Publications

2024

Esbin, M, L Dahal, V Fan, J McKenna, E Yin, X Darzacq, and R Tjian. 2024. "TFEB controls expression of human syncytins during cell-cell fusion." Genes Dev.

Graham, T, C Dugast-Darzacq, G Dailey, B Weng, X Darzacq, and R Tjian. 2024. "Single-molecule live imaging of subunit interactions and exchange within cellular regulatory complexes." bioRxiv.

Versluis, P, T Graham, V Eng, J Ebenezer, X Darzacq, W Zipfel, and J Lis. 2024. "Live-cell imaging of RNA Pol II and elongation factors distinguishes competing mechanisms of transcription regulation ." Mol Cell.

Walther, N, S Anantakrishnan, G Dailey, R Tjian, and X Darzacq. 2024. "Automated live-cell single-molecule tracking in enteroid monolayers reveals transcription factor dynamics probing lineage-determining function." bioRxiv.

2023

Zhou, J, C Cattoglio, Y Shao, H Tirumala, C Vetralla, S Bajikar, Y Li, H Chen, Q Wang, Z Wu, B Tang, M Zahabiyon, A Bajic, X Meng, J Ferrie, A LaGrone, P Zhang, J Kim, J Tang, Z Liu, X Darzacq, N Heintz, R Tjian, and H Zoghbi. 2023. "A novel pathogenic mutation of MeCP2 impairs chromatin association independent of protein levels." Genes Dev.

Collombet, S, I Rall, C Dugast-Darzacq, A Heckert, A Halavatyi, A Le Saux, G Dailey, X Darzacq, and E Heard. 2023. "RNA polymerase II depletion from the inactive X chromosome territory is not mediated by physical compartmentalization." Nat Struct Mol Biol, 1216-1223.

Dahal, L, N Walther, R Tjian, X Darzacq, and T Graham. 2023. "Single-molecule tracking (SMT): a window into live-cell transcription biochemistry." Biochem Soc Trans, 51(2):557-569.

Dahal, L, T Graham, G Dailey, A Heckert, R Tjian, and X Darzacq. 2023. "Surprising Features of Nuclear Receptor Interaction Networks Revealed by Live Cell Single Molecule Imaging." 2023.09.16.558083.

Ferrie, J, J Karr, T Graham, G Dailey, G Zhang, R Tjian, and X Darzacq. 2023. "p300 Is an Obligate Integrator of Combinatorial Transcription Factor Inputs." Mol cell.

Maurer, A. 2023. "Double-Strand Break Repair Pathways Differentially Affect Processing and Transduction by Dual AAV Vectors." bioRxiv, 2023.09.19.558438.

Zhou, J, C Cattoglio, Y Shao, H Tirumala, C Vetralla, S Bajikar, Y Li, H Chen, Q Wang, Z Wu, B Tang, M Zahabiyon, A Bajic, X Meng, J Ferrie, A LaGrone, P Zhang, J Kim, J Tang, Z Liu, X Darzacq, N Heintz, R Tjian, and H Zoghbi. 2023. "A novel pathogenic mutation of MeCP2 impairs chromatin association independent of protein levels." Genes Dev.

2022

Chen, Y, C Cattoglio, G Dailey, Q Zhu, R Tjian, and X Darzacq. 2022. "Mechanisms Governing Target Search and Binding Dynamics of Hypoxia-Inducible Factors." Elife, 11:e75064.

Chong, S, T Graham, C Dugast-Darzacq, G Dailey, X Darzacq, and R Tjian. 2022. "Tuning levels of low-complexity domain interactions to modulate endogenous oncogenic transcription." Mol Cell, 82(11):2084-2097.e5.

Ferrie , J, J Karr, R Tjian, and X Darzacq. 2022. "'Structure'-function relationships in eukaryotic transcription factors: The role of intrinsically disordered regions in gene regulation." Mol Cell, 82(21):3970-3984.

Graham , T, J Ferrie , G Dailey , R Tjian , and X Darzacq. 2022. "Detecting molecular interactions in live-cell single-molecule imaging with proximity-assisted photoactivation (PAPA)." Elife, 11:e76870.

Heckert, A, L Dahal, R Tjian, and X Darzacq. 2022. "Recovering mixtures of fast-diffusing states from short single-particle trajectories." Elife, 11:e70169.

Hsieh, T H, C Cattoglio, E Slobodyanyuk, A Hansen, X Darzacq, and R Tjian. 2022. "Enhancer-promoter interactions and transcription are largely maintained upon acute loss of CTCF, cohesin, WAPL or YY1." Nat Genet, 54(12):1919-1932.

Karr , J, J Ferrie , R Tjian , and X Darzacq. 2022. "The transcription factor activity gradient (TAG) model: contemplating a contact-independent mechanism for enhancer-promoter communication." Genes Dev, 36(1-2):7-16.

Xie, L, P Dong, Y Qi, T H Hsieh, B English, SK Jung, X Chen, M De Marzio, R Casellas, H Chang, B Zhang, R Tjian, and Z Liu. 2022. "BRD2 compartmentalizes the accessible genome." Nat Genet, 54(4):481-491.

2021

Graham, T, G Dailey, X Nguyenla, E Van Dis, M Esbin, A Abidi, S Stanley, C Dugast-Darzacq, X Darzacq, and R Tjian. 2021. "Open-source RNA extraction and RT-qPCR methods for SARS-CoV-2 detection." PLoS One, 16(2):e0246647.

Darzacq, X and R 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.

Hung, K, K Yost, 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.

Sawicka, A, G Villamil, M Lidschreiber, X Darzacq, C Dugast-Darzacq, B Schwalb, and P 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.

Hung, K, K Yost, 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.