Single-Molecule Imaging of EWS-FLI1 Condensates Assembling on DNA
Summary
Here, we describe the use of the single-molecule imaging method, DNA Curtains, to study the biophysical mechanism of EWS-FLI1 condensates assembling on DNA.
Abstract
The fusion genes resulting from chromosomal translocation have been found in many solid tumors or leukemia. EWS-FLI1, which belongs to the FUS/EWS/TAF15 (FET) family of fusion oncoproteins, is one of the most frequently involved fusion genes in Ewing sarcoma. These FET family fusion proteins typically harbor a low-complexity domain (LCD) of FET protein at their N-terminus and a DNA-binding domain (DBD) at their C-terminus. EWS-FLI1 has been confirmed to form biomolecular condensates at its target binding loci due to LCD-LCD and LCD-DBD interactions, and these condensates can recruit RNA polymerase II to enhance gene transcription. However, how these condensates are assembled at their binding sites remains unclear. Recently, a single-molecule biophysics method-DNA Curtains-was applied to visualize these assembling processes of EWS-FLI1 condensates. Here, the detailed experimental protocol and data analysis approaches are discussed for the application of DNA Curtains in studying the biomolecular condensates assembling on target DNA.
Introduction
Transcriptional regulation is a crucial step for precise gene expression in living cells. Many factors, such as chromosomal modification, transcription factors (TFs), and non-coding RNAs, participate in this complicated process1,2,3. Among these factors, TFs contribute to the specificity of transcriptional regulation by recognizing and binding to specific DNA sequences known as promoters or enhancers and subsequently recruiting other functional proteins to activate or repress transcription4,5,6,7. How these TFs manage to search for their target sites in the human genome and interact with DNA coated with histones and non-histone DNA-binding proteins has perplexed scientists for decades. In the past few years, several classical models for the target search mechanism of TFs have been built to describe how they "slide," "hop," "jump," or "intersegment transfer" along the DNA chain8,9,10,11. These models are focused on the searching behavior on the DNA of one single TF molecule. However, recent studies show that some TFs undergo liquid-liquid phase separation (LLPS) either alone in the nucleus or with the Mediator complex12. The observed droplets of TFs are associated with the promoter or enhancer regions, highlighting the role of biomolecular condensate formation in transcription and the three-dimensional genome13,14,15. These biomolecular condensates are linked to membrane-lacking compartments in vivo and in vitro. They are formed via LLPS, in which modular biomacromolecules and intrinsically disordered regions (IDRs) of proteins are two main driving forces of multivalent interactions16. Thus, TFs not only search DNA but also function synergistically within these condensates4,17,18. To date, the biophysical property of these transcription condensates on DNA remains unclear.
Therefore, this study aimed to apply a single-molecule method-DNA Curtains-to directly image the formation and dynamics of the transcription condensates formed by TFs on DNA in vitro. DNA Curtains, a high-throughput in vitro imaging platform to study the interaction between proteins and DNA, has been applied in DNA repair19,20,21, target search22, and LLPS17,23,24. The flowcell of DNA Curtains is coated with biotinylated lipid bilayers to passivate the surface and allow the biomolecules to diffuse on the surface. The nanofabricated zig-zag patterns limit the movement of DNA. Biotinylated Lambda DNA substrates can align along the barrier edges and be stretched by the oriented buffer flow. The same starting and ending sequences of all the molecules allow the tracking of the protein on DNA and describe the position distribution of the binding events25,26. Moreover, the combination of DNA Curtains with total internal reflection fluorescence microscopy (TIRFM) helps minimize the background noise and detect signals at a single-molecule level. Thus, DNA Curtains could be a promising method to investigate the dynamics of transcription condensate formation on DNA motifs. This paper describes the example of an FUS/EWS/TAF15 (FET) family fusion oncoprotein, EWS-FLI1, generated by chromosomal translocation. Lambda DNA containing 25× GGAA-the binding sequence of EWS-FLI127– was used as the DNA substrate in the DNA Curtains experiments to observe how EWS-FLI1 molecules undergo LLPS on DNA. This manuscript discusses the experimental protocol and data analysis methods in detail.
Protocol
Representative Results
Discussion
As single-molecule approaches are extremely sensitive to the contents of the reaction system, extra effort must be invested to ensure good quality of all the materials and solutions during the DNA Curtains experiments, especially the lipids prepared in sections 1 and 2 and the buffers used in section 5. Reagents of higher purity must be used to prepare buffers, and buffers must be freshly prepared for the single-molecule assay
When 500 nM mCherry-labeled EWS-FLI1 was flushed into the chamber, …
Declarações
The authors have nothing to disclose.
Acknowledgements
This work was supported by NSFC Grants No. 31670762 (Z.Q.).
Materials
| 488 nm diodepumped solid-state laser | Coherent | OBIS488LS | |
| 561 nm diodepumped solid-state laser | Coherent | OBIS561LS | |
| Agar | Rhawn | R003215-50g | |
| biotinylated DOPE | Avanti | 870273P | |
| Bovine Serum Albumin | Sigma | A7030 | |
| Chloroform | Amresco | 1595C027 | |
| Coating Electra 92 | Allresist GmbH | AR-PC 5090.02 | The conductive protective coating |
| Deoxyribonuclease I bovine | Sigma | D5139-2MG | |
| DOPC | Avanti | 850375P | |
| DTT | Sigma | D9779 | |
| Glass coverslip | Fisher Scientific | 12-544-7 | |
| Hellmanex III | Sigma | Z805939-1EA | |
| KCl | Sigma | 60130 | |
| Lambda DNA | NEB | N3013S | |
| Lambda Packing Extracts | Epicentre | MP5120 | |
| MgCl2 | Sigma | M2670 | |
| NaCl | Sigma | s3014 | |
| Nanoport | Idex | N-333-01 | |
| NheI-HF | NEB | R3131S | |
| Nikon Inverted Microscope | Nikon | Eclipse Ti | |
| NZCYM Broth | Sigma | N3643-250G | |
| PEG-2000 DOPE | Avanti | 880130P-1G | |
| PEG-8000 | Amresco | 25322-68-3 | |
| PMMA 200K, ETHYL LACTATE 4% | Allresist GmbH | AR-P 649.04 | |
| PMMA 950K, ANISOLE 2% | Allresist GmbH | AR-P 672.02 | |
| Prime 95B Scientific CMOS camera | PHOTOMETRICS | Prime95B | |
| proteinase K | NEB | P8107S | |
| Silica glass slide | G.Finkenbeiner | ||
| Six-way injection valve | Idex | MXP9900-000 | |
| Streptavidin | Thermo | S888 | Diluted with ddH2O |
| Syringe pump | Harvard Apparatus | Pump11 Elite | |
| T4 DNA Ligase | NEB | M0202S | |
| Tris base | Sigma | T6066 | |
| XhoI | NEB | R0146V | |
| YOYO-1 Iodide (491/509) | Invitrogen | Y3601 | Diluted with DMSO |
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