Chai, A Winoto, and R Tjian. 2016. "MEF2C and EBF1 Co-regulate B Cell-Specific Transcription." PLoS Genet, 12 (2).

Li, L, H Liu, P Dong, D Li, W Legant, J Grimm, L Lavis, E Betzig, R Tjian, and Z Liu. 2016. "Real-time imaging of Huntingtin aggregates diverting target search and gene transcription." eLife.

Noizet, M, E Lagoutte, M Gratigny, M Bouschbacher, I Lazareth, H Roest Crollius, X Darzacq, and C Dugast-Darzacq. 2016. "Master regulators in primary skin fibroblast fate reprogramming in a human ex vivo model of chronic wounds." Wound Repair Regen, 24 (2): 247-262.

Tantale, K, F Mueller, A Kozulic-Pirher, A Lesne, J Victor, M Robert, S Capozi, R Chouaib, V Bäcker, J Mateos-Langerak, X Darzacq, C Zimmer, E Basyuk, and E Bertrand. 2016. "A single-molecule view of transcription reveals convoys of RNA polymerases and multi-scale bursting." Nat Commun.

Teves, S, L An, A Hansen, L Xie, X Darzacq, and R Tjian. 2016. "A dynamic mode of mitotic bookmarking by transcription factors." eLife, eLife 2016;5:e22280.

Zhang, Z, B English, J Grim, S Kazane, W Hu, A Tsai, C Inouye, C You, J Piehler, P Schultz, L Lavis, A Revyakin, and R Tjian. 2016. "Rapid dynamics of general transcription factor TFIIB binding during preinitiation complex assembly revealed by single-molecule analysis." Genes Dev, 30 (18): 2106-2118.

2015

Cattoglio, C, E Zhang, I Grubisic, K Chiba, Y Fong, and R Tjian. 2015. "Functional and mechanistic studies of XPC DNA-repair complex as transcriptional coactivator in embryonic stem cells." Proc Natl Acad Sci , 112 (18).

Coleman, R, Z Liu, X Darzacq, R Tjian, R Singer, and T Lionnet. 2015. "Imaging Transcription: Past, Present, and Future." Cold Spring Harb Symp Quant Biol, 80, 1-8.

Deng, W, X Shi, R Tjian, T Lionnet, and R Singer. 2015. "CASFISH: CRISPR/Cas9-mediated in situ labeling of genomic loci in fixed cells." Proc Natl Acad Sci, 112 (38): 11870-11875.

Knight, S, L Xie, W Deng, B Guglielmi, L Witkowsky, L Bosanac, E Zhang, M El Beheiry, J Masson, M Danhan, Z Liu, J Doudna, and R Tjian. 2015. "Dynamics of CRISPR-Cas9 genome interrogation in living cells." Science, 350 (6262): 823-826.

Li, L, S Martinez, W Hu, Z Liu, and R Tjian. 2015. "A specific E3 ligase/deubiquitinase pair modulates TBP protein levels during muscle differentiation." eLife.

Normanno, D, L Boudarène, C Dugast-Darzacq, J Chen, C Richter, F Proux, O Bénichou, R Voituriez, X Darzacq, and M Dahan. 2015. "Probing the target search of DNA-binding proteins in mammalian cells using TetR as model searcher." Nat Commun.

Zhang, E, Y He, P Grob, Y Fong, E Nogales, and R Tjian. 2015. "Architecture of the human XPC DNA repair and stem cell coactivator complex." Proc Natl Acad Sci, 112 (48): 14817-14822.

Zhang, Z, Z Boskovic, M Hussain, W Hu, C Inouye, H Kim, A Abole, M Doud, T Lewis, A Koehler, S Schreiber, and R Tjian. 2015. "Chemical perturbation of an intrinsically disordered region of TFIID distinguishes two modes of transcription initiation." eLife.