Spatially coherent diffusion of human RNA Pol II depends on transcriptional state rather than chromatin motion

References

• Shaban HA, Barth R, Bystricky K. Navigating the crowd: visualizing coordination between genome dynamics, structure, and transcription. Genome Biol. 2020;21(1). DOI:10.1186/s13059-020-02185-y
   Web of Science ®Google Scholar
• van Steensel B, Furlong EEM. The role of transcription in shaping the spatial organization of the genome. Nat Rev Mol Cell Biol. 2019;20(6):327–337.
   Web of Science ®Google Scholar
• Schier AC, Taatjes DJ. Structure and mechanism of the RNA polymerase II transcription machinery. Genes Dev. 2020;34(7-8):465-88.
   Web of Science ®Google Scholar
• Sabari BR, Dall’Agnese A, Boija A, et al. Coactivator condensation at super-enhancers links phase separation and gene control. Science. 2018;361(6400):eaar3958.
   Web of Science ®Google Scholar
• Cho WK, Spille JH, Hecht M, et al. Mediator and RNA polymerase II clusters associate in transcription-dependent condensates. Science. 2018;361:412–415.
   PubMed Web of Science ®Google Scholar
• Pancholi A, Klingberg T, Zhang W, et al. RNA polymerase II clusters form in line with surface condensation on regulatory chromatin. Mol Syst Biol. 2021;17(9):e10272.
   Web of Science ®Google Scholar
• Ghamari A, van de Corput MËPC, Thongjuea S, et al. In vivo live imaging of RNA polymerase II transcription factories in primary cells. Genes Dev. 2013;27(7):767–77.
   Google Scholar
• Rippe K, Papantonis A. RNA polymerase II transcription compartments: from multivalent chromatin binding to liquid droplet formation? Nat Rev Mol Cell Biol. 2021;22(10):645–6.
   Web of Science ®Google Scholar
• Nagashima R, Hibino K, Ashwin SS, et al. Single nucleosome imaging reveals loose genome chromatin networks via active RNA polymerase II. J Cell Biol. 2019;218(5):1511–30.
   Web of Science ®Google Scholar
• Shaban HA, Barth R, Recoules L, et al. Hi-D: nanoscale mapping of nuclear dynamics in single living cells. Genome Biol. 2020;21(1):95.
   PubMed Web of Science ®Google Scholar
• Shaban HA, Seeber A. Monitoring the spatio-temporal organization and dynamics of the genome. Nucleic Acids Res. 2020;48(7):3423–34.
   Web of Science ®Google Scholar
• Li J, Dong A, Saydaminova K, et al. Single-molecule nanoscopy elucidates RNA polymerase II transcription at single genes in live cells. Cell. 2019;178(2):491–506.
   Web of Science ®Google Scholar
• Steurer B, Janssens RC, Geverts B, et al. Live-cell analysis of endogenous GFP-RPB1 uncovers rapid turnover of initiating and promoter-paused RNA Polymerase II. Proc Natl Acad Sci. 2018;115(19):E4368-76.
   Web of Science ®Google Scholar
• Cisse I II, Causse I, Boudarene SZ, et al. Real-time dynamics of RNA polymerase II clustering in live human cells. Science. 2013;341:664–667.
   PubMed Web of Science ®Google Scholar
• Forero-Quintero LS, Raymond W, Handa T, et al. Live-cell imaging reveals the spatiotemporal organization of endogenous RNA polymerase II phosphorylation at a single gene. Nat Commun. 2021;12(1):1–6.
   Web of Science ®Google Scholar
• Cho WK, Jayanth N, English BP, et al. RNA Polymerase II cluster dynamics predict mRNA output in living cells. Elife. 2016;5.
   Web of Science ®Google Scholar
• Castells-Garcia A, Ed-daoui I, González-Almela E, et al. Super resolution microscopy reveals how elongating RNA polymerase II and nascent RNA interact with nucleosome clutches. Nucleic Acids Res. 2022;50:175–190. Internet].;:. Available from.
   PubMed Web of Science ®Google Scholar
• Miron E, Oldenkamp R, Brown JM, et al. Chromatin arranges in chains of mesoscale domains with nanoscale functional topography independent of cohesin. Sci Adv. 2020;6(39):eaba8811.
   Web of Science ®Google Scholar
• Shaban HA, Barth R, Bystricky K. Formation of correlated chromatin domains at nanoscale dynamic resolution during transcription. Nucleic Acids Res. 2018;461;e77–e77.
   PubMedGoogle Scholar
• Agbleke AA, Amitai A, Buenrostro JD, et al. Advances in chromatin and chromosome research: perspectives from multiple fields. Mol Cell. 2020;79(6):881–901.
   Web of Science ®Google Scholar
• Barth R, Fourel G, Shaban HA. Dynamics as a cause for the nanoscale organization of the genome. Nucleus. 2020;11:83–98.
   PubMed Web of Science ®Google Scholar
• Barth R, Bystricky K, Shaban HA. Coupling chromatin structure and dynamics by live super-resolution imaging. Sci Adv. 2020 Jul 1;6(27):eaaz2196.
   Web of Science ®Google Scholar
• Stein ML. Interpolation of spatial data : some theory for kriging. Springer: New York; 1999.
   Google Scholar
• Ray S, Panova T, Miller G, et al. Topoisomerase IIα promotes activation of RNA polymerase I transcription by facilitating pre-initiation complex formation. Nat Commun. 2013;4:1598.
   PubMed Web of Science ®Google Scholar
• Carter DRF, Eskiw C, Cook PR. Transcription factories. Biochem Soc Trans. 2008;39(21):9085–92.
   Google Scholar
• Papantonis A, Cook PR. Transcription factories: genome organization and gene regulation. Chem Rev. 2013;113(11):8683–705.
   Web of Science ®Google Scholar
• Sehgal PB, Darnell JE, Tamm I. The inhibition of DRB (5,6-dichloro-1-β-d-ribofuranosylbenzimidazole) of hnRNA and mRNA production in HeLa cells. Cell. 1976;9(3):473–80.
   Web of Science ®Google Scholar
• Bensaude O. Inhibiting eukaryotic transcription: which compound to choose? How to evaluate its activity? Transcription. 2011;2(3):103–8.
   Google Scholar
• Mitchell JA, Fraser P. Transcription factories are nuclear subcompartments that remain in the absence of transcription. Genes Dev. 2008;22(1):20–5.
   Web of Science ®Google Scholar
• Cho WK, Jayanth N, Mullen S, et al. Super-resolution imaging of fluorescently labeled, endogenous RNA polymerase II in living cells with CRISPR/Cas9-mediated gene editing. Sci Rep. 2016;6(1):1–8.
   Web of Science ®Google Scholar
• Chiang M, Brackley CA, Marenduzzo D, et al. Predicting genome organisation and function with mechanistic modelling. Trends Genet. 2022;38(4):364–378.
   Web of Science ®Google Scholar
• Brackley CA, Taylor S, Papantonis A, et al. Nonspecific bridging-induced attraction drives clustering of DNA-binding proteins and genome organization. Proc Natl Acad Sci. 2013;110:E3605–11.
   PubMed Web of Science ®Google Scholar
• Di Pierro M, Potoyan DA, Wolynes PG, et al. Anomalous diffusion, spatial coherence, and viscoelasticity from the energy landscape of human chromosomes. Proc Natl Acad Sci. 2018;115:7753–7758.
   PubMed Web of Science ®Google Scholar
• Salari H, Di Stefano M, Jost D. Spatial organization of chromosomes leads to heterogeneous chromatin motion and drives the liquid- or gel-like dynamical behavior of chromatin. Genome Res. 2022;32:28–43.
   PubMedGoogle Scholar
• Darzacq X, Shav-Tal Y, de Turris V, et al. In vivo dynamics of RNA polymerase II transcription. Nat Struct Mol Biol. 2007;14:796–806.
   PubMed Web of Science ®Google Scholar
• Wada Y, Ohta Y, Xu M, et al. A wave of nascent transcription on activated human genes. Proc Natl Acad Sci. 2009;106:18357–18361.
   PubMed Web of Science ®Google Scholar
• Leidescher S, Ribisel J, Ullrich S, et al. Spatial organization of transcribed eukaryotic genes. Nat Cell Biol. 2022;24:327–339.
   PubMed Web of Science ®Google Scholar
• Brackley CA, Liebchen B, Michieletto D, et al. Ephemeral protein binding to DNA shapes stable nuclear bodies and chromatin domains. Biophys J. 2017;112(6):1085–93.
   Google Scholar
• Zhang S, Übelmesser N, Josipovic N, et al. RNA polymerase II is required for spatial chromatin reorganization following exit from mitosis. Sci Adv. 2021;7(43):eabg8205.
   Web of Science ®Google Scholar
• Sun D, Roth S, Black MJ. A quantitative analysis of current practices in optical flow estimation and the principles behind them. Int J Comput Vis. 2014;106:115–137.
   Web of Science ®Google Scholar
• Matérn B. Spatial variation. Springer-Verlag: Berlin Heidelberg, Germany; 1986.
   Google Scholar
• Schertzer D, Lovejoy S. Nonlinear variability in geophysics: multifractal simulations and analysis. fractals’ Phys Orig Prop. Boston MA: Springer US; 1989: 49–79.
   Google Scholar