{"id":197479,"date":"2025-06-19T15:40:11","date_gmt":"2025-06-19T15:40:11","guid":{"rendered":"https:\/\/www.europesays.com\/uk\/197479\/"},"modified":"2025-06-19T15:40:11","modified_gmt":"2025-06-19T15:40:11","slug":"rna-polymerase-ii-transcription-compartments-from-factories-to-condensates","status":"publish","type":"post","link":"https:\/\/www.europesays.com\/uk\/197479\/","title":{"rendered":"RNA polymerase II transcription compartments \u2014 from factories to condensates"},"content":{"rendered":"
  • \n

    Baum, M., Erdel, F., Wachsmuth, M. & Rippe, K. Retrieving the intracellular topology from multi-scale protein mobility mapping in living cells. Nat. Commun. 5<\/b>, 4494 (2014).<\/p>\n

    Article<\/a>\u00a0
    \n     CAS<\/a>\u00a0
    \n     PubMed<\/a>\u00a0
    \n
    \n Google Scholar<\/a>\u00a0\n <\/p>\n<\/li>\n

  • \n

    Boisvert, F. M., van Koningsbruggen, S., Navascues, J. & Lamond, A. I. The multifunctional nucleolus. Nat. Rev. Mol. Cell Biol. 8<\/b>, 574\u2013585 (2007).<\/p>\n

    Article<\/a>\u00a0
    \n     CAS<\/a>\u00a0
    \n     PubMed<\/a>\u00a0
    \n
    \n Google Scholar<\/a>\u00a0\n <\/p>\n<\/li>\n

  • \n

    Papantonis, A. & Cook, P. R. Transcription factories: genome organization and gene regulation. Chem. Rev. 113<\/b>, 8683\u20138705 (2013).<\/p>\n

    Article<\/a>\u00a0
    \n     CAS<\/a>\u00a0
    \n     PubMed<\/a>\u00a0
    \n
    \n Google Scholar<\/a>\u00a0\n <\/p>\n<\/li>\n

  • \n

    Geisler, M. S., Kemp, J. P. Jr & Duronio, R. J. Histone locus bodies: a paradigm for how nuclear biomolecular condensates control cell cycle regulated gene expression. Nucleus 14<\/b>, 2293604 (2023).<\/p>\n

    Article<\/a>\u00a0
    \n     PubMed<\/a>\u00a0
    \n     PubMed Central<\/a>\u00a0
    \n
    \n Google Scholar<\/a>\u00a0\n <\/p>\n<\/li>\n

  • \n

    Jackson, D. A., Hassan, A. B., Errington, R. J. & Cook, P. R. Visualization of focal sites of transcription within human nuclei. EMBO J. 12<\/b>, 1059\u20131065 (1993). The first visualization of discrete RNA polymerase II foci that founded the transcription factory model.<\/b><\/p>\n

    Article<\/a>\u00a0
    \n     CAS<\/a>\u00a0
    \n     PubMed<\/a>\u00a0
    \n     PubMed Central<\/a>\u00a0
    \n
    \n Google Scholar<\/a>\u00a0\n <\/p>\n<\/li>\n

  • \n

    Iborra, F. J., Pombo, A., Jackson, D. A. & Cook, P. R. Active RNA polymerases are localized within discrete transcription \u2018factories\u2019 in human nuclei. J. Cell Sci. 109<\/b>, 1427\u20131436 (1996).<\/p>\n

    Article<\/a>\u00a0
    \n     CAS<\/a>\u00a0
    \n     PubMed<\/a>\u00a0
    \n
    \n Google Scholar<\/a>\u00a0\n <\/p>\n<\/li>\n

  • \n

    Osborne, C. S. et al. Active genes dynamically colocalize to shared sites of ongoing transcription. Nat. Genet. 36<\/b>, 1065\u20131071 (2004).<\/p>\n

    Article<\/a>\u00a0
    \n     CAS<\/a>\u00a0
    \n     PubMed<\/a>\u00a0
    \n
    \n Google Scholar<\/a>\u00a0\n <\/p>\n<\/li>\n

  • \n

    Ragoczy, T., Bender, M. A., Telling, A., Byron, R. & Groudine, M. The locus control region is required for association of the murine beta-globin locus with engaged transcription factories during erythroid maturation. Genes Dev. 20<\/b>, 1447\u20131457 (2006).<\/p>\n

    Article<\/a>\u00a0
    \n     CAS<\/a>\u00a0
    \n     PubMed<\/a>\u00a0
    \n     PubMed Central<\/a>\u00a0
    \n
    \n Google Scholar<\/a>\u00a0\n <\/p>\n<\/li>\n

  • \n

    Zhou, G. L. et al. Active chromatin hub of the mouse alpha-globin locus forms in a transcription factory of clustered housekeeping genes. Mol. Cell. Biol. 26<\/b>, 5096\u20135105 (2006).<\/p>\n

    Article<\/a>\u00a0
    \n     CAS<\/a>\u00a0
    \n     PubMed<\/a>\u00a0
    \n     PubMed Central<\/a>\u00a0
    \n
    \n Google Scholar<\/a>\u00a0\n <\/p>\n<\/li>\n

  • \n

    Sutherland, H. & Bickmore, W. A. Transcription factories: gene expression in unions? Nat. Rev. Genet. 10<\/b>, 457\u2013466 (2009).<\/p>\n

    Article<\/a>\u00a0
    \n     CAS<\/a>\u00a0
    \n     PubMed<\/a>\u00a0
    \n
    \n Google Scholar<\/a>\u00a0\n <\/p>\n<\/li>\n

  • \n

    Hnisz, D., Shrinivas, K., Young, R. A., Chakraborty, A. K. & Sharp, P. A. A phase separation model for transcriptional control. Cell 169<\/b>, 13\u201323 (2017). A perspective article introducing the notion of phase separation as a potential mechanism underlying transcriptional activation via enhancers.<\/b><\/p>\n

    Article<\/a>\u00a0
    \n     CAS<\/a>\u00a0
    \n     PubMed<\/a>\u00a0
    \n     PubMed Central<\/a>\u00a0
    \n
    \n Google Scholar<\/a>\u00a0\n <\/p>\n<\/li>\n

  • \n

    Banani, S. F., Lee, H. O., Hyman, A. A. & Rosen, M. K. Biomolecular condensates: organizers of cellular biochemistry. Nat. Rev. Mol. Cell Biol. 18<\/b>, 285\u2013298 (2017).<\/p>\n

    Article<\/a>\u00a0
    \n     CAS<\/a>\u00a0
    \n     PubMed<\/a>\u00a0
    \n     PubMed Central<\/a>\u00a0
    \n
    \n Google Scholar<\/a>\u00a0\n <\/p>\n<\/li>\n

  • \n

    Boija, A. et al. Transcription factors activate genes through the phase-separation capacity of their activation domains. Cell 175<\/b>, 1842\u20131855.e16 (2018).<\/p>\n

    Article<\/a>\u00a0
    \n     CAS<\/a>\u00a0
    \n     PubMed<\/a>\u00a0
    \n
    \n Google Scholar<\/a>\u00a0\n <\/p>\n<\/li>\n

  • \n

    Sabari, B. R. et al. Coactivator condensation at super-enhancers links phase separation and gene control. Science 361<\/b>, eaar3958-17 (2018).<\/p>\n

    Article<\/a>\u00a0
    \n     PubMed<\/a>\u00a0
    \n     PubMed Central<\/a>\u00a0
    \n
    \n Google Scholar<\/a>\u00a0\n <\/p>\n<\/li>\n

  • \n

    Shrinivas, K. et al. Enhancer features that drive formation of transcriptional condensates. Mol. Cell 75<\/b>, 549\u2013561.e7 (2019).<\/p>\n

    Article<\/a>\u00a0
    \n     CAS<\/a>\u00a0
    \n     PubMed<\/a>\u00a0
    \n     PubMed Central<\/a>\u00a0
    \n
    \n Google Scholar<\/a>\u00a0\n <\/p>\n<\/li>\n

  • \n

    Wei, M. T. et al. Nucleated transcriptional condensates amplify gene expression. Nat. Cell Biol. 22<\/b>, 1187\u20131196 (2020).<\/p>\n

    Article<\/a>\u00a0
    \n     CAS<\/a>\u00a0
    \n     PubMed<\/a>\u00a0
    \n
    \n Google Scholar<\/a>\u00a0\n <\/p>\n<\/li>\n

  • \n

    Lu, Y. et al. Phase separation of TAZ compartmentalizes the transcription machinery to promote gene expression. Nat. Cell Biol. 22<\/b>, 453\u2013464 (2020).<\/p>\n

    Article<\/a>\u00a0
    \n     CAS<\/a>\u00a0
    \n     PubMed<\/a>\u00a0
    \n     PubMed Central<\/a>\u00a0
    \n
    \n Google Scholar<\/a>\u00a0\n <\/p>\n<\/li>\n

  • \n

    Uversky, V. N. Recent developments in the field of intrinsically disordered proteins: intrinsic disorder-based emergence in cellular biology in light of the physiological and pathological liquid\u2013liquid phase transitions. Annu. Rev. Biophys. 50<\/b>, 135\u2013156 (2021).<\/p>\n

    Article<\/a>\u00a0
    \n     CAS<\/a>\u00a0
    \n     PubMed<\/a>\u00a0
    \n
    \n Google Scholar<\/a>\u00a0\n <\/p>\n<\/li>\n

  • \n

    Holehouse, A. S. & Kragelund, B. B. The molecular basis for cellular function of intrinsically disordered protein regions. Nat. Rev. Mol. Cell Biol. 25<\/b>, 187\u2013211 (2024).<\/p>\n

    Article<\/a>\u00a0
    \n     CAS<\/a>\u00a0
    \n     PubMed<\/a>\u00a0
    \n
    \n Google Scholar<\/a>\u00a0\n <\/p>\n<\/li>\n

  • \n

    Musselman, C. A. & Kutateladze, T. G. Characterization of functional disordered regions within chromatin-associated proteins. iScience 24<\/b>, 102070 (2021).<\/p>\n

    Article<\/a>\u00a0
    \n     CAS<\/a>\u00a0
    \n     PubMed<\/a>\u00a0
    \n     PubMed Central<\/a>\u00a0
    \n
    \n Google Scholar<\/a>\u00a0\n <\/p>\n<\/li>\n

  • \n

    Rippe, K. Liquid\u2013liquid phase separation in chromatin. Cold Spring Harb. Perspect. Biol. 14<\/b>, a040683 (2022).<\/p>\n

    Article<\/a>\u00a0
    \n     CAS<\/a>\u00a0
    \n     PubMed<\/a>\u00a0
    \n     PubMed Central<\/a>\u00a0
    \n
    \n Google Scholar<\/a>\u00a0\n <\/p>\n<\/li>\n

  • \n

    Jonas, F., Navon, Y. & Barkai, N. Intrinsically disordered regions as facilitators of the transcription factor target search. Nat. Rev. Genet. 26<\/b>, 424\u2013435 (2025).<\/p>\n

    Article<\/a>\u00a0
    \n     CAS<\/a>\u00a0
    \n     PubMed<\/a>\u00a0
    \n
    \n Google Scholar<\/a>\u00a0\n <\/p>\n<\/li>\n

  • \n

    Soto, L. F. et al. Compendium of human transcription factor effector domains. Mol. Cell 82<\/b>, 514\u2013526 (2022). This paper presents a comprehensive catalogue of more than 900 effector domains across ~600 human transcription factor<\/b>s including charge, hydrophobicity, disorder and phosphorylation information.<\/b><\/p>\n

    Article<\/a>\u00a0
    \n     CAS<\/a>\u00a0
    \n     PubMed<\/a>\u00a0
    \n
    \n Google Scholar<\/a>\u00a0\n <\/p>\n<\/li>\n

  • \n

    Mar, M., Nitsenko, K. & Heidarsson, P. O. Multifunctional intrinsically disordered regions in transcription factors. Chemistry 29<\/b>, e202203369 (2023).<\/p>\n

    Article<\/a>\u00a0
    \n     CAS<\/a>\u00a0
    \n     PubMed<\/a>\u00a0
    \n
    \n Google Scholar<\/a>\u00a0\n <\/p>\n<\/li>\n

  • \n

    Rippe, K. & Papantonis, A. Functional organization of RNA polymerase II in nuclear subcompartments. Curr. Opin. Cell Biol. 74<\/b>, 88\u201396 (2022).<\/p>\n

    Article<\/a>\u00a0
    \n     CAS<\/a>\u00a0
    \n     PubMed<\/a>\u00a0
    \n
    \n Google Scholar<\/a>\u00a0\n <\/p>\n<\/li>\n

  • \n

    McSwiggen, D. T., Mir, M., Darzacq, X. & Tjian, R. Evaluating phase separation in live cells: diagnosis, caveats, and functional consequences. Genes Dev. 33<\/b>, 1619\u20131634 (2019).<\/p>\n

    Article<\/a>\u00a0
    \n     CAS<\/a>\u00a0
    \n     PubMed<\/a>\u00a0
    \n     PubMed Central<\/a>\u00a0
    \n
    \n Google Scholar<\/a>\u00a0\n <\/p>\n<\/li>\n

  • \n

    Stortz, M., Presman, D. M. & Levi, V. Transcriptional condensates: a blessing or a curse for gene regulation? Commun. Biol. 7<\/b>, 187 (2024).<\/p>\n

    Article<\/a>\u00a0
    \n     PubMed<\/a>\u00a0
    \n     PubMed Central<\/a>\u00a0
    \n
    \n Google Scholar<\/a>\u00a0\n <\/p>\n<\/li>\n

  • \n

    Trojanowski, J. et al. Transcription activation is enhanced by multivalent interactions independent of phase separation. Mol. Cell 82<\/b>, 1878\u20131893.e10 (2022). This study shows that assembly of transcription factors into liquid-like droplets has a neutral or even inhibitory effect on transcriptional activation.<\/b><\/p>\n

    Article<\/a>\u00a0
    \n     CAS<\/a>\u00a0
    \n     PubMed<\/a>\u00a0
    \n
    \n Google Scholar<\/a>\u00a0\n <\/p>\n<\/li>\n

  • \n

    Chong, S. et al. Tuning levels of low-complexity domain interactions to modulate endogenous oncogenic transcription. Mol. Cell 82<\/b>, 2084\u20132097.e5 (2022). This study shows that increasing intrinsically disordered region (IDR)\u2013IDR interactions of an oncogenic transcription factor to induce phase separation results in the repression of transcription of its endogenous target genes.<\/b><\/p>\n

    Article<\/a>\u00a0
    \n     CAS<\/a>\u00a0
    \n     PubMed<\/a>\u00a0
    \n
    \n Google Scholar<\/a>\u00a0\n <\/p>\n<\/li>\n

  • \n

    Meeussen, J. V. W. et al. Transcription factor clusters enable target search but do not contribute to target gene activation. Nucleic Acids Res. 51<\/b>, 5449\u20135468 (2023).<\/p>\n

    Article<\/a>\u00a0
    \n     CAS<\/a>\u00a0
    \n     PubMed<\/a>\u00a0
    \n     PubMed Central<\/a>\u00a0
    \n
    \n Google Scholar<\/a>\u00a0\n <\/p>\n<\/li>\n

  • \n

    Yang, J. et al. MYC phase separation selectively modulates the transcriptome. Nat. Struct. Mol. Biol. 31<\/b>, 1567\u20131579 (2024).<\/p>\n

    Article<\/a>\u00a0
    \n     CAS<\/a>\u00a0
    \n     PubMed<\/a>\u00a0
    \n     PubMed Central<\/a>\u00a0
    \n
    \n Google Scholar<\/a>\u00a0\n <\/p>\n<\/li>\n

  • \n

    Liu, W. et al. Pcf11\/Spt5 condensates stall RNA polymerase II to facilitate termination and piRNA-guided heterochromatin formation. Mol. Cell 85<\/b>, 929\u2013947.e10 (2025). This paper presents an example of a transcription-related condensate that acts to repress RNA polymerase II activity and promote local heterochromatinization.<\/b><\/p>\n

    Article<\/a>\u00a0
    \n     CAS<\/a>\u00a0
    \n     PubMed<\/a>\u00a0
    \n
    \n Google Scholar<\/a>\u00a0\n <\/p>\n<\/li>\n

  • \n

    Lim, B. & Levine, M. S. Enhancer\u2013promoter communication: hubs or loops? Curr. Opin. Genet. Dev. 67<\/b>, 5\u20139 (2021).<\/p>\n

    Article<\/a>\u00a0
    \n     CAS<\/a>\u00a0
    \n     PubMed<\/a>\u00a0
    \n
    \n Google Scholar<\/a>\u00a0\n <\/p>\n<\/li>\n

  • \n

    Henninger, J. E. & Young, R. A. An RNA-centric view of transcription and genome organization. Mol. Cell 84<\/b>, 3627\u20133643 (2024).<\/p>\n

    Article<\/a>\u00a0
    \n     CAS<\/a>\u00a0
    \n     PubMed<\/a>\u00a0
    \n
    \n Google Scholar<\/a>\u00a0\n <\/p>\n<\/li>\n

  • \n

    Ugolini, M. et al. Transcription bodies regulate gene expression by sequestering CDK9. Nat. Cell Biol. 26<\/b>, 604\u2013612 (2024).<\/p>\n

    Article<\/a>\u00a0
    \n     CAS<\/a>\u00a0
    \n     PubMed<\/a>\u00a0
    \n     PubMed Central<\/a>\u00a0
    \n
    \n Google Scholar<\/a>\u00a0\n <\/p>\n<\/li>\n

  • \n

    Demmerle, J., Hao, S. & Cai, D. Transcriptional condensates and phase separation: condensing information across scales and mechanisms. Nucleus 14<\/b>, 2213551 (2023).<\/p>\n

    Article<\/a>\u00a0
    \n     PubMed<\/a>\u00a0
    \n     PubMed Central<\/a>\u00a0
    \n
    \n Google Scholar<\/a>\u00a0\n <\/p>\n<\/li>\n

  • \n

    Forero-Quintero, L. S. et al. Live-cell imaging reveals the spatiotemporal organization of endogenous RNA polymerase II phosphorylation at a single gene. Nat. Commun. 12<\/b>, 3158 (2021).<\/p>\n

    Article<\/a>\u00a0
    \n     CAS<\/a>\u00a0
    \n     PubMed<\/a>\u00a0
    \n     PubMed Central<\/a>\u00a0
    \n
    \n Google Scholar<\/a>\u00a0\n <\/p>\n<\/li>\n

  • \n

    Cisse, I. I. et al. Real-time dynamics of RNA polymerase II clustering in live human cells. Science 341<\/b>, 664\u2013667 (2013).<\/p>\n

    Article<\/a>\u00a0
    \n     CAS<\/a>\u00a0
    \n     PubMed<\/a>\u00a0
    \n
    \n Google Scholar<\/a>\u00a0\n <\/p>\n<\/li>\n

  • \n

    Zhao, Z. W. et al. Spatial organization of RNA polymerase II inside a mammalian cell nucleus revealed by reflected light-sheet superresolution microscopy. Proc. Natl Acad. Sci. USA 111<\/b>, 681\u2013686 (2014).<\/p>\n

    Article<\/a>\u00a0
    \n     CAS<\/a>\u00a0
    \n     PubMed<\/a>\u00a0
    \n
    \n Google Scholar<\/a>\u00a0\n <\/p>\n<\/li>\n

  • \n

    Erdel, F. & Rippe, K. Formation of chromatin subcompartments by phase separation. Biophys. J. 114<\/b>, 2262\u20132270 (2018).<\/p>\n

    Article<\/a>\u00a0
    \n     CAS<\/a>\u00a0
    \n     PubMed<\/a>\u00a0
    \n     PubMed Central<\/a>\u00a0
    \n
    \n Google Scholar<\/a>\u00a0\n <\/p>\n<\/li>\n

  • \n

    Muzzopappa, F. et al. Detecting and quantifying liquid\u2013liquid phase separation in living cells by model-free calibrated half-bleaching. Nat. Commun. 13<\/b>, 7787 (2022).<\/p>\n

    Article<\/a>\u00a0
    \n     CAS<\/a>\u00a0
    \n     PubMed<\/a>\u00a0
    \n     PubMed Central<\/a>\u00a0
    \n
    \n Google Scholar<\/a>\u00a0\n <\/p>\n<\/li>\n

  • \n

    Jackson, D. A., Iborra, F. J., Manders, E. M. & Cook, P. R. Numbers and organization of RNA polymerases, nascent transcripts, and transcription units in HeLa nuclei. Mol. Biol. Cell 9<\/b>, 1523\u20131536 (1998).<\/p>\n

    Article<\/a>\u00a0
    \n     CAS<\/a>\u00a0
    \n     PubMed<\/a>\u00a0
    \n     PubMed Central<\/a>\u00a0
    \n
    \n Google Scholar<\/a>\u00a0\n <\/p>\n<\/li>\n

  • \n

    Eskiw, C. H., Rapp, A., Carter, D. R. & Cook, P. R. RNA polymerase II activity is located on the surface of protein-rich transcription factories. J. Cell Sci. 121<\/b>, 1999\u20132007 (2008).<\/p>\n

    Article<\/a>\u00a0
    \n     CAS<\/a>\u00a0
    \n     PubMed<\/a>\u00a0
    \n
    \n Google Scholar<\/a>\u00a0\n <\/p>\n<\/li>\n

  • \n

    Pei, G., Lyons, H., Li, P. & Sabari, B. R. Transcription regulation by biomolecular condensates. Nat. Rev. Mol. Cell Biol. 26<\/b>, 213\u2013236 (2025).<\/p>\n

    Article<\/a>\u00a0
    \n     CAS<\/a>\u00a0
    \n     PubMed<\/a>\u00a0
    \n
    \n Google Scholar<\/a>\u00a0\n <\/p>\n<\/li>\n

  • \n

    Chen, H. et al. Dynamic interplay between enhancer\u2013promoter topology and gene activity. Nat. Genet. 50<\/b>, 1296\u20131303 (2018).<\/p>\n

    Article<\/a>\u00a0
    \n     CAS<\/a>\u00a0
    \n     PubMed<\/a>\u00a0
    \n     PubMed Central<\/a>\u00a0
    \n
    \n Google Scholar<\/a>\u00a0\n <\/p>\n<\/li>\n

  • \n

    Cho, W. K. et al. Mediator and RNA polymerase II clusters associate in transcription-dependent condensates. Science 361<\/b>, 412\u2013415 (2018).<\/p>\n

    Article<\/a>\u00a0
    \n     CAS<\/a>\u00a0
    \n     PubMed<\/a>\u00a0
    \n     PubMed Central<\/a>\u00a0
    \n
    \n Google Scholar<\/a>\u00a0\n <\/p>\n<\/li>\n

  • \n

    Faro-Trindade, I. & Cook, P. R. A conserved organization of transcription during embryonic stem cell differentiation and in cells with high C value. Mol. Biol. Cell 17<\/b>, 2910\u20132920 (2006).<\/p>\n

    Article<\/a>\u00a0
    \n     CAS<\/a>\u00a0
    \n     PubMed<\/a>\u00a0
    \n     PubMed Central<\/a>\u00a0
    \n
    \n Google Scholar<\/a>\u00a0\n <\/p>\n<\/li>\n

  • \n

    Pombo, A. et al. Regional specialization in human nuclei: visualization of discrete sites of transcription by RNA polymerase III. EMBO J. 18<\/b>, 2241\u20132253 (1999).<\/p>\n

    Article<\/a>\u00a0
    \n     CAS<\/a>\u00a0
    \n     PubMed<\/a>\u00a0
    \n     PubMed Central<\/a>\u00a0
    \n
    \n Google Scholar<\/a>\u00a0\n <\/p>\n<\/li>\n

  • \n

    Eskiw, C. H. & Fraser, P. Ultrastructural study of transcription factories in mouse erythroblasts. J. Cell Sci. 124<\/b>, 3676\u20133683 (2011).<\/p>\n

    Article<\/a>\u00a0
    \n     CAS<\/a>\u00a0
    \n     PubMed<\/a>\u00a0
    \n     PubMed Central<\/a>\u00a0
    \n
    \n Google Scholar<\/a>\u00a0\n <\/p>\n<\/li>\n

  • \n

    Papantonis, A. et al. TNFalpha signals through specialized factories where responsive coding and miRNA genes are transcribed. EMBO J. 31<\/b>, 4404\u20134414 (2012).<\/p>\n

    Article<\/a>\u00a0
    \n     CAS<\/a>\u00a0
    \n     PubMed<\/a>\u00a0
    \n     PubMed Central<\/a>\u00a0
    \n
    \n Google Scholar<\/a>\u00a0\n <\/p>\n<\/li>\n

  • \n

    Brown, J. M. et al. Association between active genes occurs at nuclear speckles and is modulated by chromatin environment. J. Cell Biol. 182<\/b>, 1083\u20131097 (2008).<\/p>\n

    Article<\/a>\u00a0
    \n     CAS<\/a>\u00a0
    \n     PubMed<\/a>\u00a0
    \n     PubMed Central<\/a>\u00a0
    \n
    \n Google Scholar<\/a>\u00a0\n <\/p>\n<\/li>\n

  • \n

    Schede, H. H., Natarajan, P., Chakraborty, A. K. & Shrinivas, K. A model for organization and regulation of nuclear condensates by gene activity. Nat. Commun. 14<\/b>, 4152 (2023).<\/p>\n

    Article<\/a>\u00a0
    \n     CAS<\/a>\u00a0
    \n     PubMed<\/a>\u00a0
    \n     PubMed Central<\/a>\u00a0
    \n
    \n Google Scholar<\/a>\u00a0\n <\/p>\n<\/li>\n

  • \n

    Cook, P. R. The organization of replication and transcription. Science 284<\/b>, 1790\u20131795 (1999).<\/p>\n

    Article<\/a>\u00a0
    \n     CAS<\/a>\u00a0
    \n     PubMed<\/a>\u00a0
    \n
    \n Google Scholar<\/a>\u00a0\n <\/p>\n<\/li>\n

  • \n

    Kuznetsova, K. et al. Nanog organizes transcription bodies. Curr. Biol. 33<\/b>, 164\u2013173.e5 (2023).<\/p>\n

    Article<\/a>\u00a0
    \n     CAS<\/a>\u00a0
    \n     PubMed<\/a>\u00a0
    \n
    \n Google Scholar<\/a>\u00a0\n <\/p>\n<\/li>\n

  • \n

    Melnik, S. et al. The proteomes of transcription factories containing RNA polymerases I, II or III. Nat. Methods 8<\/b>, 963\u2013968 (2011). Biochemical isolation and characterization of distinct RNA polymerase I-, II- and III-associated supramolecular complexes with distinct and specialized compositions.<\/b><\/p>\n

    Article<\/a>\u00a0
    \n     CAS<\/a>\u00a0
    \n     PubMed<\/a>\u00a0
    \n     PubMed Central<\/a>\u00a0
    \n
    \n Google Scholar<\/a>\u00a0\n <\/p>\n<\/li>\n

  • \n

    Caudron-Herger, M., Cook, P. R., Rippe, K. & Papantonis, A. Dissecting the nascent human transcriptome by analysing the RNA content of transcription factories. Nucleic Acids Res. 43<\/b>, e95 (2015).<\/p>\n

    Article<\/a>\u00a0
    \n     PubMed<\/a>\u00a0
    \n     PubMed Central<\/a>\u00a0
    \n
    \n Google Scholar<\/a>\u00a0\n <\/p>\n<\/li>\n

  • \n

    Sabari, B. R., Hyman, A. A. & Hnisz, D. Functional specificity in biomolecular condensates revealed by genetic complementation. Nat. Rev. Genet. 26<\/b>, 279\u2013290 (2025).<\/p>\n

    Article<\/a>\u00a0
    \n     CAS<\/a>\u00a0
    \n     PubMed<\/a>\u00a0
    \n
    \n Google Scholar<\/a>\u00a0\n <\/p>\n<\/li>\n

  • \n

    Lee, C. et al. Light-induced targeting enables proteomics on endogenous condensates. Cell 187<\/b>, 7079\u20137090.e17 (2024). This paper presents a method for light-induced targeting of endogenous condensates that enables cataloguing of their protein composition.<\/b><\/p>\n

    Article<\/a>\u00a0
    \n     CAS<\/a>\u00a0
    \n     PubMed<\/a>\u00a0
    \n
    \n Google Scholar<\/a>\u00a0\n <\/p>\n<\/li>\n

  • \n

    Huang, S. K., Whitney, P. H., Dutta, S., Shvartsman, S. Y. & Rushlow, C. A. Spatial organization of transcribing loci during early genome activation in Drosophila. Curr. Biol. 31<\/b>, 5102\u20135110.e5 (2021).<\/p>\n

    Article<\/a>\u00a0
    \n     CAS<\/a>\u00a0
    \n     PubMed<\/a>\u00a0
    \n     PubMed Central<\/a>\u00a0
    \n
    \n Google Scholar<\/a>\u00a0\n <\/p>\n<\/li>\n

  • \n

    White, A. E. et al. Drosophila histone locus bodies form by hierarchical recruitment of components. J. Cell Biol. 193<\/b>, 677\u2013694 (2011).<\/p>\n

    Article<\/a>\u00a0
    \n     CAS<\/a>\u00a0
    \n     PubMed<\/a>\u00a0
    \n     PubMed Central<\/a>\u00a0
    \n
    \n Google Scholar<\/a>\u00a0\n <\/p>\n<\/li>\n

  • \n

    Kemp, J. P. Jr, Yang, X. C., Dominski, Z., Marzluff, W. F. & Duronio, R. J. Superresolution light microscopy of the Drosophila histone locus body reveals a core\u2013shell organization associated with expression of replication-dependent histone genes. Mol. Biol. Cell 32<\/b>, 942\u2013955 (2021).<\/p>\n

    Article<\/a>\u00a0
    \n     CAS<\/a>\u00a0
    \n     PubMed<\/a>\u00a0
    \n     PubMed Central<\/a>\u00a0
    \n
    \n Google Scholar<\/a>\u00a0\n <\/p>\n<\/li>\n

  • \n

    Pancholi, A. et al. RNA polymerase II clusters form in line with surface condensation on regulatory chromatin. Mol. Syst. Biol. 17<\/b>, e10272 (2021). This study used super-resolution imaging of RNA polymerase II clusters in zebrafish embryos to reveal polymorphic compartments with transcribed chromatin located around a protein-rich and DNA-depleted core.<\/b><\/p>\n

    Article<\/a>\u00a0
    \n     CAS<\/a>\u00a0
    \n     PubMed<\/a>\u00a0
    \n     PubMed Central<\/a>\u00a0
    \n
    \n Google Scholar<\/a>\u00a0\n <\/p>\n<\/li>\n

  • \n

    Castells-Garcia, A. et al. Super resolution microscopy reveals how elongating RNA polymerase II and nascent RNA interact with nucleosome clutches. Nucleic Acids Res. 50<\/b>, 175\u2013190 (2022).<\/p>\n

    Article<\/a>\u00a0
    \n     CAS<\/a>\u00a0
    \n     PubMed<\/a>\u00a0
    \n
    \n Google Scholar<\/a>\u00a0\n <\/p>\n<\/li>\n

  • \n

    Hilbert, L. et al. Transcription organizes euchromatin via microphase separation. Nat. Commun. 12<\/b>, 1360 (2021).<\/p>\n

    Article<\/a>\u00a0
    \n     CAS<\/a>\u00a0
    \n     PubMed<\/a>\u00a0
    \n     PubMed Central<\/a>\u00a0
    \n
    \n Google Scholar<\/a>\u00a0\n <\/p>\n<\/li>\n

  • \n

    Zhang, S., Ubelmesser, N., Barbieri, M. & Papantonis, A. Enhancer\u2013promoter contact formation requires RNAPII and antagonizes loop extrusion. Nat. Genet. 55<\/b>, 832\u2013840 (2023). A study establishing that RNA polymerase II is essential for enhancer\u2013promoter looping via high-resolution 3D genomics.<\/b><\/p>\n

    Article<\/a>\u00a0
    \n     CAS<\/a>\u00a0
    \n     PubMed<\/a>\u00a0
    \n
    \n Google Scholar<\/a>\u00a0\n <\/p>\n<\/li>\n

  • \n

    Yang, J. H. & Hansen, A. S. Enhancer selectivity in space and time: from enhancer\u2013promoter interactions to promoter activation. Nat. Rev. Mol. Cell Biol. 25<\/b>, 574\u2013591 (2024).<\/p>\n

    Article<\/a>\u00a0
    \n     CAS<\/a>\u00a0
    \n     PubMed<\/a>\u00a0
    \n     PubMed Central<\/a>\u00a0
    \n
    \n Google Scholar<\/a>\u00a0\n <\/p>\n<\/li>\n

  • \n

    Nagashima, R. et al. Single nucleosome imaging reveals loose genome chromatin networks via active RNA polymerase II. J. Cell Biol. 218<\/b>, 1511\u20131530 (2019).<\/p>\n

    Article<\/a>\u00a0
    \n     CAS<\/a>\u00a0
    \n     PubMed<\/a>\u00a0
    \n     PubMed Central<\/a>\u00a0
    \n
    \n Google Scholar<\/a>\u00a0\n <\/p>\n<\/li>\n

  • \n

    Kimura, H., Sugaya, K. & Cook, P. R. The transcription cycle of RNA polymerase II in living cells. J. Cell Biol. 159<\/b>, 777\u2013782 (2002).<\/p>\n

    Article<\/a>\u00a0
    \n     CAS<\/a>\u00a0
    \n     PubMed<\/a>\u00a0
    \n     PubMed Central<\/a>\u00a0
    \n
    \n Google Scholar<\/a>\u00a0\n <\/p>\n<\/li>\n

  • \n

    Ghamari, A. et al. In vivo live imaging of RNA polymerase II transcription factories in primary cells. Genes Dev. 27<\/b>, 767\u2013777 (2013).<\/p>\n

    Article<\/a>\u00a0
    \n     CAS<\/a>\u00a0
    \n     PubMed<\/a>\u00a0
    \n     PubMed Central<\/a>\u00a0
    \n
    \n Google Scholar<\/a>\u00a0\n <\/p>\n<\/li>\n

  • \n

    Chen, X. et al. Study of RNA polymerase II clustering inside live-cell nuclei using Bayesian nanoscopy. ACS Nano 10<\/b>, 2447\u20132454 (2016).<\/p>\n

    Article<\/a>\u00a0
    \n     CAS<\/a>\u00a0
    \n     PubMed<\/a>\u00a0
    \n
    \n Google Scholar<\/a>\u00a0\n <\/p>\n<\/li>\n

  • \n

    Cho, W. K. et al. RNA polymerase II cluster dynamics predict mRNA output in living cells. eLife 5<\/b>, e13617 (2016).<\/p>\n

    Article<\/a>\u00a0
    \n     PubMed<\/a>\u00a0
    \n     PubMed Central<\/a>\u00a0
    \n
    \n Google Scholar<\/a>\u00a0\n <\/p>\n<\/li>\n

  • \n

    Cho, W. K. et al. Super-resolution imaging of fluorescently labeled, endogenous RNA polymerase II in living cells with CRISPR\/Cas9-mediated gene editing. Sci. Rep. 6<\/b>, 35949 (2016).<\/p>\n

    Article<\/a>\u00a0
    \n     CAS<\/a>\u00a0
    \n     PubMed<\/a>\u00a0
    \n     PubMed Central<\/a>\u00a0
    \n
    \n Google Scholar<\/a>\u00a0\n <\/p>\n<\/li>\n

  • \n

    Basu, S. et al. Unblending of transcriptional condensates in human repeat expansion disease. Cell 181<\/b>, 1062\u20131079.e30 (2020). This study found that >20 inherited human disorders are associated with changes in the potential of cell-type-specific transcription factors to form condensates and regulate gene expression.<\/b><\/p>\n

    Article<\/a>\u00a0
    \n     CAS<\/a>\u00a0
    \n     PubMed<\/a>\u00a0
    \n     PubMed Central<\/a>\u00a0
    \n
    \n Google Scholar<\/a>\u00a0\n <\/p>\n<\/li>\n

  • \n

    Lyons, H. et al. Functional partitioning of transcriptional regulators by patterned charge blocks. Cell 186<\/b>, 327\u2013345.e28 (2023). This study shows MED1-intrinsically disordered region (IDR) condensates selectively partitioning RNA polymerase II with positive regulators for gene activation dependent on patterned charge blocks within their IDRs.<\/b><\/p>\n

    Article<\/a>\u00a0
    \n     CAS<\/a>\u00a0
    \n     PubMed<\/a>\u00a0
    \n     PubMed Central<\/a>\u00a0
    \n
    \n Google Scholar<\/a>\u00a0\n <\/p>\n<\/li>\n

  • \n

    De La Cruz, N. et al. Disorder-mediated interactions target proteins to specific condensates. Mol. Cell 84<\/b>, 3497\u20133512.e9 (2024).<\/p>\n

    Article<\/a>\u00a0
    \n     PubMed<\/a>\u00a0
    \n
    \n Google Scholar<\/a>\u00a0\n <\/p>\n<\/li>\n

  • \n

    Henninger, J. E. et al. RNA-mediated feedback control of transcriptional condensates. Cell 184<\/b>, 207\u2013225.e24 (2021).<\/p>\n

    Article<\/a>\u00a0
    \n     CAS<\/a>\u00a0
    \n     PubMed<\/a>\u00a0
    \n
    \n Google Scholar<\/a>\u00a0\n <\/p>\n<\/li>\n

  • \n

    Quinodoz, S. A. et al. RNA promotes the formation of spatial compartments in the nucleus. Cell 184<\/b>, 5775\u20135790.e30 (2021).<\/p>\n

    Article<\/a>\u00a0
    \n     CAS<\/a>\u00a0
    \n     PubMed<\/a>\u00a0
    \n     PubMed Central<\/a>\u00a0
    \n
    \n Google Scholar<\/a>\u00a0\n <\/p>\n<\/li>\n

  • \n

    Asimi, V. et al. Hijacking of transcriptional condensates by endogenous retroviruses. Nat. Genet. 54<\/b>, 1238\u20131247 (2022).<\/p>\n

    Article<\/a>\u00a0
    \n     CAS<\/a>\u00a0
    \n     PubMed<\/a>\u00a0
    \n     PubMed Central<\/a>\u00a0
    \n
    \n Google Scholar<\/a>\u00a0\n <\/p>\n<\/li>\n

  • \n

    Hur, W. et al. CDK-regulated phase separation seeded by histone genes ensures precise growth and function of histone locus bodies. Dev. Cell 54<\/b>, 379\u2013394.e6 (2020).<\/p>\n

    Article<\/a>\u00a0
    \n     CAS<\/a>\u00a0
    \n     PubMed<\/a>\u00a0
    \n     PubMed Central<\/a>\u00a0
    \n
    \n Google Scholar<\/a>\u00a0\n <\/p>\n<\/li>\n

  • \n

    Chowdhary, S., Kainth, A. S., Paracha, S., Gross, D. S. & Pincus, D. Inducible transcriptional condensates drive 3D genome reorganization in the heat shock response. Mol. Cell 82<\/b>, 4386\u20134399.e7 (2022).<\/p>\n

    Article<\/a>\u00a0
    \n     CAS<\/a>\u00a0
    \n     PubMed<\/a>\u00a0
    \n     PubMed Central<\/a>\u00a0
    \n
    \n Google Scholar<\/a>\u00a0\n <\/p>\n<\/li>\n

  • \n

    Marenduzzo, D., Finan, K. & Cook, P. R. The depletion attraction: an underappreciated force driving cellular organization. J. Cell Biol. 175<\/b>, 681\u2013686 (2006).<\/p>\n

    Article<\/a>\u00a0
    \n     CAS<\/a>\u00a0
    \n     PubMed<\/a>\u00a0
    \n     PubMed Central<\/a>\u00a0
    \n
    \n Google Scholar<\/a>\u00a0\n <\/p>\n<\/li>\n

  • \n

    Shin, Y. et al. Liquid nuclear condensates mechanically sense and restructure the genome. Cell 175<\/b>, 1481\u20131491.e13 (2018).<\/p>\n

    Article<\/a>\u00a0
    \n     CAS<\/a>\u00a0
    \n     PubMed<\/a>\u00a0
    \n     PubMed Central<\/a>\u00a0
    \n
    \n Google Scholar<\/a>\u00a0\n <\/p>\n<\/li>\n

  • \n

    Strom, A. R. et al. Condensate interfacial forces reposition DNA loci and probe chromatin viscoelasticity. Cell 187<\/b>, 5282\u20135297.e20 (2024). Together with Shin et al. (2018), this paper shows inducible condensates are used to exert forces on targeted genomic loci and modulate their spatiotemporal interactions, with chromatin behaving like a viscoelastic entity.<\/b><\/p>\n

    Article<\/a>\u00a0
    \n     CAS<\/a>\u00a0
    \n     PubMed<\/a>\u00a0
    \n
    \n Google Scholar<\/a>\u00a0\n <\/p>\n<\/li>\n

  • \n

    Cai, D. et al. Phase separation of YAP reorganizes genome topology for long-term YAP target gene expression. Nat. Cell Biol. 21<\/b>, 1578\u20131589 (2019). This study shows that that foci of the endogenous or overexpressed YAZ co-activator recruit RNA polymerase II several minutes after they initially form on chromatin.<\/b><\/p>\n

    Article<\/a>\u00a0
    \n     CAS<\/a>\u00a0
    \n     PubMed<\/a>\u00a0
    \n     PubMed Central<\/a>\u00a0
    \n
    \n Google Scholar<\/a>\u00a0\n <\/p>\n<\/li>\n

  • \n

    Morin, J. A. et al. Sequence-dependent surface condensation of a pioneer transcription factor on DNA. Nat. Phys. 18<\/b>, 271\u2013276 (2022).<\/p>\n

    Article<\/a>\u00a0
    \n     CAS<\/a>\u00a0
    \n
    \n Google Scholar<\/a>\u00a0\n <\/p>\n<\/li>\n

  • \n

    Lewis, B. A., Das, S. K., Jha, R. K. & Levens, D. Self-assembly of promoter DNA and RNA Pol II machinery into transcriptionally active biomolecular condensates. Sci. Adv. 9<\/b>, eadi4565 (2023).<\/p>\n

    Article<\/a>\u00a0
    \n     CAS<\/a>\u00a0
    \n     PubMed<\/a>\u00a0
    \n     PubMed Central<\/a>\u00a0
    \n
    \n Google Scholar<\/a>\u00a0\n <\/p>\n<\/li>\n

  • \n

    Koreski, K. P. et al. Drosophila histone locus body assembly and function involves multiple interactions. Mol. Biol. Cell 31<\/b>, 1525\u20131537 (2020).<\/p>\n

    Article<\/a>\u00a0
    \n     CAS<\/a>\u00a0
    \n     PubMed<\/a>\u00a0
    \n     PubMed Central<\/a>\u00a0
    \n
    \n Google Scholar<\/a>\u00a0\n <\/p>\n<\/li>\n

  • \n

    Larkin, J. D., Papantonis, A., Cook, P. R. & Marenduzzo, D. Space exploration by the promoter of a long human gene during one transcription cycle. Nucleic Acids Res. 41<\/b>, 2216\u20132227 (2013).<\/p>\n

    Article<\/a>\u00a0
    \n     CAS<\/a>\u00a0
    \n     PubMed<\/a>\u00a0
    \n     PubMed Central<\/a>\u00a0
    \n
    \n Google Scholar<\/a>\u00a0\n <\/p>\n<\/li>\n

  • \n

    Du, M. et al. Direct observation of a condensate effect on super-enhancer controlled gene bursting. Cell 187<\/b>, 331\u2013344.e17 (2024).<\/p>\n

    Article<\/a>\u00a0
    \n     CAS<\/a>\u00a0
    \n     PubMed<\/a>\u00a0
    \n
    \n Google Scholar<\/a>\u00a0\n <\/p>\n<\/li>\n

  • \n

    Mazzocca, M., Fillot, T., Loffreda, A., Gnani, D. & Mazza, D. The needle and the haystack: single molecule tracking to probe the transcription factor search in eukaryotes. Biochem. Soc. Trans. 49<\/b>, 1121\u20131132 (2021).<\/p>\n

    Article<\/a>\u00a0
    \n     CAS<\/a>\u00a0
    \n     PubMed<\/a>\u00a0
    \n     PubMed Central<\/a>\u00a0
    \n
    \n Google Scholar<\/a>\u00a0\n <\/p>\n<\/li>\n

  • \n

    Jana, T., Brodsky, S. & Barkai, N. Speed-specificity trade-offs in the transcription factors search for their genomic binding sites. Trends Genet. 37<\/b>, 421\u2013432 (2021).<\/p>\n

    Article<\/a>\u00a0
    \n     CAS<\/a>\u00a0
    \n     PubMed<\/a>\u00a0
    \n
    \n Google Scholar<\/a>\u00a0\n <\/p>\n<\/li>\n

  • \n

    Wei, M. et al. Nuclear actin regulates inducible transcription by enhancing RNA polymerase II clustering. Sci. Adv. 6<\/b>, eaay6515 (2020).<\/p>\n

    Article<\/a>\u00a0
    \n     CAS<\/a>\u00a0
    \n     PubMed<\/a>\u00a0
    \n     PubMed Central<\/a>\u00a0
    \n
    \n Google Scholar<\/a>\u00a0\n <\/p>\n<\/li>\n

  • \n

    Langstein-Skora, I. et al. Sequence and chemical specificity define the functional landscape of intrinsically disordered regions. Preprint at bioRxiv https:\/\/doi.org\/10.1101\/2022.02.10.480018<\/a> (2024).<\/p>\n<\/li>\n

  • \n

    Chen, L. et al. Hormone-induced enhancer assembly requires an optimal level of hormone receptor multivalent interactions. Mol. Cell 83<\/b>, 3438\u20133456.e12 (2023).<\/p>\n

    Article<\/a>\u00a0
    \n     CAS<\/a>\u00a0
    \n     PubMed<\/a>\u00a0
    \n     PubMed Central<\/a>\u00a0
    \n
    \n Google Scholar<\/a>\u00a0\n <\/p>\n<\/li>\n

  • \n

    Strom, A. R. et al. Interplay of condensation and chromatin binding underlies BRD4 targeting. Mol. Biol. Cell 35<\/b>, ar88 (2024).<\/p>\n

    Article<\/a>\u00a0
    \n     CAS<\/a>\u00a0
    \n     PubMed<\/a>\u00a0
    \n     PubMed Central<\/a>\u00a0
    \n
    \n Google Scholar<\/a>\u00a0\n <\/p>\n<\/li>\n

  • \n

    Yan, K. et al. SGF29 nuclear condensates reinforce cellular aging. Cell Discov. 9<\/b>, 110 (2023).<\/p>\n

    Article<\/a>\u00a0
    \n     CAS<\/a>\u00a0
    \n     PubMed<\/a>\u00a0
    \n     PubMed Central<\/a>\u00a0
    \n
    \n Google Scholar<\/a>\u00a0\n <\/p>\n<\/li>\n

  • \n

    Trofimov, K. et al. FER-like iron deficiency-induced transcription factor (FIT) accumulates in nuclear condensates. J. Cell Biol. 223<\/b>, e202311048 (2024).<\/p>\n

    Article<\/a>\u00a0
    \n     CAS<\/a>\u00a0
    \n     PubMed<\/a>\u00a0
    \n     PubMed Central<\/a>\u00a0
    \n
    \n Google Scholar<\/a>\u00a0\n <\/p>\n<\/li>\n

  • \n

    Zamudio, A. V. et al. Mediator condensates localize signaling factors to key cell identity genes. Mol. Cell 76<\/b>, 753\u2013766.e6 (2019).<\/p>\n

    Article<\/a>\u00a0
    \n     CAS<\/a>\u00a0
    \n     PubMed<\/a>\u00a0
    \n     PubMed Central<\/a>\u00a0
    \n
    \n Google Scholar<\/a>\u00a0\n <\/p>\n<\/li>\n

  • \n

    Hsin, J. P., Sheth, A. & Manley, J. L. RNAP II CTD phosphorylated on threonine-4 is required for histone mRNA 3\u2032 end processing. Science 334<\/b>, 683\u2013686 (2011).<\/p>\n

    Article<\/a>\u00a0
    \n     CAS<\/a>\u00a0
    \n     PubMed<\/a>\u00a0
    \n     PubMed Central<\/a>\u00a0
    \n
    \n Google Scholar<\/a>\u00a0\n <\/p>\n<\/li>\n

  • \n

    Papantonis, A. & Oudelaar, A. M. Mechanisms of enhancer-mediated gene activation in the context of the 3D genome. Annu. Rev. Genomics Hum. Genet. https:\/\/doi.org\/10.1146\/annurev-genom-120423-012301<\/a> (2025).<\/p>\n<\/li>\n

  • \n

    Seufert, I., Vargas, C., Wille, S. J. & Rippe, K. Deregulated enhancer\u2013promoter communication in cancer through altered nuclear architecture. Int. J. Cancer https:\/\/doi.org\/10.1002\/ijc.35424<\/a> (2025).<\/p>\n<\/li>\n

  • \n

    Karr, J. P., Ferrie, J. J., Tjian, R. & Darzacq, X. The transcription factor activity gradient (TAG) model: contemplating a contact-independent mechanism for enhancer\u2013promoter communication. Genes Dev. 36<\/b>, 7\u201316 (2022).<\/p>\n

    Article<\/a>\u00a0
    \n     CAS<\/a>\u00a0
    \n     PubMed<\/a>\u00a0
    \n     PubMed Central<\/a>\u00a0
    \n
    \n Google Scholar<\/a>\u00a0\n <\/p>\n<\/li>\n

  • \n

    Jiang, Y. et al. Genome-wide analyses of chromatin interactions after the loss of Pol I, Pol II, and Pol III. Genome Biol. 21<\/b>, 158 (2020).<\/p>\n

    Article<\/a>\u00a0
    \n     CAS<\/a>\u00a0
    \n     PubMed<\/a>\u00a0
    \n     PubMed Central<\/a>\u00a0
    \n
    \n Google Scholar<\/a>\u00a0\n <\/p>\n<\/li>\n

  • \n

    El Khattabi, L. et al. A pliable mediator acts as a functional rather than an architectural bridge between promoters and enhancers. Cell 178<\/b>, 1145\u20131158.e20 (2019).<\/p>\n

    Article<\/a>\u00a0
    \n     CAS<\/a>\u00a0
    \n     PubMed<\/a>\u00a0
    \n
    \n Google Scholar<\/a>\u00a0\n <\/p>\n<\/li>\n

  • \n

    Sun, F. et al. The Pol II preinitiation complex (PIC) influences mediator binding but not promoter\u2013enhancer looping. Genes Dev. 35<\/b>, 1175\u20131189 (2021).<\/p>\n

    Article<\/a>\u00a0
    \n     PubMed<\/a>\u00a0
    \n     PubMed Central<\/a>\u00a0
    \n
    \n Google Scholar<\/a>\u00a0\n <\/p>\n<\/li>\n

  • \n

    Hsieh, T. S. et al. Resolving the 3D landscape of transcription-linked mammalian chromatin folding. Mol. Cell 78<\/b>, 539\u2013553.e8 (2020).<\/p>\n

    Article<\/a>\u00a0
    \n     CAS<\/a>\u00a0
    \n     PubMed<\/a>\u00a0
    \n     PubMed Central<\/a>\u00a0
    \n
    \n Google Scholar<\/a>\u00a0\n <\/p>\n<\/li>\n

  • \n

    Hug, C. B., Grimaldi, A. G., Kruse, K. & Vaquerizas, J. M. Chromatin architecture emerges during zygotic genome activation independent of transcription. Cell 169<\/b>, 216\u2013228.e19 (2017).<\/p>\n

    Article<\/a>\u00a0
    \n     CAS<\/a>\u00a0
    \n     PubMed<\/a>\u00a0
    \n
    \n Google Scholar<\/a>\u00a0\n <\/p>\n<\/li>\n

  • \n

    Rowley, M. J. et al. Evolutionarily conserved principles predict 3D chromatin organization. Mol. Cell 67<\/b>, 837\u2013852.e7 (2017).<\/p>\n

    Article<\/a>\u00a0
    \n     CAS<\/a>\u00a0
    \n     PubMed<\/a>\u00a0
    \n     PubMed Central<\/a>\u00a0
    \n
    \n Google Scholar<\/a>\u00a0\n <\/p>\n<\/li>\n

  • \n

    Chahar, S. et al. Transcription induces context-dependent remodeling of chromatin architecture during differentiation. PLoS Biol. 21<\/b>, e3002424 (2023).<\/p>\n

    Article<\/a>\u00a0
    \n     CAS<\/a>\u00a0
    \n     PubMed<\/a>\u00a0
    \n     PubMed Central<\/a>\u00a0
    \n
    \n Google Scholar<\/a>\u00a0\n <\/p>\n<\/li>\n

  • \n

    Hoencamp, C. & Rowland, B. D. Genome control by SMC complexes. Nat. Rev. Mol. Cell Biol. 24<\/b>, 633\u2013650 (2023).<\/p>\n

    Article<\/a>\u00a0
    \n     CAS<\/a>\u00a0
    \n     PubMed<\/a>\u00a0
    \n
    \n Google Scholar<\/a>\u00a0\n <\/p>\n<\/li>\n

  • \n

    Rao, S. S. P. et al. Cohesin loss eliminates all loop domains. Cell 171<\/b>, 305\u2013320.e24 (2017).<\/p>\n

    Article<\/a>\u00a0
    \n     CAS<\/a>\u00a0
    \n     PubMed<\/a>\u00a0
    \n     PubMed Central<\/a>\u00a0
    \n
    \n Google Scholar<\/a>\u00a0\n <\/p>\n<\/li>\n

  • \n

    Aljahani, A. et al. Analysis of sub-kilobase chromatin topology reveals nano-scale regulatory interactions with variable dependence on cohesin and CTCF. Nat. Commun. 13<\/b>, 2139 (2022).<\/p>\n

    Article<\/a>\u00a0
    \n     CAS<\/a>\u00a0
    \n     PubMed<\/a>\u00a0
    \n     PubMed Central<\/a>\u00a0
    \n
    \n Google Scholar<\/a>\u00a0\n <\/p>\n<\/li>\n

  • \n

    Goronzy, I. N. et al. Simultaneous mapping of 3D structure and nascent RNAs argues against nuclear compartments that preclude transcription. Cell Rep. 41<\/b>, 111730 (2022).<\/p>\n

    Article<\/a>\u00a0
    \n     CAS<\/a>\u00a0
    \n     PubMed<\/a>\u00a0
    \n     PubMed Central<\/a>\u00a0
    \n
    \n Google Scholar<\/a>\u00a0\n <\/p>\n<\/li>\n

  • \n

    Beagrie, R. A. et al. Complex multi-enhancer contacts captured by genome architecture mapping. Nature 543<\/b>, 519\u2013524 (2017).<\/p>\n

    Article<\/a>\u00a0
    \n     CAS<\/a>\u00a0
    \n     PubMed<\/a>\u00a0
    \n     PubMed Central<\/a>\u00a0
    \n
    \n Google Scholar<\/a>\u00a0\n <\/p>\n<\/li>\n

  • \n

    Ramasamy, S. et al. The Mediator complex regulates enhancer\u2013promoter interactions. Nat. Struct. Mol. Biol. 30<\/b>, 991\u20131000 (2023).<\/p>\n

    Article<\/a>\u00a0
    \n     CAS<\/a>\u00a0
    \n     PubMed<\/a>\u00a0
    \n     PubMed Central<\/a>\u00a0
    \n
    \n Google Scholar<\/a>\u00a0\n <\/p>\n<\/li>\n

  • \n

    Penagos-Puig, A. et al. RNA polymerase II pausing regulates chromatin organization in erythrocytes. Nat. Struct. Mol. Biol. 30<\/b>, 1092\u20131104 (2023).<\/p>\n

    Article<\/a>\u00a0
    \n     CAS<\/a>\u00a0
    \n     PubMed<\/a>\u00a0
    \n
    \n Google Scholar<\/a>\u00a0\n <\/p>\n<\/li>\n

  • \n

    Papantonis, A. et al. Active RNA polymerases: mobile or immobile molecular machines? PLoS Biol. 8<\/b>, e1000419 (2010).<\/p>\n

    Article<\/a>\u00a0
    \n     PubMed<\/a>\u00a0
    \n     PubMed Central<\/a>\u00a0
    \n
    \n Google Scholar<\/a>\u00a0\n <\/p>\n<\/li>\n

  • \n

    Heist, T., Fukaya, T. & Levine, M. Large distances separate coregulated genes in living Drosophila embryos. Proc. Natl Acad. Sci. USA 116<\/b>, 15062\u201315067 (2019).<\/p>\n

    Article<\/a>\u00a0
    \n     CAS<\/a>\u00a0
    \n     PubMed<\/a>\u00a0
    \n     PubMed Central<\/a>\u00a0
    \n
    \n Google Scholar<\/a>\u00a0\n <\/p>\n<\/li>\n

  • \n

    Benabdallah, N. S. et al. Decreased enhancer\u2013promoter proximity accompanying enhancer activation. Mol. Cell 76<\/b>, 473\u2013484.e7 (2019).<\/p>\n

    Article<\/a>\u00a0
    \n     CAS<\/a>\u00a0
    \n     PubMed<\/a>\u00a0
    \n     PubMed Central<\/a>\u00a0
    \n
    \n Google Scholar<\/a>\u00a0\n <\/p>\n<\/li>\n

  • \n

    Alexander, J. M. et al. Live-cell imaging reveals enhancer-dependent Sox2 transcription in the absence of enhancer proximity. eLife 8<\/b>, e41769 (2019).<\/p>\n

    Article<\/a>\u00a0
    \n     PubMed<\/a>\u00a0
    \n     PubMed Central<\/a>\u00a0
    \n
    \n Google Scholar<\/a>\u00a0\n <\/p>\n<\/li>\n

  • \n

    Cheng, L., De, C., Li, J. & Pertsinidis, A. Mechanisms of transcription control by distal enhancers from high-resolution single-gene imaging. Preprint at bioRxiv https:\/\/doi.org\/10.1101\/2023.03.19.533190<\/a> (2023).<\/p>\n<\/li>\n

  • \n

    Kim, Y. J. et al. Light-activated macromolecular phase separation modulates transcription by reconfiguring chromatin interactions. Sci. Adv. 9<\/b>, eadg1123 (2023).<\/p>\n

    Article<\/a>\u00a0
    \n     CAS<\/a>\u00a0
    \n     PubMed<\/a>\u00a0
    \n     PubMed Central<\/a>\u00a0
    \n
    \n Google Scholar<\/a>\u00a0\n <\/p>\n<\/li>\n

  • \n

    Wang, W. et al. A histidine cluster determines YY1-compartmentalized coactivators and chromatin elements in phase-separated enhancer clusters. Nucleic Acids Res. 50<\/b>, 4917\u20134937 (2022).<\/p>\n

    Article<\/a>\u00a0
    \n     CAS<\/a>\u00a0
    \n     PubMed<\/a>\u00a0
    \n     PubMed Central<\/a>\u00a0
    \n
    \n Google Scholar<\/a>\u00a0\n <\/p>\n<\/li>\n

  • \n

    Lu, H. et al. Phase-separation mechanism for C-terminal hyperphosphorylation of RNA polymerase II. Nature 558<\/b>, 318\u2013323 (2018).<\/p>\n

    Article<\/a>\u00a0
    \n     CAS<\/a>\u00a0
    \n     PubMed<\/a>\u00a0
    \n     PubMed Central<\/a>\u00a0
    \n
    \n Google Scholar<\/a>\u00a0\n <\/p>\n<\/li>\n

  • \n

    Uchino, S. et al. Live imaging of transcription sites using an elongating RNA polymerase II-specific probe. J. Cell Biol. 221<\/b>, e202104134 (2022).<\/p>\n

    Article<\/a>\u00a0
    \n     CAS<\/a>\u00a0
    \n     PubMed<\/a>\u00a0
    \n
    \n Google Scholar<\/a>\u00a0\n <\/p>\n<\/li>\n

  • \n

    Lee, R. et al. CTCF-mediated chromatin looping provides a topological framework for the formation of phase-separated transcriptional condensates. Nucleic Acids Res. 50<\/b>, 207\u2013226 (2022).<\/p>\n

    Article<\/a>\u00a0
    \n     CAS<\/a>\u00a0
    \n     PubMed<\/a>\u00a0
    \n
    \n Google Scholar<\/a>\u00a0\n <\/p>\n<\/li>\n

  • \n

    Darzacq, X. et al. In vivo dynamics of RNA polymerase II transcription. Nat. Struct. Mol. Biol. 14<\/b>, 796\u2013806 (2007).<\/p>\n

    Article<\/a>\u00a0
    \n     CAS<\/a>\u00a0
    \n     PubMed<\/a>\u00a0
    \n     PubMed Central<\/a>\u00a0
    \n
    \n Google Scholar<\/a>\u00a0\n <\/p>\n<\/li>\n

  • \n

    Leidescher, S. et al. Spatial organization of transcribed eukaryotic genes. Nat. Cell Biol. 24<\/b>, 327\u2013339 (2022).<\/p>\n

    Article<\/a>\u00a0
    \n     CAS<\/a>\u00a0
    \n     PubMed<\/a>\u00a0
    \n     PubMed Central<\/a>\u00a0
    \n
    \n Google Scholar<\/a>\u00a0\n <\/p>\n<\/li>\n

  • \n

    Espinola, S. M. et al. Cis-regulatory chromatin loops arise before TADs and gene activation, and are independent of cell fate during early Drosophila development. Nat. Genet. 53<\/b>, 477\u2013486 (2021).<\/p>\n

    Article<\/a>\u00a0
    \n     CAS<\/a>\u00a0
    \n     PubMed<\/a>\u00a0
    \n
    \n Google Scholar<\/a>\u00a0\n <\/p>\n<\/li>\n

  • \n

    Ladouceur, A. M. et al. Clusters of bacterial RNA polymerase are biomolecular condensates that assemble through liquid\u2013liquid phase separation. Proc. Natl Acad. Sci. USA 117<\/b>, 18540\u201318549 (2020).<\/p>\n

    Article<\/a>\u00a0
    \n     CAS<\/a>\u00a0
    \n     PubMed<\/a>\u00a0
    \n     PubMed Central<\/a>\u00a0
    \n
    \n Google Scholar<\/a>\u00a0\n <\/p>\n<\/li>\n

  • \n

    de Laat, W. & Grosveld, F. Spatial organization of gene expression: the active chromatin hub. Chr. Res. 11<\/b>, 447\u2013459 (2003).<\/p>\n

    Article<\/a>\u00a0
    \n
    \n Google Scholar<\/a>\u00a0\n <\/p>\n<\/li>\n

  • \n

    Chong, S. et al. Imaging dynamic and selective low-complexity domain interactions that control gene transcription. Science 361<\/b>, eaar2555-17 (2018). This study observed transcriptionally active transcription factor assemblies and intrinsically disordered region-mediated interactions at physiological concentrations at endogenous chromosomal loci in the absence of phase separation.<\/b><\/p>\n

    Article<\/a>\u00a0
    \n     PubMed<\/a>\u00a0
    \n     PubMed Central<\/a>\u00a0
    \n
    \n Google Scholar<\/a>\u00a0\n <\/p>\n<\/li>\n

  • \n

    Dufourt, J. et al. Temporal control of gene expression by the pioneer factor Zelda through transient interactions in hubs. Nat. Commun. 9<\/b>, 5194 (2018).<\/p>\n

    Article<\/a>\u00a0
    \n     PubMed<\/a>\u00a0
    \n     PubMed Central<\/a>\u00a0
    \n
    \n Google Scholar<\/a>\u00a0\n <\/p>\n<\/li>\n

  • \n

    Fallacaro, S. et al. A fine kinetic balance of interactions directs transcription factor hubs to genes. Preprint at bioRxiv https:\/\/doi.org\/10.1101\/2024.04.16.589811<\/a> (2024).<\/p>\n<\/li>\n

  • \n

    Duronio, R. J. & Marzluff, W. F. Coordinating cell cycle-regulated histone gene expression through assembly and function of the histone locus body. RNA Biol. 14<\/b>, 726\u2013738 (2017).<\/p>\n

    Article<\/a>\u00a0
    \n     PubMed<\/a>\u00a0
    \n     PubMed Central<\/a>\u00a0
    \n
    \n Google Scholar<\/a>\u00a0\n <\/p>\n<\/li>\n

  • \n

    Christopher, J. A. et al. Subcellular proteomics. Nat. Rev. Methods Primers\u00a01<\/b>, 32 (2021).<\/p>\n

    Article<\/a>\u00a0
    \n     CAS<\/a>\u00a0
    \n     PubMed<\/a>\u00a0
    \n     PubMed Central<\/a>\u00a0
    \n
    \n Google Scholar<\/a>\u00a0\n <\/p>\n<\/li>\n

  • \n

    Zhou, Y. et al. RNA damage compartmentalization by DHX9 stress granules. Cell 187<\/b>, 1701\u20131718.e28 (2024).<\/p>\n

    Article<\/a>\u00a0
    \n     CAS<\/a>\u00a0
    \n     PubMed<\/a>\u00a0
    \n
    \n Google Scholar<\/a>\u00a0\n <\/p>\n<\/li>\n

  • \n

    Kar, M. et al. Solutes unmask differences in clustering versus phase separation of FET proteins. Nat. Commun. 15<\/b>, 4408 (2024).<\/p>\n

    Article<\/a>\u00a0
    \n     CAS<\/a>\u00a0
    \n     PubMed<\/a>\u00a0
    \n     PubMed Central<\/a>\u00a0
    \n
    \n Google Scholar<\/a>\u00a0\n <\/p>\n<\/li>\n

  • \n

    Mittag, T. & Pappu, R. V. A conceptual framework for understanding phase separation and addressing open questions and challenges. Mol. Cell 82<\/b>, 2201\u20132214 (2022).<\/p>\n

    Article<\/a>\u00a0
    \n     CAS<\/a>\u00a0
    \n     PubMed<\/a>\u00a0
    \n     PubMed Central<\/a>\u00a0
    \n
    \n Google Scholar<\/a>\u00a0\n <\/p>\n<\/li>\n

  • \n

    Holehouse, A. S. & Alberti, S. Molecular determinants of condensate composition. Mol. Cell 85<\/b>, 290\u2013308 (2025).<\/p>\n

    Article<\/a>\u00a0
    \n     CAS<\/a>\u00a0
    \n     PubMed<\/a>\u00a0
    \n
    \n Google Scholar<\/a>\u00a0\n <\/p>\n<\/li>\n

  • \n

    Jia, L., Gao, S. & Qiao, Y. Optical control over liquid\u2013liquid phase separation. Small Methods 8<\/b>, e2301724 (2024).<\/p>\n

    Article<\/a>\u00a0
    \n     PubMed<\/a>\u00a0
    \n
    \n Google Scholar<\/a>\u00a0\n <\/p>\n<\/li>\n

  • \n

    Erdel, F. et al. Mouse heterochromatin adopts digital compaction states without showing hallmarks of HP1-driven liquid\u2013liquid phase separation. Mol. Cell 78<\/b>, 236\u2013249.e7 (2020).<\/p>\n

    Article<\/a>\u00a0
    \n     CAS<\/a>\u00a0
    \n     PubMed<\/a>\u00a0
    \n     PubMed Central<\/a>\u00a0
    \n
    \n Google Scholar<\/a>\u00a0\n <\/p>\n<\/li>\n

  • \n

    Michieletto, D. & Marenda, M. Rheology and viscoelasticity of proteins and nucleic acids condensates. JACS Au 2<\/b>, 1506\u20131521 (2022).<\/p>\n

    Article<\/a>\u00a0
    \n     CAS<\/a>\u00a0
    \n     PubMed<\/a>\u00a0
    \n     PubMed Central<\/a>\u00a0
    \n
    \n Google Scholar<\/a>\u00a0\n <\/p>\n<\/li>\n

  • \n

    Conte, M. et al. Loop-extrusion and polymer phase-separation can co-exist at the single-molecule level to shape chromatin folding. Nat. Commun. 13<\/b>, 4070 (2022).<\/p>\n

    Article<\/a>\u00a0
    \n     CAS<\/a>\u00a0
    \n     PubMed<\/a>\u00a0
    \n     PubMed Central<\/a>\u00a0
    \n
    \n Google Scholar<\/a>\u00a0\n <\/p>\n<\/li>\n

  • \n

    Park, J., Kim, J. J. & Ryu, J. K. Mechanism of phase condensation for chromosome architecture and function. Exp. Mol. Med. 56<\/b>, 809\u2013819 (2024).<\/p>\n

    Article<\/a>\u00a0
    \n     CAS<\/a>\u00a0
    \n     PubMed<\/a>\u00a0
    \n     PubMed Central<\/a>\u00a0
    \n
    \n Google Scholar<\/a>\u00a0\n <\/p>\n<\/li>\n","protected":false},"excerpt":{"rendered":"Baum, M., Erdel, F., Wachsmuth, M. & Rippe, K. Retrieving the intracellular topology from multi-scale protein mobility mapping…\n","protected":false},"author":2,"featured_media":197480,"comment_status":"","ping_status":"","sticky":false,"template":"","format":"standard","meta":{"footnotes":""},"categories":[3846],"tags":[3971,3973,3967,3970,71089,3972,3968,267,3969,80107,70,16,15],"class_list":{"0":"post-197479","1":"post","2":"type-post","3":"status-publish","4":"format-standard","5":"has-post-thumbnail","7":"category-genetics","8":"tag-agriculture","9":"tag-animal-genetics-and-genomics","10":"tag-biomedicine","11":"tag-cancer-research","12":"tag-chromosomes","13":"tag-gene-function","14":"tag-general","15":"tag-genetics","16":"tag-human-genetics","17":"tag-nuclear-organization","18":"tag-science","19":"tag-uk","20":"tag-united-kingdom"},"share_on_mastodon":{"url":"https:\/\/pubeurope.com\/@uk\/114710793245845230","error":""},"_links":{"self":[{"href":"https:\/\/www.europesays.com\/uk\/wp-json\/wp\/v2\/posts\/197479","targetHints":{"allow":["GET"]}}],"collection":[{"href":"https:\/\/www.europesays.com\/uk\/wp-json\/wp\/v2\/posts"}],"about":[{"href":"https:\/\/www.europesays.com\/uk\/wp-json\/wp\/v2\/types\/post"}],"author":[{"embeddable":true,"href":"https:\/\/www.europesays.com\/uk\/wp-json\/wp\/v2\/users\/2"}],"replies":[{"embeddable":true,"href":"https:\/\/www.europesays.com\/uk\/wp-json\/wp\/v2\/comments?post=197479"}],"version-history":[{"count":0,"href":"https:\/\/www.europesays.com\/uk\/wp-json\/wp\/v2\/posts\/197479\/revisions"}],"wp:featuredmedia":[{"embeddable":true,"href":"https:\/\/www.europesays.com\/uk\/wp-json\/wp\/v2\/media\/197480"}],"wp:attachment":[{"href":"https:\/\/www.europesays.com\/uk\/wp-json\/wp\/v2\/media?parent=197479"}],"wp:term":[{"taxonomy":"category","embeddable":true,"href":"https:\/\/www.europesays.com\/uk\/wp-json\/wp\/v2\/categories?post=197479"},{"taxonomy":"post_tag","embeddable":true,"href":"https:\/\/www.europesays.com\/uk\/wp-json\/wp\/v2\/tags?post=197479"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}