Astyanax mexicanus      Scaffold


※ Scaffold introduction

    Scaffolds were defined as the drivers of LLPS essential for the structural integrity of MLOs, and the major components which, alone or with co-scaffolds, undergo LLPS (1-4). A minimum set of six experimental tests, including the assembly of spherical droplets, the observation of fusion events, and the identification of mutations that abolish or inhibit LLPS in vitro and in cells have been proposed for rigorous analysis of LLPS processes (1). For each known scaffold protein, descriptions on performed assays of the minimum set of experiments were presented on its gene page. For example, the human fused in sarcoma (FUS), a well-characterized RNA-binding protein undergoing LLPS involved in formation of multiple biomolecular condensates (5,6-8), forms liquid-like droplets both in cells and at near physiological conditions in vitro. All the six experimental tests were performed to analyze the LLPS properties of FUS (9).

References
1. Alberti, S., Gladfelter, A. and Mittag, T. (2019) Considerations and challenges in studying liquid-liquid phase separation and biomolecular condensates. Cell, 176, 419-434. PMID: 30682370
2. Banani, S.F., Lee, H.O., Hyman, A.A. and Rosen, M.K. (2017) Biomolecular condensates: organizers of cellular biochemistry. Nat. Rev. Mol. Cell Biol. 18, 285-298. PMID: 28225081
3. Banani, S.F., Rice, A.M., Peeples, W.B., Lin, Y., Jain, S., Parker, R. and Rosen, M.K. (2016) Compositional control of phase-separated cellular bodies. Cell, 166, 651-663. PMID: 27374333
4. Hyman, A.A. and Simons, K. (2012) Cell biology. Beyond oil and water--phase transitions in cells. Science, 337, 1047-1049. PMID: 22936764
5. Hofweber, M., Hutten, S., Bourgeois, B., Spreitzer, E., Niedner-Boblenz, A., Schifferer, M., Ruepp, M.D., Simons, M., Niessing, D., Madl, T. et al. (2018) Phase Separation of FUS Is Suppressed by Its Nuclear Import Receptor and Arginine Methylation. Cell, 173, 706-719 e713. PMID: 29677514
6. Murray, D.T., Kato, M., Lin, Y., Thurber, K.R., Hung, I., McKnight, S.L. and Tycko, R. (2017) Structure of FUS Protein Fibrils and Its Relevance to Self-Assembly and Phase Separation of Low-Complexity Domains. Cell, 171, 615-627 e61. PMID: 28942918
7. Guo, L., Kim, H.J., Wang, H., Monaghan, J., Freyermuth, F., Sung, J.C., O'Donovan, K., Fare, C.M., Diaz, Z., Singh, N. et al. (2018) Nuclear-Import Receptors Reverse Aberrant Phase Transitions of RNA-Binding Proteins with Prion-like Domains. Cell, 173, 677-692 e20. PMID: 29677512
8. Yoshizawa, T., Ali, R., Jiou, J., Fung, H.Y.J., Burke, K.A., Kim, S.J., Lin, Y., Peeples, W.B., Saltzberg, D., Soniat, M. et al. (2018) Nuclear Import Receptor Inhibits Phase Separation of FUS through Binding to Multiple Sites. Cell, 173, 693-705 e22. PMID: 29677513
9. Patel, A., Lee, H.O., Jawerth, L., Maharana, S., Jahnel, M., Hein, M.Y., Stoynov, S., Mahamid, J., Saha, S., Franzmann, T.M. et al. (2015) A Liquid-to-Solid Phase Transition of the ALS Protein FUS Accelerated by Disease Mutation. Cell, 57, 162, 1066-1077. PMID: 26317470


There are 73 genes.  Reviewed (0 or Unreviewed (73

No.StatusDrLLPS IDEnsemble Gene IDUniProt AccessionGene Name
1
LLPS-Asm-0009
ENSAMXG00000009499.2
W5KQE3
2
LLPS-Asm-0082
ENSAMXG00000037884.1
A0A3B1JNE3
3
LLPS-Asm-0085
ENSAMXG00000003041.2
A0A3B1K216
4
LLPS-Asm-0111
ENSAMXG00000017485.2
A0A3B1K3K4
5
LLPS-Asm-0155
ENSAMXG00000033981.1
A0A3B1IXY6
6
LLPS-Asm-0241
ENSAMXG00000020869.2
A0A3B1IMN5
7
LLPS-Asm-0250
ENSAMXG00000006688.2
A0A3B1JUV7
8
LLPS-Asm-0295
ENSAMXG00000020046.2
A0A3B1J9R7
9
LLPS-Asm-0336
ENSAMXG00000015752.2
A0A3B1INH9
10
LLPS-Asm-0340
ENSAMXG00000037730.1
A0A3B1IV80
11
LLPS-Asm-0344
ENSAMXG00000030819.1
A0A3B1KFC6
12
LLPS-Asm-0350
ENSAMXG00000038511.1
A0A3B1II24
13
LLPS-Asm-0354
ENSAMXG00000030817.1
A0A3B1KD55
14
LLPS-Asm-0406
ENSAMXG00000018462.2
A0A3B1J371
15
LLPS-Asm-0462
ENSAMXG00000020288.2
W5LM42
16
LLPS-Asm-0489
ENSAMXG00000010892.2
W5KUB9
17
LLPS-Asm-0516
ENSAMXG00000020362.2
W5LMB3
18
LLPS-Asm-0517
ENSAMXG00000036881.1
A0A3B1KFJ6
19
LLPS-Asm-0554
ENSAMXG00000014034.2
W5L3N7
20
LLPS-Asm-0577
ENSAMXG00000041598.1
A0A3B1IKI3
21
LLPS-Asm-0599
ENSAMXG00000019677.2
W5LK95
22
LLPS-Asm-0607
ENSAMXG00000021025.2
W5LP82
23
LLPS-Asm-0660
ENSAMXG00000012704.2
W5KZU3
24
LLPS-Asm-0750
ENSAMXG00000008599.2
W5KMP6
25
LLPS-Asm-0786
ENSAMXG00000001381.2
W5K1F4
26
LLPS-Asm-0889
ENSAMXG00000010833.2
A0A3B1JZK7
27
LLPS-Asm-0911
ENSAMXG00000030795.1
A0A3B1JA12
28
LLPS-Asm-0927
ENSAMXG00000001495.2
W5K1Q4
29
LLPS-Asm-1096
ENSAMXG00000001589.2
W5K217
30
LLPS-Asm-1164
ENSAMXG00000008707.2
W5KN07
31
LLPS-Asm-1174
ENSAMXG00000015612.2
A0A3B1IPD2
32
LLPS-Asm-1242
ENSAMXG00000024615.2
A0A3B1JIU6
33
LLPS-Asm-1273
ENSAMXG00000019286.2
A0A3B1IRG6
34
LLPS-Asm-1284
ENSAMXG00000009544.2
A0A3B1IRI3
35
LLPS-Asm-1295
ENSAMXG00000004471.2
A0A3B1JST6
36
LLPS-Asm-1298
ENSAMXG00000004497.2
W5KAJ6
37
LLPS-Asm-1346
ENSAMXG00000006975.2
A0A3B1J6D6
38
LLPS-Asm-1397
ENSAMXG00000006302.2
W5KFV6
39
LLPS-Asm-1400
ENSAMXG00000041903.1
A0A3B1IWI3
40
LLPS-Asm-1410
ENSAMXG00000018871.2
A0A3B1IYJ7
41
LLPS-Asm-1536
ENSAMXG00000012546.2
W5KZ85
42
LLPS-Asm-1540
ENSAMXG00000032883.1
A0A3B1IX29
43
LLPS-Asm-1650
ENSAMXG00000021280.2
W5LPS2
44
LLPS-Asm-1656
ENSAMXG00000037402.1
A0A3B1IKH1
45
LLPS-Asm-1662
ENSAMXG00000002931.2
W5K5Y3
46
LLPS-Asm-1734
ENSAMXG00000012436.2
W5KYW6
47
LLPS-Asm-1821
ENSAMXG00000014974.2
A0A3B1JNR3
48
LLPS-Asm-1866
ENSAMXG00000011526.2
W5KW74
49
LLPS-Asm-2008
ENSAMXG00000021477.2
W5LQ40
50
LLPS-Asm-2024
ENSAMXG00000031223.1
A0A3B1J8Q2
51
LLPS-Asm-2037
ENSAMXG00000002781.2
W5K5L6
52
LLPS-Asm-2113
ENSAMXG00000019553.2
A0A3B1JGQ7
53
LLPS-Asm-2278
ENSAMXG00000019066.2
W5LIH6
54
LLPS-Asm-2322
ENSAMXG00000042718.1
A0A3B1ILE2
55
LLPS-Asm-2359
ENSAMXG00000037761.1
A0A3B1IH92
56
LLPS-Asm-2425
ENSAMXG00000024785.2
A0A3B1JYW4
57
LLPS-Asm-2584
ENSAMXG00000042316.1
A0A3B1IGV8
58
LLPS-Asm-2746
ENSAMXG00000018993.2
A0A3B1JHS3
59
LLPS-Asm-2753
ENSAMXG00000036639.1
A0A3B1J8W0
60
LLPS-Asm-2895
ENSAMXG00000005466.2
W5KDE0
61
LLPS-Asm-2913
ENSAMXG00000010155.2
W5KSB7
62
LLPS-Asm-2924
ENSAMXG00000010288.2
W5KSP0
63
LLPS-Asm-3107
ENSAMXG00000043028.1
A0A3B1J8Q7
64
LLPS-Asm-3121
ENSAMXG00000001477.2
W5K1Q0
65
LLPS-Asm-3540
ENSAMXG00000005167.2
A0A3B1IBU4
66
LLPS-Asm-3560
ENSAMXG00000008212.2
W5KLH6
67
LLPS-Asm-3690
ENSAMXG00000036979.1
A0A3B1JIH3
68
LLPS-Asm-3999
ENSAMXG00000000904.2
W5K017
69
LLPS-Asm-4087
ENSAMXG00000032407.1
A0A3B1IHW2
70
LLPS-Asm-4143
ENSAMXG00000009680.2
W5KQW1
71
LLPS-Asm-0287
ENSAMXG00000014587.2
A0A3B1KLJ8
AGO2
72
LLPS-Asm-3337
ENSAMXG00000016932.2
A0A3B1K237
LSM4
73
LLPS-Asm-1202
ENSAMXG00000031427.1
W5KVZ7
LYZ (1 of many)