Entry created on 1 July 2019 (Revision 1.0) Annotator: Rita Pancsa
Basic protein information
Accession Q14781
Common name CBX2
Gene CBX2
Organism Homo sapiens
Uniprot name Chromobox protein homolog 2
Basic LLPS information
Organelle PcG protein complex; euchromatin; heterochromatin; PcG chromatin condensates
Type of experimental evidence
Protein region(s) mediating LLPS
1
-
532
Full protein sequence contributes to LLPS: AT-hook, phosphorylable S-tract, IDR with positive charges
Based on the experimental results of the following publication: 30514760
Molecular features viewer
PDB structures
Extended LLPS information
Functional description
The Polycomb-repressive complex 1 (PRC1) family complexes are central to maintaining the repression of genes whose expression would generate inappropriately specified cells. PRC1 protein chromobox 2 (CBX2), a member of the CBX protein family, undergoes phase separation to form condensates and that the CBX2 condensates exhibit liquid-like properties. CBX2 acts as a scaffold, while other subunits of CBX2-PRC1 are clients. However, the absence of CBX2-PRC1 subunits leading to irregular shapes of CBX2 condensates suggests that the trimeric client has critical roles in regulating the material properties of CBX2-PRC1 condensates as well as the assembly of PcG condensates. CBX2 condensates colocalize CBX2-PRC1 subunits and H3K27m3-marked chromatin regions. CBX2 dynamically exchanges with the surrounding environment within condensates and has liquid-like properties. CBX2 can undergo LLPS to form condensates in vitro. CBX2 condensates can concentrate DNA and nucleosomes in vitro. CBX2 contains a high content of Lys and Arg. Conserved residues (positive-negative charge patterns) within the IDR that are critical for the LLPS of CBX2. Perturbation of these charged clusters reduces the phase separation of CBX2 both in vitro and in vivo. H3K27me3 contributes little to the formation of CBX2 condensates in living cells (PMID:30514760). Reconstituted PRC1 readily phase-separates into droplets in vitro at low concentrations and physiological salt conditions. Point mutationsin an internal domain of Cbx2 eliminate phase separation. These same point mutations eliminate the formation of puncta in cells and have been shown previously to eliminate nucleosome compaction in vitro and generate axial patterning defects in mice (PMID:31171700).
Literature supporting the LLPS: 30514760, 31171700
Functional class of membraneless organelle: protective storage/reservoir; biomolecular filter/selectivity barrier
Binding partners (at biological protein concentrations)
1) DNA with H3K27me3 (not required)
Type of RNA(s) required/used for the LLPS at biological protein concentrations
Not required.
Molecular interaction types contributing to LLPS
electrostatic (cation-anion) interaction (PMID:30514760)
Determinants of phase separation and droplet properties
1) protein concentration of CBX2 2) salt concentration
Membrane cluster No
Partner-dependent No
RNA-dependent No
PTM required No
Domain-motif interactions No
Discrete oligomerization No
Regulation and disease
Post-translational modifications affecting LLPS
Position Residue PTM Effect Reference Modifying enzyme Notes
Isoforms known to affect LLPS
Isoform Effect Reference
All known isoforms containing sequence changes in the LLPS region(s)
Position type Isoform names from UniProt
Disease mutations affecting LLPS
Mutation dbSNP Disease OMIM Effect Reference Notes
Experimental information
Experimental techniques applied to prove/investigate LLPS
Overexpressing YFP-Cbx2 and HaloTag (HT)-Cbx2 (fusion proteins) in transgenic PGK12.1 mouse embryonic stem cells in vivo and examining them by fluorescence live-cell imaging showed that both YFP-CBX2 and HT-CBX2 formed condensates in living wild-type mES (particle size and count) cells and that the CBX2 condensates exhibit liquid-like properties (FRAP). Under the basal expression, the protein level of YFP-CBX2 was similar to that of the endogenous protein CBX2, the distribution of YFP-CBX2 and HT-CBX2 in Cbx2-/- mES cells was similar to that in wild-type mES cells (particle size and count by microscopy). YFP-CBX2 condensates colocalized with condensates of other PRC1 complex subunits RING1B and PHC1 in vivo. Immunofluorescence of H3K27me3 and YFP-CBX2 showed that CBX2 condensates colocalize with chromatin with the dense H3K27me3 mark suggesting that PcG-targeted genes are recruited to CBX2 condensates, or vice versa. CBX2 condensates were protein concentration-dependent. Recombinant GST-CBX2-FLAG (GST-CBX2) did not undergo LLPS in vitro at high salt concentration or in the presence of glutathione. After dialyzing the high salt of GST-CBX2 fusion to 140 mM NaCl at 4 °C overnight and transferring 10 μl of sample to coverslip CBX2 condensates with a size of a few hundred nanometers were observed by DIC microscopy. So did FLAG-CBX2. In vitro phase separation of CBX2 was protein concentration-dependent. In vitro treatment of CBX2 condensates with increasing concentrations of NaCl and Triton X-100 caused a reduction in the number of CBX2 condensates (particle size and count by microscopy). Fluorescent dye-labelled 24-bp double-stranded DNA and similarly labeled nucleosomes did not form condensates, however, in the presence of CBX2, DNA was concentrated and CBX2 condensates colocalized with the concentrated DNA or nucleosomes. Site-directed mutagenesis studies demonstrated that the conserved residues of CBX2 within the intrinsically disordered region (IDR), which is the region for compaction of chromatin in vitro, promote the condensate formation both in vitro and in vivo. Genetic engineering studies implied that trimethylation of Lys-27 at histone H3 (H3K27me3), a marker of heterochromatin formation produced by PRC2, had minimal effects on the CBX2 condensate formation (particle size and count) (PMID:30514760). EGFP-CBX2+ RING1b could form dense spherical droplets in the presence of volume excluder that increased in size as a function of concentration and could fuse with each other (particle size and count bz microscopy). Mutational studies suggested that the positive charges within the CBX2 LCDR are critical for phase separation in vitro in addition to the previously described roles in chromatin compaction and proper axial patterning in vivo, in mice. At higher salt concentration, the preformed droplets drastically reduced in number and size (particle size and count by microscopy). Reducing the salt concentration to 100 mM KCl resulted in reformation of droplets. In vivo results recapitulated the findings of in vitro assays and underscore the importance of positively charged residues in the CBX2 LCDR for PRC1 phase separation (PMID:31171700).
Experimental observations supporting the liquid material state of the condensate
dynamic movement/reorganization of molecules within the droplet (PMID:30514760) dynamic exchange of molecules with surrounding solvent (PMID:30514760, PMID:31171700) sensitivity to 1,6-hexanediol (PMID:30514760, PMID:31171700) reversibility of formation and dissolution (PMID:31171700)