Table 1.

Nuclear Condensates

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