Single-Molecule Imaging of the Phase Separation-Modulated DNA Compaction to Study Transcriptional Repression

  • Protocol
  • First Online:
Phase-Separated Biomolecular Condensates

Part of the book series: Methods in Molecular Biology ((MIMB,volume 2563))

  • 2857 Accesses

Abstract

Liquid-liquid phase separation (LLPS) often induces the formation of biomolecule condensates at the cellular level. The importance of this phenomenon has been demonstrated in many important biological functions, such as in transcription. However, the biophysical nature of LLPS containing transcriptional machinery has not yet been carefully examined. Here, we give an overview of a novel high-throughput single-molecule technique, termed as DNA Curtains. It was established recently to dissect the DNA compaction process in real time. The experimental procedures are further discussed in detail in the context of the biomolecular condensates of a transcription repressor.

This is a preview of subscription content, log in via an institution to check access.

Access this chapter

Subscribe and save

Springer+ Basic
EUR 32.99 /Month
  • Get 10 units per month
  • Download Article/Chapter or Ebook
  • 1 Unit = 1 Article or 1 Chapter
  • Cancel anytime
Subscribe now

Buy Now

Protocol
USD 49.95
Price excludes VAT (Brazil)
  • Available as PDF
  • Read on any device
  • Instant download
  • Own it forever
eBook
USD 89.00
Price excludes VAT (Brazil)
  • Available as EPUB and PDF
  • Read on any device
  • Instant download
  • Own it forever
Softcover Book
USD 119.99
Price excludes VAT (Brazil)
  • Compact, lightweight edition
  • Dispatched in 3 to 5 business days
  • Free ship** worldwide - see info
Hardcover Book
USD 169.99
Price excludes VAT (Brazil)
  • Durable hardcover edition
  • Dispatched in 3 to 5 business days
  • Free ship** worldwide - see info

Tax calculation will be finalised at checkout

Purchases are for personal use only

Institutional subscriptions

Similar content being viewed by others

References

  1. Hnisz D, Shrinivas K, Young RA, Chakraborty AK, Sharp PA (2017) A phase separation model for transcriptional control. Cell 169(1):13–23. https://doi.org/10.1016/j.cell.2017.02.007

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  2. Banani SF, Lee HO, Hyman AA, Rosen MK (2017) Biomolecular condensates: organizers of cellular biochemistry. Nat Rev Mol Cell Biol 18(5):285–298. https://doi.org/10.1038/nrm.2017.7

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  3. Berry J, Brangwynne CP, Haataja M (2018) Physical principles of intracellular organization via active and passive phase transitions. Rep Prog Phys 80(4):ARTN 046601. https://doi.org/10.1088/1361-6633/aaa61e

    Article  CAS  Google Scholar 

  4. Brangwynne CP, Eckmann CR, Courson DS, Rybarska A, Hoege C, Gharakhani J, Julicher F, Hyman AA (2009) Germline P granules are liquid droplets that localize by controlled dissolution/condensation. Science 324(5935):1729–1732. https://doi.org/10.1126/science.1172046

    Article  CAS  PubMed  Google Scholar 

  5. Boeynaems S, Alberti S, Fawzi NL, Mittag T, Polymenidou M, Rousseau F, Schymkowitz J, Shorter J, Wolozin B, Van den Bosch L, Tompa P, Fuxreiter M (2018) Protein phase separation: a new phase in cell biology. Trends Cell Biol 28(6):420–435. https://doi.org/10.1016/j.tcb.2018.02.004

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  6. Uversky VN (2017) Intrinsically disordered proteins in overcrowded milieu: membrane-less organelles, phase separation, and intrinsic disorder. Curr Opin Struct Biol 44:18–30. https://doi.org/10.1016/j.sbi.2016.10.015

    Article  CAS  PubMed  Google Scholar 

  7. Li PL, Banjade S, Cheng HC, Kim S, Chen B, Guo L, Llaguno M, Hollingsworth JV, King DS, Banani SF, Russo PS, Jiang QX, Nixon BT, Rosen MK (2012) Phase transitions in the assembly of multivalent signalling proteins. Nature 483(7389):336–U129. https://doi.org/10.1038/nature10879

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  8. Greene EC, Wind S, Fazio T, Gorman J, Visnapuu ML (2010) DNA curtains for high-throughput single-molecule optical imaging. In: Walter NG (ed) Methods in enzymology, Vol 472: single molecule tools, Pt a: fluorescence based approaches, vol 472. Methods in enzymology. Elsevier Academic Press Inc, San Diego, pp 293–315. https://doi.org/10.1016/s0076-6879(10)72006-1

    Chapter  Google Scholar 

  9. Zhao YL, Jiang YZ, Qi Z (2017) Visualizing biological reaction intermediates with DNA curtains. J Phys D-Appl Phys 50(15):16. https://doi.org/10.1088/1361-6463/aa59cf

    Article  CAS  Google Scholar 

  10. Zuo L, Zhang G, Massett M, Cheng J, Guo Z, Wang L, Gao Y, Li R, Huang X, Li P, Qi Z (2021) Loci-specific phase separation of FET fusion oncoproteins promotes gene transcription. Nat Commun 12(1):1491. https://doi.org/10.1038/s41467-021-21690-7

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  11. Zhou H, Song Z, Zhong S, Zuo L, Qi Z, Qu L-J, Lai L (2019) Mechanism of DNA-induced phase separation for transcriptional repressor VRN1. Angew Chem Int Ed Engl 58(15):4858–4862. https://doi.org/10.1002/anie.201810373

    Article  CAS  PubMed  Google Scholar 

  12. Larson AG, Elnatan D, Keenen MM, Trnka MJ, Ohnston JBJ, Burlingame AL, Agard DA, Redding S, Narlikar GJ (2017) Liquid droplet formation by HP1 alpha suggests a role for phase separation in heterochromatin. Nature 547(7662):236–23+. https://doi.org/10.1038/nature22822

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  13. Strom AR, Emelyanov AV, Mir M, Fyodorov DV, Darzacq X, Karpen GH (2017) Phase separation drives heterochromatin domain formation. Nature 547(7662):241–24+. https://doi.org/10.1038/nature22989

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  14. Collins BE, Ye LF, Duzdevich D, Greene EC (2014) DNA curtains: novel tools for imaging protein-nucleic acid interactions at the single-molecule level. Methods Cell Biol 123:217–234. https://doi.org/10.1016/B978-0-12-420138-5.00012-4

    Article  PubMed  Google Scholar 

Download references

Acknowledgments

We thank Dr. Xu Huang (University of Glasgow) for comments and edits on our manuscript. This work was supported in part by National Natural Science Foundation of China (No. 31670762 (Z.Q.) and 21633001 (L.L.)).

Author information

Authors and Affiliations

Authors

Corresponding authors

Correspondence to Luhua Lai or Zhi Qi .

Editor information

Editors and Affiliations

Rights and permissions

Reprints and permissions

Copyright information

© 2023 The Author(s), under exclusive license to Springer Science+Business Media, LLC, part of Springer Nature

About this protocol

Check for updates. Verify currency and authenticity via CrossMark

Cite this protocol

Zuo, L., Lai, L., Qi, Z. (2023). Single-Molecule Imaging of the Phase Separation-Modulated DNA Compaction to Study Transcriptional Repression. In: Zhou, HX., Spille, JH., Banerjee, P.R. (eds) Phase-Separated Biomolecular Condensates. Methods in Molecular Biology, vol 2563. Humana, New York, NY. https://doi.org/10.1007/978-1-0716-2663-4_10

Download citation

  • DOI: https://doi.org/10.1007/978-1-0716-2663-4_10

  • Published:

  • Publisher Name: Humana, New York, NY

  • Print ISBN: 978-1-0716-2662-7

  • Online ISBN: 978-1-0716-2663-4

  • eBook Packages: Springer Protocols

Publish with us

Policies and ethics

Navigation