Table 1.
Name | Function | Refs | Condensate features | Regulation |
---|---|---|---|---|
Nucleolus | rRNA transcription, processing, and preribosome assembly | [27–30,40] | Multilayered organization with functional division of labor: rRNA transcription, rRNA processing, and preribosome assembly. nucleated by local RNA synthesis | -NPM1 has two conserved acidic tracts necessary for R-motif engagement -NPM1 has a nucleic acid binding domain necessary for binding rDNA |
Cajal body | snRNA transcription and processing | [3,58,114–117] | Concentrates RNA processing enzymes responsible for spliceosomal RNA maturation. | Nucleated by local RNA synthesis |
Superenhancers | Transcription of cell-identity mRNA | [20,21,23] | Concentrates relevant cofactors, phosphorylation-regulated partitioning of RNA Pol II, seeded by specific enhancer features, DNA-dependent assembly, and reduces search space for signaling factors | -Serine residues in MED1 necessary for phase separation -Acidic residues in OCT4 help interactions with MED1 droplets -Length of RNA Pol II CTD is important -DNA sequence is important -Aromatic residues in b-cat are required to partition |
Histone locus body | Histone mRNA transcription and processing | [118–121] | Coordinated expression of arrayed repeats of replication-dependent histone genes during early S phase. Both the RNA Pol II transcriptional machinery and histone mRNA processing enzymes are concentrated | -CDK phosphorylation of NPAT -Size dependent on underlying number of histone genes |
Estrogen receptor | Estrogen-responsive gene regulation | [122] | Concentrates the RNA Pol II machinery in an estrogen-dependent manner | Chronic estrogen stimulation leads to changes in material properties and irreversibility |
YAP | Response to hyperosmotic stress | [123] | Selective partitioning of TEAD and TAZ for target gene activation upon hyperosmotic shock | |
Speckles | Cotranscriptional mRNA processing and processing | [25,26,48,124] | Concentrates the mRNA processing machinery. Phosphorylation-regulated partitioning of RNA Pol II, seeded by RNA machinery storage | Phosphorylation of RNA Pol II CTD leads to association synthesis |
Paraspeckle | Storage of RNA and protein | [38,69,70] | NEAT1 RNA and various RNA-binding proteins are essential components. Core shell architecture. | Synthesis of NEAT1 RNA isoforms regulates formation |
CTCF clusters | Genome structure | [125,126] | Reduced search space for CTCF, nucleated by RNA binding | RNA binding domain required for CTCF clustering |
DNA damage | Double strand break repair | [18,19] | Seeded by PARP, 53BP1 phase separation selectively partitions p53 | Seeded by DNA damage induced PARylation |
DNA replication origins | Specification of DNA replication origin | [17] | Coordinates replication initiation of clusters sites. ORC, Cdc6, and Cdt1 are proposed scaffold. DNA-dependent formation. Selective partitioning of Mcm2–7 promotes loading and replication origin choice. | Phosphorylation regulated |
Chromatin | Physiological form of genetic material | [16] | Regulates access to underlying regulatory and coding sequence | -Acetyl-lysine-driven dissolution -Nucleosome-spacing-driven compaction |
Constitutive heterochromatin | Repression of repetitive elements | [12,14–16,88] | HP1α proposed as scaffold, creates highly dynamic concentrations of chromatin. | -Phosphorylation of HP1 promotes phase separation -Dynamic PTM regulation: H3K9me3 promotes HP1/swi6 binding and condensate formation, Lysine acetylation promotes chromatin decompaction |
Facultative heterochromatin (PcG bodies) | Repression of cell-type specific and developmental mRNA | [127] | Concentrates CBX2. Amino acids that drive phase separation also drive chromatin compaction and are necessary for proper segmentation during development | Basic patch in CBX2 is required |
PML bodies | Various functions proposed | [128] | PML protein is essential component. Partitions several chromatin-associated factors. | SUMOylation regulates partitioning by binding to SUMO-interaction motifs found on PML |
SPOP/DAXX | Protein ubiquitination | [129] | Concentrates cullin3–RING ubiquitin ligases and substrates | Substrate mediated co-condensation |
Lge1/Bre1 | Gene body histone ubiquitination | [77] | Concentrates ubiquitination enzymes and nucleosomal substrate | |
Barr body | Mammalian dosage compensation | [71,72] | lncRNA | Local synthesis of lncRNA initiates X inactivation |
Abbreviations: CBX2, chromobox protein homolog 2; CTCF, CCCTC-binding factor; NPAT, nuclear protein, coactivator of histone transcription; NPM1, nucleophosmin 1; OCT4, octamer-binding transcription factor 4; PARP, poly (ADP-ribose) polymerase; PML, promyelocytic leukemia; SPOP, speckle-type POZ protein; SUMO, small ubiquitin-like modifier; YAP, Yes-associated protein