Publications

2021

Graham, Thomas, Gina Dailey, Xammy Nguyenla, Erik Van Dis, Meagan Esbin, Abrar Abidi, Sarah Stanley, Xavier Darzacq, Claire Dugast-Darzacq, and Robert Tjian. 2021. "Open-source RNA extraction and RT-qPCR methods for SARS-CoV-2 detection." PLoS One, 16(2):e0246647.

Chong, Shasha, Claire Darzacq, Gina Dailey, Thomas Graham, Xavier Darzacq, and Robert Tjian. 2021. "Tuning levels of low-complexity domain interactions to modulate endogenous oncogenic transcription." bioRxiv, Posted 17 August 2021.

Chen, Yu, Claudia Cattoglio, Gina Dailey, Quilin Zhu, Robert Tjian, and Xavier Darzacq. 2021. "Mechanisms Governing Target Search and Binding Dynamics of Hypoxia-Inducible Factors.".

Darzacq, Xavier and Robert Tjian. 2021. "Weak Multivalent Biomolecular Interactions: A Strength vs Numbers Tug of War with Implications for Phase Partitioning." RNA.

Graham, T, C Dugast-Darzacq, G Dailey, X Darzacq, and R Tjian. 2021. "Simple, Inexpensive RNA Isolation and One-Step RT-qPCR Methods for SARS-CoV-2 Detection and General Use." Curr Protoc.

Heckert, Alec, Liza Dahal, Robert Tjian, and Xavier Darzacq. 2021. "Recovering mixtures of fast diffusing states from short single particle trajectories.".

Yost, K, K Hung, L Xie, Q Shi, K Helmsauer, J Luebeck, R Schöpflin, J Lange, R Chamorro González, N Weiser, C Chen, M Valieva, I Wong, S Wu, S Dehkordi, C Duffy, K Kraft, J Tang, J Belk, J Rose, M Corces, J Granja, R Li, U Rajkumar, J Friedlein, A Bagchi, A Satpathy, R Tjian, S Mundlos, V Bafna, A Henssen, P Mischel, Z Liu, and H Chang. 2021. "ecDNA hubs drive cooperative intermolecular oncogene expression. ." Nature.

Narlikar, G, S Myong, D Larson, K Maeshima, N Francis, K Rippe, B Sabari, L Strader, and R Tjian. 2021. "Is transcriptional regulation just going through a phase? ." Mol Cell, 81 (8): 1579-1585.

Nogales, E, D Herbst, M Esbin, R Louder, C Dugast-Darzacq, G Dailey, Q Fang, X Darzacq, and R Tjian. 2021. "Structure of the human SAGA coactivator complex." Nat Struct Mol Biol.

Collombet, Samuel, Isabell Rall, Claire Dugast-Darzacq, Alec Heckert, Aliaksandr Halavatyi, Agnes Le Saux, Gina Dailey, Xavier Darzacq, and Edith Heard. 2021. "RNA polymerase II depletion from the inactive X chromosome territory is not mediated by physical compartmentalization.".

Sawicka, Anna, Gabriel Villamil, Michael Lidschreiber, Xavier Darzacq, Claire Dugast-Darzacq, Björn Schwalb, and Patrick Cramer. 2021. "Transcription activation depends on the length of the RNA polymerase II C-terminal domain." EMBO J., 40, 9.

Seong, B, N Dharia, S Lin, K Donovan, S Chong, A Robichaud, A Conway, A Hamze, L Ross, G Alexe, B Adane, B Nabet, F Ferguson, B Stolte, E Wang, J Sun, X Darzacq, F Piccioni, N Gray, E Fischer, and K Stegmaier. 2021. "TRIM8 modulates the EWS/FLI oncoprotein to promote survival in Ewing sarcoma." Cancer Cell.

Whitney, O, L Kennedy, V Fan, A Hinkle, R Kantor, H Greenwald, A Crits-Christoph, B Al-Shayeb, M Chaplin, A Maurer, R Tjian, and K Nelson. 2021. "Sewage, Salt, Silica, and SARS-CoV-2 (4S): An Economical Kit-Free Method for Direct Capture of SARS-CoV-2 RNA from Wastewater." Environ Sci Technol.

Yost, K, K Hung, L Xie, Q Shi, K Helmsauer, J Luebeck, R Schöpflin, J Lange, R Chamorro González, N Weiser, C Chen, M Valieva, I Wong, S Wu, S Dehkordi, C Duffy, K Kraft, J Tang, J Belk, J Rose, M Corces, J Granja, R Li, U Rajkumar, J Friedlein, A Bagchi, A Satpathy, R Tjian, S Mundlos, V Bafna, A Henssen, P Mischel, Z Liu, and H Chang. 2021. "ecDNA hubs drive cooperative intermolecular oncogene expression. ." Nature.

2020

Cattoglio, C, I Pustova, X Darzacq, R Tjian, and A Hansen. 2020. "Assessing Self-interaction of Mammalian Nuclear Proteins by Co-immunoprecipitation." bio-protocol, 10 (4): February 20.

Cattoglio, C, X Darzacq, R Tjian, and A Hansen. 2020. "Estimating Cellular Abundances of Halo-tagged Proteins in Live Mammalian Cells by Flow Cytometry." bio-protocol, 10 (4): February 20.

Chan, W, S Chong, A Liang, X Cui, L Gates, T Carroll, Y Li, L Feng, G Chen, S Wang, M Ortiz, S Daley, X Wang, H Xuan, A Kentsis, T Muir, R Roeder, H Li, W Li, R Tjian, H Wen, and C Allis. 2020. "Impaired cell fate through gain-of-function mutations in a chromatin reader ." Nature, 577 (2020): 121-126.

Chen, Z, A Shaw, H Wilson, M Woringer, X Daerzacq, S Marqusee, Q Wang, and C Bustamante. 2020. "Single-molecule diffusometry reveals no catalysis-induced diffusion enhancement of alkaline phosphatase as proposed by FCS experiments." Proc Natl Acad Sci U S A, 117 (35): 21328-21335.

Costantino, L, T Hsieh, R Lamothe, X Darzacq, and D Koshland. 2020. "Cohesin residency determines chromatin loop patterns." Elife, 9 (e59889).

Esbin, M and R Tjian. 2020. "Distinct Handoff Mechanism for TBP-TATA DNA Engagement Revealed by SAGA Structures." Biochemistry, May 5, 59 (17): 1647-1649. American Chemical Society.

Esbin, M, O Whitney, S Chong, A Maurer, X Darzacq, and R Tjian. 2020. "Overcoming the bottleneck to widespread testing: A rapid review of nucleic acid testing approaches for COVID-19 detection." RNA, Jul, 26 (7): 771-783.

Hansen, A, A Amitai, C Cattoglio, R Tjian, and X Darzacq. 2020. "Guided nuclear exploration increases CTCF target search efficiency." Nat Chem Biol, 16 (2020): 257-266.

Hsieh, T, C Cattoglio, E Slobodyanyuk, A Hansen, O Rando, R Tjian, and X Darzacq. 2020. "Resolving the 3D Landscape of Transcription-Linked Mammalian Chromatin Folding." Mol Cell, 78 (3): 539.

Maurer, A and M Weitzman. 2020. "Adeno-Associated Virus Genome Interactions Important for Vector Production and Transduction." Human Gene Therapy, 8 May 2020.

Park, S, J Hauver, Y Zhang, R Coleman, R Tjian, S Chu, and A Pertsinidis. 2020. "A Single-Molecule Surface-Based Platform to Detect the Assembly and Function of the Human RNA Polymerase II Transcription Machinery." Structure, Aug 4, S0969-2126 (20): 30242-2.

Wang, A, L Chen, R Wu, Y Hao, D McSwiggen, A Heckert, C Richardson, B Gowen, K Kazane, J Vu, S Wyman, J Shin, X Darzacq, J Walter, and J Corn. 2020. "The Histone Chaperone FACT Induces Cas9 Multi-turnover Behavior and Modifies Genome Manipulation in Human Cells." Mol Cell, Jun 23, S1097-2765 (20): 30399-3.

Xie, L, P Dong, X Chen, T Hsieh, S Banala, M DeMarzio, B English, Y Qi, S Jung, K Kieffer-Kwon, W Legant, A Hansen, A Schulmann, R Casellas, B Zhang, E Betzig, L Lavis, H Chang, R Tjian, and Z Liu. 2020. "3D ATAC-PALM: super-resolution imaging of the accessible genome ." Nat Methods, Apr, 17 (4): 430-436.

2019

Cattoglio, C, I Pustova, N Walther, J Ho, M Hantsche-Grininger, C Inouye, M Hossain, G Dailey, J Ellenberg, X Darzacq, R Tjian, and A Hansen. 2019. "Determining cellular CTCF and cohesin abundances to constrain 3D genome models." Elife, 2019, 8 (e40164).

Hansen, A, TH Hsieh, C Cattoglio, I Pustova, R Saldaña-Meyer, D Reinberg, X Darzacq, and R Tjian. 2019. "Distinct Classes of Chromatin Loops Revealed by Deletion of an RNA-Binding Region in CTCF. ." Mol Cell, S1097-2765, (19), 30594-30595.

Hollerer, I, J Barker, V Jorgensen, A Tresenrider, C Dugast-Darzacq, L Chan, X Darzacq, R Tjian, E Ünal, and G Brar. 2019. "Evidence for an Integrated Gene Repression Mechanism Based on mRNA Isoform Toggling in Human Cells." G3 (Bethesda) (9): 4, 1045-1053.

McSwiggen, D, M Mir, X Darzacq, and R Tjian. 2019. "Evaluating phase separation in live cells: diagnosis, caveats, and functional consequences." Genes Dev, Oct 8.

McSwiggen, D, A Hansen, S Teves, H Marie-Nelly, Y Hao, A Heckert, K Umemoto, C Dugast-Darzacq, R Tjian, and X Darzacq. 2019. "Evidence for DNA-mediated nuclear compartmentalization distinct from phase separation. ." Elife, 8, 47098.

Oomen, M, A Hansen, Y Liu, X Darzacq, and J Dekker. 2019. "CTCF sites display cell cycle-dependent dynamics in factor binding and nucleosome positioning." Genome Res (29): 2, 236-249.

Parker, M, M Bell, M Mir, J Kao, X Darzacq, M Botchan, and J Berger. 2019. "A new class of disordered elements controls DNA replication through initiator self-assembly." Elife, 2019 Sep 27;8, pii: e48562.

Piccolo, F, Z Liu, P Dong, C Hsu, E Stoyanova, A Rao, R Tjian, and N Heintz. 2019. "MeCP2 nuclear dynamics in live neurons results from low and high affinity chromatin interactions. ." elife, Dec23, 8.

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 carboxy-terminal domain phase separation." Nat Struct Mol Biol., sep, 25(9), 833-840.

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.

Knight, S, R Tjian, and J Doudna. 2018. "Genomes in Focus: Development and Applications of CRISPR-Cas9 Imaging Technologies." Angew Chem int Ed Engl (Apr 9): 16, 4329-4337.

Liu, Z and R Tjian. 2018. "Visualizing transcription factor dynamics in living cells. ." J Cell Biol. (217): 4, 1181-1191.

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.

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." Elife, 7.

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.

Strom, A, A Emelyanov, M Mir, D Fyodorov, X Darzacq, and G Karpen. 2018. "Phase Separation Drives Heterochromatin Domain Formation." Biophysical Journal, 114, 445.

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." Biochem Soc Trans (46): 4, 945-956.

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.

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.