Xiphophorus maculatus      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 72 genes.  Reviewed (0 or Unreviewed (72

No.StatusDrLLPS IDEnsemble Gene IDUniProt AccessionGene Name
1
LLPS-Xim-0002
ENSXMAG00000003753.2
M3ZNI2
2
LLPS-Xim-0005
ENSXMAG00000018792.2
M4AWN6
3
LLPS-Xim-0025
ENSXMAG00000009677.2
A0A3B5R029
4
LLPS-Xim-0059
ENSXMAG00000019151.2
A0A3B5R9K6
5
LLPS-Xim-0135
ENSXMAG00000003437.2
M3ZMK0
6
LLPS-Xim-0138
ENSXMAG00000000039.2
A0A3B5PRQ0
7
LLPS-Xim-0171
ENSXMAG00000017701.2
M4ATF7
8
LLPS-Xim-0179
ENSXMAG00000014141.2
A0A3B5QDY8
9
LLPS-Xim-0207
ENSXMAG00000023528.1
A0A3B5PSL5
10
LLPS-Xim-0338
ENSXMAG00000026861.1
A0A3B5PVA5
11
LLPS-Xim-0349
ENSXMAG00000000396.2
M3ZDV3
12
LLPS-Xim-0357
ENSXMAG00000008522.2
A0A3B5QE15
13
LLPS-Xim-0360
ENSXMAG00000002511.2
M3ZJY7
14
LLPS-Xim-0490
ENSXMAG00000002593.2
M3ZK58
15
LLPS-Xim-0500
ENSXMAG00000013524.2
A0A3B5R7C0
16
LLPS-Xim-0525
ENSXMAG00000014898.2
M4AKH7
17
LLPS-Xim-0572
ENSXMAG00000012882.2
A0A3B5Q5A3
18
LLPS-Xim-0732
ENSXMAG00000015925.2
M4ANC5
19
LLPS-Xim-0762
ENSXMAG00000015676.2
M4AML4
20
LLPS-Xim-0859
ENSXMAG00000019255.2
M4AXV4
21
LLPS-Xim-0881
ENSXMAG00000019336.2
M4AY37
22
LLPS-Xim-0975
ENSXMAG00000004985.2
M3ZRZ3
23
LLPS-Xim-0985
ENSXMAG00000009362.2
M4A4J0
24
LLPS-Xim-1048
ENSXMAG00000016713.2
M4AQK6
25
LLPS-Xim-1081
ENSXMAG00000012546.2
A0A3B5Q6Y2
26
LLPS-Xim-1093
ENSXMAG00000013547.2
M4AGK8
27
LLPS-Xim-1138
ENSXMAG00000023539.1
A0A3B5PRJ4
28
LLPS-Xim-1229
ENSXMAG00000007090.2
M3ZY09
29
LLPS-Xim-1246
ENSXMAG00000010836.2
A0A3B5PZ68
30
LLPS-Xim-1287
ENSXMAG00000015687.2
M4AMP3
31
LLPS-Xim-1551
ENSXMAG00000007377.2
M3ZYW0
32
LLPS-Xim-1628
ENSXMAG00000010451.2
M4A7N7
33
LLPS-Xim-1630
ENSXMAG00000028666.1
M3ZRD7
34
LLPS-Xim-1672
ENSXMAG00000026757.1
A0A3B5QRF3
35
LLPS-Xim-1682
ENSXMAG00000007623.2
M3ZZL0
36
LLPS-Xim-1721
ENSXMAG00000017366.2
A0A3B5R5R7
37
LLPS-Xim-1781
ENSXMAG00000006766.2
M3ZX50
38
LLPS-Xim-1813
ENSXMAG00000024335.1
A0A3B5R2K7
39
LLPS-Xim-1865
ENSXMAG00000008323.2
M4A1L6
40
LLPS-Xim-1903
ENSXMAG00000004959.2
M3ZRX6
41
LLPS-Xim-1986
ENSXMAG00000016090.2
A0A3B5Q5T5
42
LLPS-Xim-2054
ENSXMAG00000002128.2
A0A3B5RFG2
43
LLPS-Xim-2067
ENSXMAG00000013527.2
M4AGG7
44
LLPS-Xim-2125
ENSXMAG00000010683.2
M4A8C5
45
LLPS-Xim-2135
ENSXMAG00000027915.1
A0A3B5Q5N7
46
LLPS-Xim-2217
ENSXMAG00000024608.1
A0A3B5QF04
47
LLPS-Xim-2400
ENSXMAG00000022975.1
A0A3B5QKF7
48
LLPS-Xim-2416
ENSXMAG00000028057.1
A0A3B5QRL7
49
LLPS-Xim-2543
ENSXMAG00000007353.2
A0A3B5R002
50
LLPS-Xim-2659
ENSXMAG00000003481.2
A0A3B5Q6U1
51
LLPS-Xim-2729
ENSXMAG00000001707.2
M3ZHM0
52
LLPS-Xim-2786
ENSXMAG00000011153.2
M4A9N9
53
LLPS-Xim-2850
ENSXMAG00000022050.1
A0A3B5PWU7
54
LLPS-Xim-2912
ENSXMAG00000009720.2
M4A5K5
55
LLPS-Xim-3279
ENSXMAG00000003247.2
M3ZM12
56
LLPS-Xim-3287
ENSXMAG00000014963.2
M4AKJ2
57
LLPS-Xim-3363
ENSXMAG00000008513.2
M4A247
58
LLPS-Xim-3447
ENSXMAG00000009357.2
M4A4I4
59
LLPS-Xim-3558
ENSXMAG00000000827.2
M3ZF41
60
LLPS-Xim-3589
ENSXMAG00000011345.2
M4AA79
61
LLPS-Xim-3646
ENSXMAG00000025560.1
A0A3B5PUF5
62
LLPS-Xim-3662
ENSXMAG00000029896.1
A0A3B5QBG3
63
LLPS-Xim-3818
ENSXMAG00000006763.2
M3ZX48
64
LLPS-Xim-4072
ENSXMAG00000017725.2
M4ATI0
65
LLPS-Xim-4171
ENSXMAG00000013851.2
M4AHG6
66
LLPS-Xim-0827
ENSXMAG00000000787.2
M3ZF21
AGO2
67
LLPS-Xim-2899
ENSXMAG00000002316.2
M3ZJC4
GAR1
68
LLPS-Xim-1391
ENSXMAG00000029150.1
A0A3B5QVQ1
HNRNPA0 (1 of many)
69
LLPS-Xim-1668
ENSXMAG00000026672.1
A0A3B5QNL6
LSM4
70
LLPS-Xim-0153
ENSXMAG00000005154.2
M3ZSH7
NUP62
71
LLPS-Xim-1204
ENSXMAG00000004091.2
M3ZPG6
RPL5 (1 of many)
72
LLPS-Xim-1735
ENSXMAG00000015716.2
Q92143
tp53