Trends in Genetics
ReviewPhase Separation as a Melting Pot for DNA Repeats
Section snippets
Repetitive DNA Loci, Heterochromatin, and Phase Separation
Genomes contain large amounts of repetitive DNA sequences that constitute, for example, >70% of the human genome [1]. Previously referred to as ‘junk’ DNA, these sequences, which comprise both coding and noncoding sequences, are now clearly vital for genome function. Key examples of repetitive DNA regions include the life-sustaining rDNA (see Glossary) loci, chromosome-protecting telomeres, and the genome-reorganizing transposable elements (TEs). Due to their vulnerability to DNA damage and
Roles of Phase Separation at rDNA Repeats and the Nucleolus
rDNA loci are spatially isolated from the rest of the nuclear DNA, forming one or a small number of membraneless nucleolar compartments. In human cells, rDNA is tandemly arranged across chromosomes 13, 14, 15, 21, and 22, with ~70 units per chromosome [18]. The rRNA genes within rDNA are transcribed by RNA polymerase I (Pol I) into a precursor ribosomal RNA (pre-rRNA), which undergoes processing and maturation into 18S, 5.8S, and 28S rRNAs as it migrates from the center to the periphery of the
Phase Separation Impacts Telomeres via Heterochromatin Modulation, Nuclear Compartmentalization, and DNA Repair Control
Telomeres are repetitive DNA sequences that are positioned at the ends of linear chromosomes to prevent their attrition and fusion. Recent evidence suggests that telomeres are regulated by phase separation-dependent mechanisms. For example, HP1, which phase separates and promotes the formation of liquid-like heterochromatin domains, is required for the establishment of telomeric silent chromatin 3., 4., 36.. This silencing is integral to the dynamic nature of telomere elongation. Specifically,
Transposable Elements, Nuclear Compartments, and Phase Separation
TEs are jumping genes that often drive genome reorganization. TEs can move through copy-and-paste (retrotransposons) and cut-and-paste (DNA transposons) mechanisms, with the former requiring an RNA intermediate [58]. Retrotransposons comprise up to 45% of the human genome, and their dysregulation is implicated in various diseases, including neurodegeneration and cancer, as well as aging 1., 59., 60.. Human autonomous long interspersed element 1 (LINE1) encodes two proteins, ORF1p and ORF2p,
Phase Separation and Repetitive DNA in Human Disease
Thus far, we have discussed connections between repetitive DNA loci and compartments that are phase separated and liquid like. However, phase separation can yield compartments with a range of physical properties. For example, the contents can range from low- to high-viscosity liquids and even solid-like structures. In some cases, phase-separated molecules can transition back and forth through these phases. In human disease, these phase separations and transitions can be defining pathological
Concluding Remarks
Here, we have highlighted crosstalks between phase separation, nuclear compartmentalization, and major repetitive DNA loci that are critical to genome organization, chromosome protection, and cellular lifespan. We speculate that DNA repeats are particularly susceptible to regulation by phase separation for two main reasons. First, DNA repeats form the bulk of eukaryotic genomes and represent a risk to genome stability. Phase separation may provide the cell with a broad and energy-efficient
Outstanding Questions
What are the signals controlling the phase separation or transition of factors that establish nuclear compartments critical to the regulation of repetitive DNA loci?
Following cell division, how does the cell coordinate chromosome folding or chromatin tethering to nuclear landmarks with the phase separation-driven genesis of nuclear compartments?
Can aging and diseases related to the dysfunction of repetitive DNA loci be countered or halted by using molecules that alter the phase separation
Acknowledgments
A.C.H is funded by a Doctoral Award (152283) from the Canadian Institutes of Health Research (CIHR). L.A.O. is funded by an Ontario Graduate Scholarship (OGS). This work was supported by grants to K.M. from the CIHR (388041, 399687) and Canada Research Chairs Program (CRC; 950-230661). We thank members of the Mekhail laboratory for fruitful discussions.
Glossary
- Cajal body (CB)
- subnuclear membraneless compartments that are the site of small nuclear RNA (snRNA) and small nucleolar RNA (snoRNA) modification and the assembly site of their respective RNPs.
- Heterochromatin
- epigenetic silencing mechanism where DNA is highly condensed, thereby inhibiting transcription at these regions. Heterochromatin can be either constitutive (consistently silent) or facultative (with gene expression potential).
- Intrinsically disordered domain
- polypeptide domain sequences that
References (97)
Protein phase separation: a new phase in cell biology
Trends Cell Biol.
(2018)- et al.
Modulation of intrinsically disordered protein function by post-translational modifications
J. Biol. Chem.
(2016) Double-strand breaks in heterochromatin move outside of a dynamic HP1a domain to complete recombinational repair
Cell
(2011)Nuclear condensates of the Polycomb protein chromobox 2 (CBX2) assemble through phase separation
J. Biol. Chem.
(2019)New insights into nucleolar architecture and activity
Int. Rev. Cytol.
(2006)Perinuclear cohibin complexes maintain replicative life span via roles at distinct silent chromatin domains
Dev. Cell
(2011)Elimination of replication block protein Fob1 extends the life span of yeast mother cells
Mol. Cell
(1999)Redistribution of silencing proteins from telomeres to the nucleolus is associated with extension of life span in S. cerevisiae
Cell
(1997)- et al.
Extrachromosomal rDNA circles--a cause of aging in yeast
Cell
(1997) The effect of replication initiation on gene amplification in the rDNA and its relationship to aging
Mol. Cell
(2009)
Coexisting liquid phases underlie nucleolar subcompartments
Cell
Mechanisms of functional promiscuity by HP1 proteins
Trends Cell Biol.
Human telomerase RNA accumulation in Cajal bodies facilitates telomerase recruitment to telomeres and telomere elongation
Mol. Cell
Coilin displays differential affinity for specific RNAs in vivo and is linked to telomerase RNA biogenesis
J. Mol. Biol.
The coilin interactome identifies hundreds of small noncoding RNAs that traffic through Cajal bodies
Mol. Cell
Shelterin protects chromosome ends by compacting telomeric chromatin
Cell
Live cell imaging of telomerase RNA dynamics reveals cell cycle-dependent clustering of telomerase at elongating telomeres
Mol. Cell
The tip of the iceberg: RNA-binding proteins with prion-like domains in neurodegenerative disease
Brain Res.
A Liquid-to-solid phase transition of the ALS protein FUS accelerated by disease mutation
Cell
Adaptation to stressors by systemic protein amyloidogenesis
Dev. Cell
Immobilization of proteins in the nucleolus by ribosomal intergenic spacer noncoding RNA
Mol. Cell
Roles for Pbp1 and caloric restriction in genome and lifespan maintenance via suppression of RNA-DNA hybrids
Dev. Cell
Transcription termination and RNA degradation contribute to silencing of RNA polymerase II transcription within heterochromatin
Mol. Cell
Non-coding RNA molecules connect calorie restriction and lifespan
J. Mol. Biol.
Profilin reduces aggregation and phase separation of huntingtin N-terminal fragments by preferentially binding to soluble monomers and oligomers
J. Biol. Chem.
RNA Controls PolyQ protein phase transitions
Mol. Cell
Tau activates transposable elements in Alzheimer's disease
Cell Rep.
Initial sequencing and analysis of the human genome
Nature
Chromatin dynamics in genome stability: roles in suppressing endogenous DNA damage and facilitating DNA repair
Int. J. Mol. Sci.
Phase separation drives heterochromatin domain formation
Nature
Liquid droplet formation by HP1alpha suggests a role for phase separation in heterochromatin
Nature
Thermodynamically driven assemblies and liquid-liquid phase separations in biology
Soft Matter
Acetylation disfavors Tau phase separation
Int. J. Mol. Sci.
Friend or foe – post-translational modifications as regulators of phase separation and RNP granule dynamics
J. Biol. Chem.
An acetylation mimicking mutation, K274Q, in tau imparts neurotoxicity by enhancing tau aggregation and inhibiting tubulin polymerization
Biochem. J.
Acetylation of intrinsically disordered regions regulates phase separation
Nat. Chem. Biol.
Liquid-liquid phase separation in biology
Annu. Rev. Cell Dev. Biol.
A conformational switch in HP1 releases auto-inhibition to drive heterochromatin assembly
Nature
Heterochromatin: guardian of the genome
Annu. Rev. Cell Dev. Biol.
The role of phase separation in heterochromatin formation, function, and regulation
Biochemistry
The nuclear envelope in genome organization, expression and stability
Nat. Rev. Mol. Cell Biol.
Enrichment of dynamic chromosomal crosslinks drive phase separation of the nucleolus
Nucleic Acids Res.
Role for perinuclear chromosome tethering in maintenance of genome stability
Nature
The Smc5-Smc6 complex and SUMO modification of Rad52 regulates recombinational repair at the ribosomal gene locus
Nat. Cell Biol.
The SIR2/3/4 complex and SIR2 alone promote longevity in Saccharomyces cerevisiae by two different mechanisms
Genes Dev.
Accelerated aging and nucleolar fragmentation in yeast sgs1 mutants
Science
Enforcement of a lifespan-sustaining distribution of Sir2 between telomeres, mating-type loci, and rDNA repeats by Rif1
Aging Cell
A localized nucleolar DNA damage response facilitates recruitment of the homology-directed repair machinery independent of cell cycle stage
Genes Dev.
Cited by (21)
Chromatin localization of nucleophosmin organizes ribosome biogenesis
2022, Molecular CellCitation Excerpt :Ribosome biogenesis starts in the nucleolus, which is organized around the genomic rDNA tandem, each encoding three of the four ribosomal RNAs (rRNAs), 18S, 5.8S, and 25S. The mammalian nucleolus has three compartments: the fibrillar center containing chromatin and rDNA repeats (FC), the dense fibrillar component (DFC) enriched in fibrillarin, and the granular component (GC) enriched in nucleophosmin (NPM1).4,5 By contrast, yeast nucleoli seem to have a bipartite organization, with the two central compartments incompletely separated, as the central fibrillar clusters of rDNA repeats show characteristics of both the FC and DFC.6
Phase separation in genome organization across evolution
2021, Trends in Cell BiologyPredicting protein condensate formation using machine learning
2021, Cell ReportsCitation Excerpt :It is interesting to note that RNA binding-related GO terms are associated with high PPS probabilities. While we aimed to exclude the possibility that this is partially the result of the presence of RNA-binding proteins in our training set, our observations are in line with the notion that nucleotide binding is a feature that is well known to be associated with and supportive of phase separation (Garcia-Jove Navarro et al., 2019; Hall et al., 2019; Wheeler et al., 2016). Recently, the mRNA modification m6A was also shown to be important for regulating phase separation of m6A readers, such as the YTHDF proteins (Fu and Zhuang, 2020; Ries et al., 2019).
RNA-seeded membraneless bodies: Role of tandemly repeated RNA
2021, Advances in Protein Chemistry and Structural BiologyRepetitive RNAs as Regulators of Chromatin-Associated Subcompartment Formation by Phase Separation
2020, Journal of Molecular BiologyCitation Excerpt :For example, it was shown that enrichment of Pol II and transcription factors in replication compartments of the herpes simplex virus appeared to be mostly driven by the creation of nucleosome free unspecific DNA binding sites and not by LLPS [134]. Repetitive DNA sequences have been implicated in PS processes as reviewed recently [135]. With respect to the corresponding repRNA counterparts, L1 and Alu sequences are among the most abundantly transcribed TE species.
Mobility and Repair of Damaged DNA: Random or Directed?
2020, Trends in Cell BiologyCitation Excerpt :One possibility may be the efficient relocation of breaks to specific repair-conducive compartments such as the nuclear pore complex. Moreover, in the context of phase separation, forces generated by motors and the cytoskeleton could allow breaks to escape or enter phase-separated nuclear domains [86]. Further, how does directed motion intersect with the random motion of damaged DNA?
- 3
These authors contributed equally