Recent trends in studies of biomolecular phase separation |
Kim, Chan-Geun
(Department of Chemistry, Pusan National University)
Hwang, Da-Eun (Department of Chemistry, Pusan National University) Kumar, Rajeev (Department of Chemistry, Pusan National University) Chung, Min (Department of Chemistry, Pusan National University) Eom, Yu-Gon (Department of Chemistry, Pusan National University) Kim, Hyunji (Department of Chemistry, Pusan National University) Koo, Da-Hyun (Department of Chemistry, Pusan National University) Choi, Jeong-Mo (Department of Chemistry, Pusan National University) |
1 | Jia P, Li X, Wang X et al (2021) ZMYND8 mediated liquid condensates spatiotemporally decommission the latent super-enhancers during macrophage polarization. Nat Commun 12, 6535 |
2 | Banani SF, Lee HO, Hyman AA and Rosen MK (2017) Biomolecular condensates: organizers of cellular biochemistry. Nat Rev Mol Cell Biol 18, 285-298 DOI |
3 | Harmon TS, Holehouse AS, Rosen MK and Pappu RV (2017) Intrinsically disordered linkers determine the interplay between phase separation and gelation in multivalent proteins. eLife 6, e30294 |
4 | Ryu JK, Hwang DE and Choi JM (2021) Current understanding of molecular phase separation in chromosomes. Int J Mol Sci 22, 10736 |
5 | Banani SF, Rice AM, Peeples WB et al (2016) Compositional control of phase-separated cellular bodies. Cell 166, 651-663 DOI |
6 | Banjade S and Rosen MK (2014) Phase transitions of multivalent proteins can promote clustering of membrane receptors. eLife 3, e04123 |
7 | Kroschwald S and Alberti S (2017) Gel or Die: phase separation as a survival strategy. Cell 168, 947-948 DOI |
8 | Sheu-Gruttadauria J and MacRae IJ (2018) Phase transitions in the assembly and function of human miRISC. Cell 173, 946-957.e916 DOI |
9 | Molliex A, Temirov J, Lee J et al (2015) Phase separation by low complexity domains promotes stress granule assembly and drives pathological fibrillization. Cell 163, 123-133 DOI |
10 | Cho WK, Spille JH, Hecht M et al (2018) Mediator and RNA polymerase II clusters associate in transcription-dependent condensates. Science 361, 412-415 DOI |
11 | Boyko S and Surewicz WK (2022) Tau liquid-liquid phase separation in neurodegenerative diseases. Trends Cell Biol 32, 611-623 DOI |
12 | Alberti S and Dormann D (2019) Liquid-liquid phase separation in disease. Ann Rev Genet 53, 171-194 DOI |
13 | Brangwynne Clifford P, Tompa P and Pappu Rohit V (2015) Polymer physics of intracellular phase transitions. Nat Phys 11, 899-904 DOI |
14 | Hyman AA, Weber CA and Julicher F (2014) Liquid-liquid phase separation in biology. Annu Rev Cell Dev Biol 30, 39-58 DOI |
15 | Dolgin E (2018) What lava lamps and vinaigrette can teach us about cell biology. Nature 555, 300-303 DOI |
16 | Wang J, Choi JM, Holehouse AS et al (2018) A molecular grammar governing the driving forces for phase separation of prion-like RNA binding proteins. Cell 174, 688-699.e616 DOI |
17 | Rubinstein M and Semenov AN (1998) Thermoreversible gelation in solutions of associating polymers. 2. Linear dynamics. Macromolecules 31, 1386-1397 DOI |
18 | Huggins ML (1942) Theory of solutions of high polymers1. J Am Chem Soc 64, 1712-1719 DOI |
19 | Wippich F, Bodenmiller B, Trajkovska Maria G, Wanka S, Aebersold R and Pelkmans L (2013) Dual specificity kinase dyrk3 couples stress granule condensation/ dissolution to mTORC1 signaling. Cell 152, 791-805 DOI |
20 | Fujioka Y, Alam JM, Noshiro D et al (2020) Phase separation organizes the site of autophagosome formation. Nature 578, 301-305 DOI |
21 | Abbas M, Lipinski WP, Nakashima KK, Huck WTS and Spruijt E (2021) A short peptide synthon for liquid-liquid phase separation. Nat Chem 13, 1046-1054 DOI |
22 | Scott WA, Gharakhanian EG, Bell AG et al (2021) Active controlled and tunable coacervation using side-chain functional α-helical homopolypeptides. J Am Chem Soc 143, 18196-18203 DOI |
23 | Sato Y and Takinoue M (2022) Capsule-like DNA hydrogels with patterns formed by lateral phase separation of DNA nanostructures. J Am Chem Soc Au 2, 159-168 |
24 | Agarwal A, Rai SK, Avni A and Mukhopadhyay S (2021) An intrinsically disordered pathological prion variant Y145Stop converts into self-seeding amyloids via liquid-liquid phase separation. Proc Natl Acad Sci U S A 118, e2100968118 |
25 | Azaldegui CA, Vecchiarelli AG and Biteen JS (2021) The emergence of phase separation as an organizing principle in bacteria. Biophys J 120, 1123-1138 DOI |
26 | Grese ZR, Bastos AC, Mamede LD, French RL, Miller TM and Ayala YM (2021) Specific RNA interactions promote TDP-43 multivalent phase separation and maintain liquid properties. EMBO Rep 22, e53632 |
27 | Shao W, Bi X, Pan Y et al (2022) Phase separation of RNA-binding protein promotes polymerase binding and transcription. Nat Chem Biol 18, 70-80 DOI |
28 | Li P, Banjade S, Cheng HC et al (2012) Phase transitions in the assembly of multivalent signalling proteins. Nature 483, 336-340 DOI |
29 | Fritsch AW, Diaz-Delgadillo AF, Adame-Arana O et al (2021) Local thermodynamics govern formation and dissolution of Caenorhabditis elegans P granule condensates. Proc Natl Acad Sci U S A 118, e2102772118 |
30 | Hong K, Song D and Jung Y (2020) Behavior control of membrane-less protein liquid condensates with metal ion-induced phase separation. Nat Commun 11, 5554 |
31 | Zbinden A, Perez-Berlanga M, De Rossi P and Polymenidou M (2020) Phase separation and neurodegenerative diseases: a disturbance in the force. Dev Cell 55, 45-68 DOI |
32 | Wang B, Zhang L, Dai T et al (2021) Liquid-liquid phase separation in human health and diseases. Signal Transduct Target Ther 6, 290-290 DOI |
33 | Lednev IK (2014) Amyloid fibrils: the eighth wonder of the world in protein folding and aggregation. Biophys J 106, 1433-1435 DOI |
34 | Bremer A, Farag M, Borcherds WM et al (2022) Deciphering how naturally occurring sequence features impact the phase behaviours of disordered prion-like domains. Nat Chem 14, 196-207 DOI |
35 | Malki A, Teulon J-M, Camacho-Zarco AR et al (2022) Intrinsically disordered tardigrade proteins self-assemble into fibrous gels in response to environmental stress. Angew Chem Int Ed 61, e202109961 |
36 | Shen C, Li R, Negro R et al (2021) Phase separation drives RNA virus-induced activation of the NLRP6 inflammasome. Cell 184, 5759-5774.e5720 DOI |
37 | Bergeron-Sandoval LP, Kumar S, Heris HK et al (2021) Endocytic proteins with prion-like domains form viscoelastic condensates that enable membrane remodeling. Proc Natl Acad Sci U S A 118, e2113789118 |
38 | Perez-Schindler J, Kohl B, Schneider-Heieck K et al (2021) RNA-bound PGC-1α controls gene expression in liquid-like nuclear condensates. Proc Natl Acad Sci U S A 118, e2105951118 |
39 | Shi Y, Chen J, Zeng WJ et al (2021) Formation of nuclear condensates by the mediator complex subunit Med15 in mammalian cells. BMC Biol 19, 245 |
40 | Zhang H, Ji X, Li P et al (2020) Liquid-liquid phase separation in biology: mechanisms, physiological functions and human diseases. Sci China Life Sci 63, 953-985 DOI |
41 | Buchan JR and Parker R (2009) Eukaryotic stress granules: the ins and outs of translation. Mol Cell 36, 932-941 DOI |
42 | Song D, Jo Y, Choi JM and Jung Y (2020) Client proximity enhancement inside cellular membrane-less compartments governed by client-compartment interactions. Nat Commun 11, 1-13 DOI |
43 | Ruff KM, Dar F and Pappu RV (2021) Ligand effects on phase separation of multivalent macromolecules. Proc Natl Acad Sci U S A 118, 10, e2017184118 |
44 | Kim GH and Kwon I (2021) Distinct roles of hnRNPH1 low-complexity domains in splicing and transcription. Proc Natl Acad Sci U S A 118, e2109668118 |
45 | Hallegger M, Chakrabarti AM, Lee FC et al (2021) TDP-43 condensation properties specify its RNA-binding and regulatory repertoire. Cell 184, 4680-4696. e4622 DOI |
46 | Sawner AS, Ray S, Yadav P et al (2021) Modulating α-synuclein liquid-liquid phase separation. Biochemistry 60, 3676-3696 DOI |
47 | Wurtz JD and Lee CF (2018) Chemical-reaction-controlled phase separated drops: formation, size selection, and coarsening. Phys Rev Lett 120, 078102 |
48 | Babl L, Giacomelli G, Ramm B, Gelmroth AK, Bramkamp M and Schwille P (2022) CTP-controlled liquid-liquid phase separation of ParB. J Mol Biol 434, 167401 |
49 | Zhu P, Lister C and Dean C (2021) Cold-induced Arabidopsis FRIGIDA nuclear condensates for FLC repression. Nature 599, 657-661 DOI |
50 | Sun M, Jia M, Ren H et al (2021) NuMA regulates mitotic spindle assembly, structural dynamics and function via phase separation. Nat Commun 12, 7157 |
51 | Hnisz D, Shrinivas K, Young RA, Chakraborty AK and Sharp PA (2017) A phase separation model for transcriptional control. Cell 169, 13-23 DOI |
52 | Palacio M and Taatjes DJ (2022) Merging established mechanisms with new insights: condensates, hubs, and the regulation of rna polymerase II transcription. J Mol Biol 434, 167216 |
53 | Ishiguro A, Lu J, Ozawa D, Nagai Y and Ishihama A (2021) ALS-linked FUS mutations dysregulate G-quadruplex-dependent liquid-liquid phase separation and liquid-to-solid transition. J Biol Chem 297, 101284 |
54 | Qi Y and Zhang B (2021) Chromatin network retards nucleoli coalescence. Nat Commun 12, 6824 |
55 | Lee T, Do S, Lee JG, Kim DN and Shin Y (2021) The flexibility-based modulation of DNA nanostar phase separation. Nanoscale 13, 17638-17647 DOI |
56 | Shin Y and Brangwynne CP (2017) Liquid phase condensation in cell physiology and disease. Science 357, eaaf4382 |
57 | Lee R, Kang MK, Kim YJ et al (2022) CTCF-mediated chromatin looping provides a topological framework for the formation of phase-separated transcriptional condensates. Nucleic Acid Res 50, 207-226 DOI |
58 | Folkmann AW, Putnam A, Lee CF and Seydoux G (2021) Regulation of biomolecular condensates by interfacial protein clusters. Science 373, 1218-1224 DOI |
59 | Liu Q, Li J, Zhang W et al (2021) Glycogen accumulation and phase separation drives liver tumor initiation. Cell 184, 5559-5576.e5519 DOI |
60 | Long Q, Zhou Y, Wu H et al (2021) Phase separation drives the self-assembly of mitochondrial nucleoids for transcriptional modulation. Nat Struct Mol Biol 28, 900-908 DOI |
61 | Feric M, Vaidya N, Harmon TS et al (2016) Coexisting liquid phases underlie nucleolar subcompartments. Cell 165, 1686-1697 DOI |
62 | Riback JA, Katanski CD, Kear-Scott JL et al (2017) Stress-triggered phase separation is an adaptive, evolutionarily tuned response. Cell 168, 1028-1040.e1019 DOI |
63 | Xiao Q, McAtee CK and Su X (2022) Phase separation in immune signalling. Nat Rev Immunol 22, 188-199 DOI |
64 | Nicolas E, Parisot P, Pinto-Monteiro C, de Walque R, De Vleeschouwer C and Lafontaine DLJ (2016) Involvement of human ribosomal proteins in nucleolar structure and p53-dependent nucleolar stress. Nat Commun 7, 11390 |
65 | Wang B, Zhang L, Dai T et al (2021) Liquid-liquid phase separation in human health and diseases. Signal Transduct Target Ther 6, 290 |
66 | Flory PJ (1942) Thermodynamics of high polymer solutions. J Chem Phys 10, 51-61 DOI |
67 | Martin EW, Holehouse AS, Peran I et al (2020) Valence and patterning of aromatic residues determine the phase behavior of prion-like domains. Science 367, 694-699 DOI |
68 | Choi J-M, Hyman AA and Pappu RV (2020) Generalized models for bond percolation transitions of associative polymers. Phys Rev E 102, 042403 |
69 | Paloni M, Bailly R, Ciandrini L and Barducci A (2020) Unraveling molecular interactions in liquid-liquid phase separation of disordered proteins by atomistic simulations. J Phys Chem B 124, 9009-9016 DOI |
70 | Choi J-M, Holehouse AS and Pappu RV (2020) Physical principles underlying the complex biology of intracellular phase transitions. Annu Rev Biophys 49, 107-133 DOI |
71 | Fong K, Li Y, Wang W et al (2013) Whole-genome screening identifies proteins localized to distinct nuclear bodies. J Cell Biol 203, 149-164 DOI |
72 | Rhine K, Vidaurre V and Myong S (2020) RNA droplets. Annu Rev Biophys 49, 247-265 DOI |
73 | Roden C and Gladfelter AS (2021) RNA contributions to the form and function of biomolecular condensates. Nat Rev Mol Cell Biol 22, 183-195 DOI |
74 | Wei MT, Elbaum-Garfinkle S, Holehouse AS et al (2017) Phase behaviour of disordered proteins underlying low density and high permeability of liquid organelles. Nat Chem 9, 1118-1125 DOI |
75 | Le Vay K, Song EY, Ghosh B, Tang TYD and Mutschler H (2021) Enhanced ribozyme-catalyzed recombination and oligonucleotide assembly in peptide-RNA condensates. Angew Chem Int Ed 60, 26096-26104 DOI |
![]() |