Co-condensation of proteins with single- and double-stranded DNA

Renger, Roman; Morín, José A.; Lemaitre, Regis; Ruer, Martine; Jülicher, Frank; Hermann, Andreas; Grill, Stephan W.

doi:10.1073/pnas.2107871119

Cited by 38 publications

(37 citation statements)

References 77 publications

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“…Notably, nucleic-acid–based condensates can be generated by monolayer protein recruitment: a mechanism described by means of the FUS protein is an example ( 57 ). FUS consists of a nucleic-acid–binding domain and a disordered low-complexity domain (LCD) that mediates FUS self-attraction.…”

Section: Rna In Biomolecular Condensatesmentioning

confidence: 99%

“…FUS consists of a nucleic-acid–binding domain and a disordered low-complexity domain (LCD) that mediates FUS self-attraction. Its adsorption on DNA gives rise to a self-interacting protein–nucleic acid polymer that collapses with the formation of FUS-DNA condensates ( 57 ) (see Figure 1A ). FUS condensation with RNA is realized in a similar manner: RNA serves as a multivalent platform, whose length controls the valency of FUS (one FUS unit occupies ∼20−25 nts) ( 58 ).…”

Section: Rna In Biomolecular Condensatesmentioning

confidence: 99%

“… A mechanism for the formation of nucleic-acid-based condensates. ( A ) Monolayer FUS recruitment on DNA ( 57 ). ( B ) FUS interaction with PAR and formation of compartments, concentrating PAR, FUS and damaged DNA ( 5 , 6 , 59 ).…”

Section: Rna In Biomolecular Condensatesmentioning

confidence: 99%

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A sePARate phase? Poly(ADP-ribose) versus RNA in the organization of biomolecular condensates

Alemasova

Lavrik

2022

Nucleic Acids Research

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Condensates are biomolecular assemblies that concentrate biomolecules without the help of membranes. They are morphologically highly versatile and may emerge via distinct mechanisms. Nucleic acids–DNA, RNA and poly(ADP-ribose) (PAR) play special roles in the process of condensate organization. These polymeric scaffolds provide multiple specific and nonspecific interactions during nucleation and ‘development’ of macromolecular assemblages. In this review, we focus on condensates formed with PAR. We discuss to what extent the literature supports the phase separation origin of these structures. Special attention is paid to similarities and differences between PAR and RNA in the process of dynamic restructuring of condensates during their functioning.

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Section: Rna In Biomolecular Condensatesmentioning

confidence: 99%

Section: Rna In Biomolecular Condensatesmentioning

confidence: 99%

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A sePARate phase? Poly(ADP-ribose) versus RNA in the organization of biomolecular condensates

Alemasova

Lavrik

2022

Nucleic Acids Research

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“…For studying chromosome organization in the eukaryotic nucleus or in bacterial cells, numerous studies have been made on live or fixed cells through imaging (Bintu et al, 2018;Ricci et al, 2015), chromosome conformation capture techniques (Brandão et al, 2021;Falk et al, 2019), etc., while in vitro protein-DNA interactions are often characterized at the single-molecule level using techniques such as Atomic Force Microscopy (Dame et al, 2000;Japaridze et al, 2017;Liang et al, 2017), magnetic (Kaczmarczyk et al, 2020;Sun et al, 2013) and optical tweezers (Lin et al, 2021;Renger et al, 2022), and DNA visualization assays (Davidson et al, 2019;Ganji et al, 2018;Golfier et al, 2020;Greene et al;Kim et al, 2019). While these complementary approaches have yielded great insights, they leave a significant gap since typical single-molecule methods address the ~kilobasepair (kbp) scale while actual genomes consist of 10 5 -10 11 bp long DNA.…”

Section: Introductionmentioning

confidence: 99%

Extracting and characterizing protein-free megabasepair DNA for in vitro experiments

Holub

Birnie

Japaridze

et al. 2022

Preprint

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Chromosome structure and function is studied in cells using imaging and chromosome-conformation-based methods as well as in vitro with a range of single-molecule techniques. Here we present a method to obtain genome-size (megabasepair length) deproteinated DNA for in vitro studies, which provides DNA substrates that are two orders of magnitude longer than typically studied in single-molecule experiments. We isolated chromosomes from bacterial cells and enzymatically digested the native proteins. Mass spectrometry indicated that 97-100% of DNA-binding proteins are removed from the sample. Upon protein removal, we observed an increase in the radius of gyration of the DNA polymers, while quantification of the fluorescence intensities showed that the length of the DNA objects remained megabasepair sized. In first proof-of-concept experiments using these deproteinated long DNA molecules, we observed DNA compaction upon adding the DNA-binding protein Fis or PEG crowding agents and showed that it is possible to track the motion of a fluorescently labelled DNA locus. These results indicate the practical feasibility of a "genome-in-a-box" approach to study chromosome organization from the bottom up.

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“…FUS is an intrinsically disordered protein composed of a N-terminal low-complexity domain (LCD) with prion-like sequences, three arginine/glycine/glycine (RGG)-rich regions, a conserved RNA recognition motif (RRM), a zinc finger (ZnF) motif, and a pro-line-tyrosine nuclear localization signal (PY-NLS) at the C terminus [ 4 ]. The LCD, also called the prion-like domain, has been shown to promote FUS self-assembly into higher-order structures, which contributes to either liquid–solid or liquid–liquid phase separation (LSPS or LLPS) of FUS either alone or in combination with other proteins and/or nucleic acids [ 5 , 6 , 7 , 8 , 9 , 10 ].…”

Section: Introductionmentioning

confidence: 99%

FUS Microphase Separation: Regulation by Nucleic Acid Polymers and DNA Repair Proteins

Sukhanova

Anarbaev

Maltseva

et al. 2022

IJMS

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Fused in sarcoma (FUS) is involved in the regulation of RNA and DNA metabolism. FUS participates in the formation of biomolecular condensates driven by phase transition. FUS is prone to self-aggregation and tends to undergo phase transition both with or without nucleic acid polymers. Using dynamic light scattering and fluorescence microscopy, we examined the formation of FUS high-order structures or FUS-rich microphases induced by the presence of RNA, poly(ADP-ribose), ssDNA, or dsDNA and evaluated effects of some nucleic-acid-binding proteins on the phase behavior of FUS–nucleic acid systems. Formation and stability of FUS-rich microphases only partially correlated with FUS’s affinity for a nucleic acid polymer. Some proteins—which directly interact with PAR, RNA, ssDNA, and dsDNA and are possible components of FUS-enriched cellular condensates—disrupted the nucleic-acid-induced assembly of FUS-rich microphases. We found that XRCC1, a DNA repair factor, underwent a microphase separation and formed own microdroplets and coassemblies with FUS in the presence of poly(ADP-ribose). These results probably indicated an important role of nucleic-acid-binding proteins in the regulation of FUS-dependent formation of condensates and imply the possibility of the formation of XRCC1-dependent phase-separated condensates in the cell.

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Co-condensation of proteins with single- and double-stranded DNA

Cited by 38 publications

References 77 publications

A sePARate phase? Poly(ADP-ribose) versus RNA in the organization of biomolecular condensates

A sePARate phase? Poly(ADP-ribose) versus RNA in the organization of biomolecular condensates

Extracting and characterizing protein-free megabasepair DNA for in vitro experiments

FUS Microphase Separation: Regulation by Nucleic Acid Polymers and DNA Repair Proteins

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