Abstract
Fate decisions during immune cell development require temporally precise changes in gene expression. Evidence suggests that the dynamic modulation of these changes is associated with the formation of diverse, membrane-less nucleoprotein assemblies that are termed biomolecular condensates. These condensates are thought to orchestrate fate-determining transcriptional and post-transcriptional processes by locally and transiently concentrating DNA or RNA molecules alongside their regulatory proteins. Findings have established a link between condensate formation and the gene regulatory networks that ensure the proper development of immune cells. Conversely, condensate dysregulation has been linked to impaired immune cell fates, including ageing and malignant transformation. This Review explores the putative mechanistic links between condensate assembly and the gene regulatory frameworks that govern normal and pathological development in the immune system.
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References
Flajnik, M. F. & Kasahara, M. Origin and evolution of the adaptive immune system: genetic events and selective pressures. Nat. Rev. Genet. 11, 47–59 (2010).
Litman, G. W., Rast, J. P. & Fugmann, S. D. The origins of vertebrate adaptive immunity. Nat. Rev. Immunol. 10, 543–553 (2010).
Carpenter, S. & O’Neill, L. A. J. From periphery to center stage: 50 years of advancements in innate immunity. Cell 187, 2030–2051 (2024).
Chi, H., Pepper, M. & Thomas, P. G. Principles and therapeutic applications of adaptive immunity. Cell 187, 2052–2078 (2024).
Pinho, S. & Frenette, P. S. Haematopoietic stem cell activity and interactions with the niche. Nat. Rev. Mol. Cell Biol. 20, 303–320 (2019).
Orkin, S. H. & Zon, L. I. Hematopoiesis: an evolving paradigm for stem cell biology. Cell 132, 631–644 (2008).
Wilkinson, A. C., Igarashi, K. J. & Nakauchi, H. Haematopoietic stem cell self-renewal in vivo and ex vivo. Nat. Rev. Genet. 21, 541–554 (2020).
Stadhouders, R., Filion, G. J. & Graf, T. Transcription factors and 3D genome conformation in cell-fate decisions. Nature 569, 345–354 (2019).
Chua, B. A., Van Der Werf, I., Jamieson, C. & Signer, R. A. J. Post-transcriptional regulation of homeostatic, stressed, and malignant stem cells. Cell Stem Cell 26, 138–159 (2020).
Raj, A. & van Oudenaarden, A. Nature, nurture, or chance: stochastic gene expression and its consequences. Cell 135, 216–226 (2008).
Sabari, B. R. Biomolecular condensates and gene activation in development and disease. Dev. Cell 55, 84–96 (2020).
Banani, S. F., Lee, H. O., Hyman, A. A. & Rosen, M. K. Biomolecular condensates: organizers of cellular biochemistry. Nat. Rev. Mol. Cell Biol. 18, 285–298 (2017).
Li, P. et al. High-throughput and proteome-wide discovery of endogenous biomolecular condensates. Nat. Chem. 16, 1101–1112 (2024).
Gorsheneva, N. A., Sopova, J. V., Azarov, V. V., Grizel, A. V. & Rubel, A. A. Biomolecular condensates: structure, functions, methods of research. Biochemistry 89, S205–S223 (2024).
Zacco, E. et al. RNA: the unsuspected conductor in the orchestra of macromolecular crowding. Chem. Rev. 124, 4734–4777 (2024).
Wadsworth, G. M. et al. RNA-driven phase transitions in biomolecular condensates. Mol. Cell 84, 3692–3705 (2024).
Roden, C. & Gladfelter, A. S. RNA contributions to the form and function of biomolecular condensates. Nat. Rev. Mol. Cell Biol. 22, 183–195 (2021).
Cech, T. R. RNA in biological condensates. RNA 28, 1–2 (2022).
Rangachari, V. Biomolecular condensates — extant relics or evolving microcompartments? Commun. Biol. 6, 656 (2023).
Mitrea, D. M., Mittasch, M., Gomes, B. F., Klein, I. A. & Murcko, M. A. Modulating biomolecular condensates: a novel approach to drug discovery. Nat. Rev. Drug. Discov. 21, 841–862 (2022).
Sabari, B. R., Dall’Agnese, A. & Young, R. A. Biomolecular condensates in the nucleus. Trends Biochem. Sci. 45, 961–977 (2020).
Sharp, P. A., Chakraborty, A. K., Henninger, J. E. & Young, R. A. RNA in formation and regulation of transcriptional condensates. RNA 28, 52–57 (2022).
Hnisz, D., Shrinivas, K., Young, R. A., Chakraborty, A. K. & Sharp, P. A. A phase separation model for transcriptional control. Cell 169, 13–23 (2017).
Du, M. et al. Direct observation of a condensate effect on super-enhancer controlled gene bursting. Cell 187, 331–344.e317 (2024).
Sabari, B. R. et al. Coactivator condensation at super-enhancers links phase separation and gene control. Science 361, eaar3958 (2018). This study provides experimental evidence that components of the transcriptional machinery, specifically BRD4 and MED1, can form condensates at super-enhancer-regulated genes.
Kilgore, H. R. et al. Distinct chemical environments in biomolecular condensates. Nat. Chem. Biol. 20, 291–301 (2024).
Lyons, H. et al. Functional partitioning of transcriptional regulators by patterned charge blocks. Cell 186, 327–345.e328 (2023).
Cisse, I. I. et al. Real-time dynamics of RNA polymerase II clustering in live human cells. Science 341, 664–667 (2013).
Cho, W. K. et al. Mediator and RNA polymerase II clusters associate in transcription-dependent condensates. Science 361, 412–415 (2018).
Ryu, K., Park, G. & Cho, W. K. Emerging insights into transcriptional condensates. Exp. Mol. Med. 56, 820–826 (2024).
Brodsky, S., Jana, T. & Barkai, N. Order through disorder: the role of intrinsically disordered regions in transcription factor binding specificity. Curr. Opin. Struct. Biol. 71, 110–115 (2021).
Brodsky, S. et al. Intrinsically disordered regions direct transcription factor in vivo binding specificity. Mol. Cell 79, 459–471.e454 (2020).
Boija, A. et al. Transcription factors activate genes through the phase-separation capacity of their activation domains. Cell 175, 1842–1855.e1816 (2018).
Lavering, E. D., Gandhamaneni, M. & Weeks, D. L. Intrinsically disordered regions are not sufficient to direct the compartmental localization of nucleolar proteins in the nucleus. PLoS Biol. 21, e3002378 (2023).
He, J. et al. Dual-role transcription factors stabilize intermediate expression levels. Cell 187, 2746–2766.e2725 (2024).
Cho, W. K. et al. RNA polymerase II cluster dynamics predict mRNA output in living cells. Elife 5, e13617 (2016).
Ilik, I. A. & Aktas, T. Nuclear speckles: dynamic hubs of gene expression regulation. FEBS J. 289, 7234–7245 (2022).
Chen, Y. & Belmont, A. S. Genome organization around nuclear speckles. Curr. Opin. Genet. Dev. 55, 91–99 (2019).
Spector, D. L. & Lamond, A. I. Nuclear speckles. Cold Spring Harb. Perspect. Biol. 3, a000646 (2011).
Giudice, J. & Jiang, H. Splicing regulation through biomolecular condensates and membraneless organelles. Nat. Rev. Mol. Cell Biol. 25, 683–700 (2024).
Carter, K. C., Taneja, K. L. & Lawrence, J. B. Discrete nuclear domains of poly(A) RNA and their relationship to the functional organization of the nucleus. J. Cell Biol. 115, 1191–1202 (1991).
Bhat, P. et al. Genome organization around nuclear speckles drives mRNA splicing efficiency. Nature 629, 1165–1173 (2024). This work uncovers a functional role for nuclear speckles in splicing, showing that spatial organization of actively transcribed genes near speckles boosts splicing efficiency of their pre-mRNAs.
Kim, J., Venkata, N. C., Hernandez Gonzalez, G. A., Khanna, N. & Belmont, A. S. Gene expression amplification by nuclear speckle association. J. Cell Biol. 219, e201904046 (2020).
Alexander, K. A. et al. p53 mediates target gene association with nuclear speckles for amplified RNA expression. Mol. Cell 81, 1666–1681.e1666 (2021).
Chan, S. P. & Slack, F. J. microRNA-mediated silencing inside P-bodies. RNA Biol. 3, 97–100 (2006).
Decker, C. J. & Parker, R. P-bodies and stress granules: possible roles in the control of translation and mRNA degradation. Cold Spring Harb. Perspect. Biol. 4, a012286 (2012).
Eulalio, A., Behm-Ansmant, I. & Izaurralde, E. P bodies: at the crossroads of post-transcriptional pathways. Nat. Rev. Mol. Cell. Biol. 8, 9–22 (2007).
Kulkarni, M., Ozgur, S. & Stoecklin, G. On track with P-bodies. Biochem. Soc. Trans. 38, 242–251 (2010).
Luo, Y., Na, Z. & Slavoff, S. A. P-bodies: composition, properties, and functions. Biochemistry 57, 2424–2431 (2018).
Parker, R. & Sheth, U. P bodies and the control of mRNA translation and degradation. Mol. Cell 25, 635–646 (2007).
Riggs, C. L., Kedersha, N., Ivanov, P. & Anderson, P. Mammalian stress granules and P bodies at a glance. J. Cell Sci. 133, jcs242487 (2020).
Standart, N. & Weil, D. P-bodies: cytosolic droplets for coordinated mRNA storage. Trends Genet. 34, 612–626 (2018).
Freimer, J. W., Hu, T. J. & Blelloch, R. Decoupling the impact of microRNAs on translational repression versus RNA degradation in embryonic stem cells. Elife 7, e38014 (2018).
Buchan, J. R. mRNP granules. Assembly, function, and connections with disease. RNA Biol. 11, 1019–1030 (2014).
Wang, C. et al. Context-dependent deposition and regulation of mRNAs in P-bodies. Elife 7, e29815 (2018).
Mathys, H. et al. Structural and biochemical insights to the role of the CCR4–NOT complex and DDX6 ATPase in microRNA repression. Mol. Cell 54, 751–765 (2014).
Cardona, A. H. et al. Self-demixing of mRNA copies buffers mRNA:mRNA and mRNA:regulator stoichiometries. Cell 186, 4310–4324.e4323 (2023). This study demonstrates how RNA condensates, specifically P-bodies, can robustly and selectively buffer translationally repressed mRNAs and counters the notion that P-bodies have limited storage capacity.
Brothers, W. R., Ali, F., Kajjo, S. & Fabian, M. R. The EDC4–XRN1 interaction controls P-body dynamics to link mRNA decapping with decay. EMBO J. 42, e113933 (2023).
Blake, L. A., Watkins, L., Liu, Y., Inoue, T. & Wu, B. A rapid inducible RNA decay system reveals fast mRNA decay in P-bodies. Nat. Commun. 15, 2720 (2024).
Millar, S. R. et al. A new phase of networking: the molecular composition and regulatory dynamics of mammalian stress granules. Chem. Rev. 123, 9036–9064 (2023).
Protter, D. S. W. & Parker, R. Principles and properties of stress granules. Trends Cell Biol. 26, 668–679 (2016).
Redding, A. & Grabocka, E. Stress granules and hormetic adaptation of cancer. Trends Cancer 9, 995–1005 (2023).
Riback, J. A. et al. Stress-triggered phase separation is an adaptive, evolutionarily tuned response. Cell 168, 1028–1040.e1019 (2017).
Hofmann, S., Kedersha, N., Anderson, P. & Ivanov, P. Molecular mechanisms of stress granule assembly and disassembly. Biochim. Biophys. Acta Mol. Cell Res. 1868, 118876 (2021).
Ries, R. J., Pickering, B. F., Poh, H. X., Namkoong, S. & Jaffrey, S. R. m6A governs length-dependent enrichment of mRNAs in stress granules. Nat. Struct. Mol. Biol. 30, 1525–1535 (2023).
Park, J. et al. Poly(GR) interacts with key stress granule factors promoting its assembly into cytoplasmic inclusions. Cell Rep. 42, 112822 (2023).
Ries, R. J. et al. m6A enhances the phase separation potential of mRNA. Nature 571, 424–428 (2019).
Khong, A., Matheny, T., Huynh, T. N., Babl, V. & Parker, R. Limited effects of m6A modification on mRNA partitioning into stress granules. Nat. Commun. 13, 3735 (2022).
Pelletier, J., Thomas, G. & Volarevic, S. Ribosome biogenesis in cancer: new players and therapeutic avenues. Nat. Rev. Cancer 18, 51–63 (2018).
Lafontaine, D. L. J., Riback, J. A., Bascetin, R. & Brangwynne, C. P. The nucleolus as a multiphase liquid condensate. Nat. Rev. Mol. Cell Biol. 22, 165–182 (2021).
Mensah, M. A. et al. Aberrant phase separation and nucleolar dysfunction in rare genetic diseases. Nature 614, 564–571 (2023).
Corman, A., Sirozh, O., Lafarga, V. & Fernandez-Capetillo, O. Targeting the nucleolus as a therapeutic strategy in human disease. Trends Biochem. Sci. 48, 274–287 (2023).
Riback, J. A. et al. Composition-dependent thermodynamics of intracellular phase separation. Nature 581, 209–214 (2020).
Russell, J. & Zomerdijk, J. C. RNA-polymerase-I-directed rDNA transcription, life and works. Trends Biochem. Sci. 30, 87–96 (2005).
Bernardi, R. & Pandolfi, P. P. Structure, dynamics and functions of promyelocytic leukaemia nuclear bodies. Nat. Rev. Mol. Cell Biol. 8, 1006–1016 (2007).
Lallemand-Breitenbach, V. & de The, H. PML nuclear bodies. Cold Spring Harb. Perspect. Biol. 2, a000661 (2010).
Boisvert, F. M., Hendzel, M. J. & Bazett-Jones, D. P. Promyelocytic leukemia (PML) nuclear bodies are protein structures that do not accumulate RNA. J. Cell Biol. 148, 283–292 (2000).
Vertegaal, A. C. O. Signalling mechanisms and cellular functions of SUMO. Nat. Rev. Mol. Cell Biol. 23, 715–731 (2022).
Shen, T. H., Lin, H. K., Scaglioni, P. P., Yung, T. M. & Pandolfi, P. P. The mechanisms of PML-nuclear body formation. Mol. Cell 24, 331–339 (2006).
Olson, O. C., Kang, Y. A. & Passegue, E. Normal hematopoiesis is a balancing act of self-renewal and regeneration. Cold Spring Harb. Perspect. Med. 10, a035519 (2020).
Li, Z. et al. Suppression of m6A reader Ythdf2 promotes hematopoietic stem cell expansion. Cell Res. 28, 904–917 (2018).
Cheng, Y. et al. m6A RNA methylation maintains hematopoietic stem cell identity and symmetric commitment. Cell Rep. 28, 1703–1716.e1706 (2019).
Lee, H. et al. Stage-specific requirement for Mettl3-dependent m6A mRNA methylation during haematopoietic stem cell differentiation. Nat. Cell Biol. 21, 700–709 (2019).
Zhang, C. et al. m6A modulates haematopoietic stem and progenitor cell specification. Nature 549, 273–276 (2017).
Yao, Q. J. et al. Mettl3–Mettl14 methyltransferase complex regulates the quiescence of adult hematopoietic stem cells. Cell Res. 28, 952–954 (2018).
Gao, Y. et al. ALKBH5 modulates hematopoietic stem and progenitor cell energy metabolism through m6A modification-mediated RNA stability control. Cell Rep. 42, 113163 (2023).
Sharma, A., Takata, H., Shibahara, K., Bubulya, A. & Bubulya, P. A. Son is essential for nuclear speckle organization and cell cycle progression. Mol. Biol. Cell 21, 650–663 (2010).
Luo, H. et al. SON is an essential m6A target for hematopoietic stem cell fate. Cell Stem Cell 30, 1658–1673.e1610 (2023).
Ilik, I. A. et al. SON and SRRM2 are essential for nuclear speckle formation. Elife 9, e60579 (2020).
Lu, X. et al. SON connects the splicing-regulatory network with pluripotency in human embryonic stem cells. Nat. Cell Biol. 15, 1141–1152 (2013).
Signer, R. A., Magee, J. A., Salic, A. & Morrison, S. J. Haematopoietic stem cells require a highly regulated protein synthesis rate. Nature 509, 49–54 (2014).
Courel, M. et al. GC content shapes mRNA storage and decay in human cells. Elife 8, e49708 (2019).
Brengues, M., Teixeira, D. & Parker, R. Movement of eukaryotic mRNAs between polysomes and cytoplasmic processing bodies. Science 310, 486–489 (2005).
Di Stefano, B. et al. The RNA helicase DDX6 controls cellular plasticity by modulating P-body homeostasis. Cell Stem Cell 25, 622–638.e613 (2019).
Hubstenberger, A. et al. P-body purification reveals the condensation of repressed mRNA regulons. Mol. Cell 68, 144–157.e145 (2017).
Teixeira, D., Sheth, U., Valencia-Sanchez, M. A., Brengues, M. & Parker, R. Processing bodies require RNA for assembly and contain nontranslating mRNAs. RNA 11, 371–382 (2005).
Aizer, A. et al. Quantifying mRNA targeting to P-bodies in living human cells reveals their dual role in mRNA decay and storage. J. Cell Sci. 127, 4443–4456 (2014).
Ayache, J. et al. P-body assembly requires DDX6 repression complexes rather than decay or Ataxin2/2L complexes. Mol. Biol. Cell 26, 2579–2595 (2015).
Kamenska, A. et al. The DDX6–4E-T interaction mediates translational repression and P-body assembly. Nucleic Acids Res. 44, 6318–6334 (2016).
Kodali, S. et al. RNA sequestration in P-bodies sustains myeloid leukaemia. Nat. Cell Biol. 26, 1745–1758 (2024).
Schoedel, K. B. et al. The bulk of the hematopoietic stem cell population is dispensable for murine steady-state and stress hematopoiesis. Blood 128, 2285–2296 (2016).
Pietras, E. M. et al. Functionally distinct subsets of lineage-biased multipotent progenitors control blood production in normal and regenerative conditions. Cell Stem Cell 17, 35–46 (2015).
Pradeu, T., Thomma, B., Girardin, S. E. & Lemaitre, B. The conceptual foundations of innate immunity: taking stock 30 years later. Immunity 57, 613–631 (2024).
Okabe, Y. & Medzhitov, R. Tissue-specific signals control reversible program of localization and functional polarization of macrophages. Cell 157, 832–844 (2014).
Ochando, J., Mulder, W. J. M., Madsen, J. C., Netea, M. G. & Duivenvoorden, R. Trained immunity — basic concepts and contributions to immunopathology. Nat. Rev. Nephrol. 19, 23–37 (2023).
Akashi, K., Traver, D., Miyamoto, T. & Weissman, I. L. A clonogenic common myeloid progenitor that gives rise to all myeloid lineages. Nature 404, 193–197 (2000).
Suh, H. C. et al. C/EBPα determines hematopoietic cell fate in multipotential progenitor cells by inhibiting erythroid differentiation and inducing myeloid differentiation. Blood 107, 4308–4316 (2006).
Xie, H., Ye, M., Feng, R. & Graf, T. Stepwise reprogramming of B cells into macrophages. Cell 117, 663–676 (2004).
Bussmann, L. H. et al. A robust and highly efficient immune cell reprogramming system. Cell Stem Cell 5, 554–566 (2009).
Christou-Kent, M. et al. CEBPA phase separation links transcriptional activity and 3D chromatin hubs. Cell Rep. 42, 112897 (2023). This work links the condensation ability of the crucial myeloid transcription factor C/EBPα to its ability to rewire chromatin organization and transcription.
Naderi, J. et al. An activity-specificity trade-off encoded in human transcription factors. Nat. Cell Biol. 26, 1309–1321 (2024).
Lawrence, T. & Natoli, G. Transcriptional regulation of macrophage polarization: enabling diversity with identity. Nat. Rev. Immunol. 11, 750–761 (2011).
Gosselin, D. et al. Environment drives selection and function of enhancers controlling tissue-specific macrophage identities. Cell 159, 1327–1340 (2014).
Kaikkonen, M. U. et al. Remodeling of the enhancer landscape during macrophage activation is coupled to enhancer transcription. Mol. Cell 51, 310–325 (2013).
Jia, P. et al. ZMYND8 mediated liquid condensates spatiotemporally decommission the latent super-enhancers during macrophage polarization. Nat. Commun. 12, 6535 (2021). This study shows how condensate formation by the chromatin reader ZMYND8 acts as a brake on de novo super-enhancer activity in polarized macrophages to limit inflammation.
Kondo, M. Lymphoid and myeloid lineage commitment in multipotent hematopoietic progenitors. Immunol. Rev. 238, 37–46 (2010).
Lin, H. & Grosschedl, R. Failure of B-cell differentiation in mice lacking the transcription factor EBF. Nature 376, 263–267 (1995).
Morgan, D. & Tergaonkar, V. Unraveling B cell trajectories at single cell resolution. Trends Immunol. 43, 210–229 (2022).
Wang, Y. et al. A prion-like ___domain in transcription factor EBF1 promotes phase separation and enables B cell programming of progenitor chromatin. Immunity 53, 1151–1167.e1156 (2020). This work links transcriptional condensates to B cell differentiation, showing that the intrinsically disordered ___domain of the transcription factor EBF1 enables it to open closed chromatin at B cell fate-instructive genes.
Boller, S. et al. Pioneering activity of the C-terminal ___domain of EBF1 shapes the chromatin landscape for B cell programming. Immunity 44, 527–541 (2016).
Ravindran, R. & Michnick, S. W. Biomolecular condensates as drivers of membrane trafficking and remodelling. Curr. Opin. Cell Biol. 89, 102393 (2024).
Akkaya, M., Kwak, K. & Pierce, S. K. B cell memory: building two walls of protection against pathogens. Nat. Rev. Immunol. 20, 229–238 (2020).
Cyster, J. G. & Allen, C. D. C. B cell responses: cell interaction dynamics and decisions. Cell 177, 524–540 (2019).
Kastenhuber, E. R. & Lowe, S. W. Putting p53 in context. Cell 170, 1062–1078 (2017).
Diaz-Munoz, M. D. et al. Tia1 dependent regulation of mRNA subcellular ___location and translation controls p53 expression in B cells. Nat. Commun. 8, 530 (2017).
Gilks, N. et al. Stress granule assembly is mediated by prion-like aggregation of TIA-1. Mol. Biol. Cell 15, 5383–5398 (2004).
Curdy, N. et al. The proteome and transcriptome of stress granules and P bodies during human T lymphocyte activation. Cell Rep. 42, 112211 (2023).
Glasmacher, E. et al. Roquin binds inducible costimulator mRNA and effectors of mRNA decay to induce microRNA-independent post-transcriptional repression. Nat. Immunol. 11, 725–733 (2010). This work establishes a link between localization of specific transcripts within condensates and autoimmunity, showing that the RNA-binding protein Roquin1 must localize to P-bodies to repress transcripts that encode ICOS, which is a driver of T cell activation.
Zuniga-Pflucker, J. C. T-cell development made simple. Nat. Rev. Immunol. 4, 67–72 (2004).
Hosokawa, H. & Rothenberg, E. V. How transcription factors drive choice of the T cell fate. Nat. Rev. Immunol. 21, 162–176 (2021).
Johnson, J. L. et al. Lineage-determining transcription factor TCF-1 initiates the epigenetic identity of T cells. Immunity 48, 243–257.e210 (2018).
Gounari, F. & Khazaie, K. TCF-1: a maverick in T cell development and function. Nat. Immunol. 23, 671–678 (2022).
Goldman, N. et al. Intrinsically disordered ___domain of transcription factor TCF-1 is required for T cell developmental fidelity. Nat. Immunol. 24, 1698–1710 (2023). This study implicates transcriptional condensates in early T cell development, showing that the intrinsically disordered region of the transcription factor TCF-1 is required to enforce T cell lineage commitment.
Kunzli, M. & Masopust, D. CD4+ T cell memory. Nat. Immunol. 24, 903–914 (2023).
Chapman, N. M., Boothby, M. R. & Chi, H. Metabolic coordination of T cell quiescence and activation. Nat. Rev. Immunol. 20, 55–70 (2020).
Zhou, L. et al. T cell proliferation requires ribosomal maturation in nucleolar condensates dependent on DCAF13. J. Cell Biol. 222, e202201096 (2023). This work examines the role of nucleolar organization in T cell activation, providing evidence that the nucleolar protein DCAF13 promotes condensation of the ribosomal assembly machinery with ribosomal components.
Zhang, J. et al. Mammalian nucleolar protein DCAF13 is essential for ovarian follicle maintenance and oocyte growth by mediating rRNA processing. Cell Death Differ. 26, 1251–1266 (2019).
Bleichert, F., Granneman, S., Osheim, Y. N., Beyer, A. L. & Baserga, S. J. The PINc ___domain protein Utp24, a putative nuclease, is required for the early cleavage steps in 18S rRNA maturation. Proc. Natl Acad. Sci. USA 103, 9464–9469 (2006).
Allan, R. S. et al. An epigenetic silencing pathway controlling T helper 2 cell lineage commitment. Nature 487, 249–253 (2012).
Allshire, R. C. & Madhani, H. D. Ten principles of heterochromatin formation and function. Nat. Rev. Mol. Cell Biol. 19, 229–244 (2018).
Strom, A. R. et al. Phase separation drives heterochromatin ___domain formation. Nature 547, 241–245 (2017).
Larson, A. G. et al. Liquid droplet formation by HP1α suggests a role for phase separation in heterochromatin. Nature 547, 236–240 (2017).
Tortora, M. M. C., Brennan, L. D., Karpen, G. & Jost, D. HP1-driven phase separation recapitulates the thermodynamics and kinetics of heterochromatin condensate formation. Proc. Natl Acad. Sci. USA 120, e2211855120 (2023).
Erdel, F. et al. Mouse heterochromatin adopts digital compaction states without showing hallmarks of HP1-driven liquid-liquid phase separation. Mol. Cell 78, 236–249.e237 (2020).
Tough, D. F., Rioja, I., Modis, L. K. & Prinjha, R. K. Epigenetic regulation of T cell memory: recalling therapeutic implications. Trends Immunol. 41, 29–45 (2020).
Cuartero, S., Stik, G. & Stadhouders, R. Three-dimensional genome organization in immune cell fate and function. Nat. Rev. Immunol. 23, 206–221 (2023).
Acemel, R. D. & Lupianez, D. G. Evolution of 3D chromatin organization at different scales. Curr. Opin. Genet. Dev. 78, 102019 (2023).
Zheng, H. & Xie, W. The role of 3D genome organization in development and cell differentiation. Nat. Rev. Mol. Cell Biol. 20, 535–550 (2019).
Onrust-van Schoonhoven, A. et al. 3D chromatin reprogramming primes human memory TH2 cells for rapid recall and pathogenic dysfunction. Sci. Immunol. 8, eadg3917 (2023). This study uncovers the compartmentalization of recall response genes and their regulatory elements in memory T cells, linking spatial organization of chromatin to immunological memory.
Crotty, S. T follicular helper cell differentiation, function, and roles in disease. Immunity 41, 529–542 (2014).
Vinuesa, C. G. et al. A RING-type ubiquitin ligase family member required to repress follicular helper T cells and autoimmunity. Nature 435, 452–458 (2005).
Tavernier, S. J. et al. A human immune dysregulation syndrome characterized by severe hyperinflammation with a homozygous nonsense Roquin-1 mutation. Nat. Commun. 10, 4779 (2019).
Ross, S. H. & Cantrell, D. A. Signaling and function of interleukin-2 in T lymphocytes. Annu. Rev. Immunol. 36, 411–433 (2018).
Spolski, R. et al. Distinct use of super-enhancer elements controls cell type-specific CD25 transcription and function. Sci. Immunol. 8, eadi8217 (2023). This study uncovers the differential use of super-enhancer elements to achieve cell type-specific expression patterns of a key cytokine receptor gene, CD25, in distinct T cell lineages.
Blayney, J. W. et al. Super-enhancers include classical enhancers and facilitators to fully activate gene expression. Cell 186, 5826–5839.e5818 (2023).
Mogilenko, D. A., Shchukina, I. & Artyomov, M. N. Immune ageing at single-cell resolution. Nat. Rev. Immunol. 22, 484–498 (2022).
Goodell, M. A. & Rando, T. A. Stem cells and healthy aging. Science 350, 1199–1204 (2015).
Sun, D. et al. Epigenomic profiling of young and aged HSCs reveals concerted changes during aging that reinforce self-renewal. Cell Stem Cell 14, 673–688 (2014).
Tang, B. et al. Aging-disturbed FUS phase transition impairs hematopoietic stem cells by altering chromatin structure. Blood 143, 124–138 (2024).
Lv, K. et al. HectD1 controls hematopoietic stem cell regeneration by coordinating ribosome assembly and protein synthesis. Cell Stem Cell 28, 1275–1290.e1279 (2021).
Maneix, L. et al. Cyclophilin A supports translation of intrinsically disordered proteins and affects haematopoietic stem cell ageing. Nat. Cell Biol. 26, 593–603 (2024). This study links impaired chaperone support for translation of key condensate regulators to haematopoietic stem cell ageing.
Flach, J. et al. Replication stress is a potent driver of functional decline in ageing haematopoietic stem cells. Nature 512, 198–202 (2014). This work connects nucleolar stress signalling to impaired ribosome assembly and the age-associated decline of haematopoietic stem cell function.
Morganti, C. et al. NPM1 ablation induces HSC aging and inflammation to develop myelodysplastic syndrome exacerbated by p53 loss. EMBO Rep. 23, e54262 (2022).
Boisvert, F. M., van Koningsbruggen, S., Navascues, J. & Lamond, A. I. The multifunctional nucleolus. Nat. Rev. Mol. Cell Biol. 8, 574–585 (2007).
Salim, D. et al. DNA replication stress restricts ribosomal DNA copy number. PLoS Genet. 13, e1007006 (2017).
Mitchell, C. in Genetics and Development. PhD thesis, Columbia Univ. Irving Medical Center (2024).
Perry, R. P. The cellular sites of synthesis of ribosomal and 4s RNA. Proc. Natl Acad. Sci. USA 48, 2179–2186 (1962).
Brunetti, L. et al. Mutant NPM1 maintains the leukemic state through HOX expression. Cancer Cell 34, 499–512.e499 (2018).
Oka, M. et al. Chromatin-bound CRM1 recruits SET-Nup214 and NPM1c onto HOX clusters causing aberrant HOX expression in leukemia cells. Elife 8, e46667 (2019).
Wang, X. Q. D. et al. Mutant NPM1 hijacks transcriptional hubs to maintain pathogenic gene programs in acute myeloid leukemia. Cancer Discov. 13, 724–745 (2023). This work indicates that a mutant form of the nucleolar protein NPM1, which is commonly expressed in acute myeloid leukaemia, can bind specific chromatin regions and form aberrant transcriptional condensates that sustain transcription of leukaemic genes.
Uckelmann, H. J. et al. Mutant NPM1 directly regulates oncogenic transcription in acute myeloid leukemia. Cancer Discov. 13, 746–765 (2023). This study also supports a model in which mutant NPM1 binds specific chromatin targets and forms transcriptional condensates that maintain leukaemic transcription.
Liu, Y. et al. Condensate-promoting ENL mutation drives tumorigenesis in vivo through dynamic regulation of histone modifications and gene expression. Cancer Discov. 14, 1522–1546 (2024).
Song, L. et al. Hotspot mutations in the structured ENL YEATS ___domain link aberrant transcriptional condensates and cancer. Mol. Cell 82, 4080–4098.e4012 (2022).
Guo, C. et al. ENL initiates multivalent phase separation of the super elongation complex (SEC) in controlling rapid transcriptional activation. Sci. Adv. 6, eaay4858 (2020).
Sanalkumar, R. et al. Highly connected 3D chromatin networks established by an oncogenic fusion protein shape tumor cell identity. Sci. Adv. 9, eabo3789 (2023).
Quiroga, I. Y., Ahn, J. H., Wang, G. G. & Phanstiel, D. Oncogenic fusion proteins and their role in three-dimensional chromatin structure, phase separation, and cancer. Curr. Opin. Genet. Dev. 74, 101901 (2022).
Nussenzweig, A. & Nussenzweig, M. C. Origin of chromosomal translocations in lymphoid cancer. Cell 141, 27–38 (2010).
Riedel, S. S. et al. Intrinsically disordered Meningioma-1 stabilizes the BAF complex to cause AML. Mol. Cell 81, 2332–2348.e2339 (2021).
Ahn, J. H. et al. Phase separation drives aberrant chromatin looping and cancer development. Nature 595, 591–595 (2021).
Chandra, B. et al. Phase separation mediates NUP98 fusion oncoprotein leukemic transformation. Cancer Discov. 12, 1152–1169 (2022).
Oka, M. et al. Phase-separated nuclear bodies of nucleoporin fusions promote condensation of MLL1/CRM1 and rearrangement of 3D genome structure. Cell Rep. 42, 112884 (2023).
Michmerhuizen, N. L., Klco, J. M. & Mullighan, C. G. Mechanistic insights and potential therapeutic approaches for NUP98-rearranged hematologic malignancies. Blood 136, 2275–2289 (2020).
Voisset, E. et al. Pml nuclear body disruption cooperates in APL pathogenesis and impairs DNA damage repair pathways in mice. Blood 131, 636–648 (2018).
Daniel, M. T. et al. PML protein expression in hematopoietic and acute promyelocytic leukemia cells. Blood 82, 1858–1867 (1993).
Dyck, J. A. et al. A novel macromolecular structure is a target of the promyelocyte-retinoic acid receptor oncoprotein. Cell 76, 333–343 (1994).
Bercier, P. et al. Structural basis of PML–RARA oncoprotein targeting by arsenic unravels a cysteine rheostat controlling PML body assembly and function. Cancer Discov. 13, 2548–2565 (2023).
Zhang, Y. et al. Phase separation of PML/RARα and BRD4 coassembled microspeckles governs transcriptional dysregulation in acute promyelocytic leukemia. Proc. Natl Acad. Sci. USA 121, e2406519121 (2024). This study uncovers an unexpected function for PML condensates in acute promyelocytic leukaemia, showing that they sequester the transcription cofactor BRD4, redistributing it to oncogenic super-enhancers and broad promoters, thereby promoting leukaemic gene transcription.
Pi, W. C. et al. E2A–PBX1 functions as a coactivator for RUNX1 in acute lymphoblastic leukemia. Blood 136, 11–23 (2020).
Lee, Y. L. et al. Mediator subunit MED1 is required for E2A–PBX1-mediated oncogenic transcription and leukemic cell growth. Proc. Natl Acad. Sci. USA 118, e1922864118 (2021).
Gozdecka, M. et al. UTX-mediated enhancer and chromatin remodeling suppresses myeloid leukemogenesis through noncatalytic inverse regulation of ETS and GATA programs. Nat. Genet. 50, 883–894 (2018).
Shi, B. et al. UTX condensation underlies its tumour-suppressive activity. Nature 597, 726–731 (2021).
Dominguez, P. M. et al. TET2 deficiency causes germinal center hyperplasia, impairs plasma cell differentiation, and promotes B-cell lymphomagenesis. Cancer Discov. 8, 1632–1653 (2018).
Delhommeau, F. et al. Mutation in TET2 in myeloid cancers. N. Engl. J. Med. 360, 2289–2301 (2009).
Couronne, L., Bastard, C. & Bernard, O. A. TET2 and DNMT3A mutations in human T-cell lymphoma. N. Engl. J. Med. 366, 95–96 (2012).
Guo, L. et al. Perturbing TET2 condensation promotes aberrant genome-wide DNA methylation and curtails leukaemia cell growth. Nat. Cell Biol. 26, 2154–2167 (2024).
Wu, X. & Zhang, Y. TET-mediated active DNA demethylation: mechanism, function and beyond. Nat. Rev. Genet. 18, 517–534 (2017).
Fonteneau, G. et al. Stress granules determine the development of obesity-associated pancreatic cancer. Cancer Discov. 12, 1984–2005 (2022).
Biancon, G. et al. Precision analysis of mutant U2AF1 activity reveals deployment of stress granules in myeloid malignancies. Mol. Cell 82, 1107–1122.e1107 (2022). This work reveals stress granule components as targets of aberrant splicing in malignant myeloid cells, which leads to increased stress granule formation.
Truitt, M. L. & Ruggero, D. New frontiers in translational control of the cancer genome. Nat. Rev. Cancer 16, 288–304 (2016).
Paris, J. et al. Targeting the RNA m6A reader YTHDF2 selectively compromises cancer stem cells in acute myeloid leukemia. Cell Stem Cell 25, 137–148.e136 (2019).
Barbieri, I. et al. Promoter-bound METTL3 maintains myeloid leukaemia by m6A-dependent translation control. Nature 552, 126–131 (2017).
Vu, L. P. et al. The N6-methyladenosine (m6A)-forming enzyme METTL3 controls myeloid differentiation of normal hematopoietic and leukemia cells. Nat. Med. 23, 1369–1376 (2017).
Li, Z. et al. FTO plays an oncogenic role in acute myeloid leukemia as a N6-methyladenosine RNA demethylase. Cancer Cell 31, 127–141 (2017).
Shen, C. et al. RNA demethylase ALKBH5 selectively promotes tumorigenesis and cancer stem cell self-renewal in acute myeloid leukemia. Cell Stem Cell 27, 64–80 e69 (2020).
Meyer, K. D. & Jaffrey, S. R. Rethinking m6A readers, writers, and erasers. Annu. Rev. Cell Dev. Biol. 33, 319–342 (2017).
Cheng, Y. et al. N6-methyladenosine on mRNA facilitates a phase-separated nuclear body that suppresses myeloid leukemic differentiation. Cancer Cell 39, 958–972.e958 (2021). This study connects aberrant nuclear condensate formation to the misregulation of m6A-modified RNAs in the context of myeloid leukaemia.
Zhu, G. et al. Phase separation of disease-associated SHP2 mutants underlies MAPK hyperactivation. Cell 183, 490–502.e418 (2020).
Pandey, R., Saxena, M. & Kapur, R. Role of SHP2 in hematopoiesis and leukemogenesis. Curr. Opin. Hematol. 24, 307–313 (2017).
Bracha, D., Walls, M. T. & Brangwynne, C. P. Probing and engineering liquid-phase organelles. Nat. Biotechnol. 37, 1435–1445 (2019).
Dai, Y., You, L. & Chilkoti, A. Engineering synthetic biomolecular condensates. Nat. Rev. Bioeng. 1, 466–480 (2023).
Femino, A. M., Fay, F. S., Fogarty, K. & Singer, R. H. Visualization of single RNA transcripts in situ. Science 280, 585–590 (1998).
Xia, C., Colognori, D., Jiang, X., Xu, K. & Doudna, J. A. Single-molecule live-cell RNA imaging with CRISPR-Csm. Preprint at bioRxiv https://doi.org/10.1101/2024.07.14.603457 (2024).
Qin, W., Cho, K. F., Cavanagh, P. E. & Ting, A. Y. Deciphering molecular interactions by proximity labeling. Nat. Methods 18, 133–143 (2021).
Ren, J., Luo, S., Shi, H. & Wang, X. Spatial omics advances for in situ RNA biology. Mol. Cell 84, 3737–3757 (2024).
Wang, X. et al. N6-methyladenosine modification of MALAT1 promotes metastasis via reshaping nuclear speckles. Dev. Cell 56, 702–715.e708 (2021).
Markmiller, S. et al. Context-dependent and disease-specific diversity in protein interactions within stress granules. Cell 172, 590–604.e513 (2018).
Lam, S. S. et al. Directed evolution of APEX2 for electron microscopy and proximity labeling. Nat. Methods 12, 51–54 (2015).
Lobingier, B. T. et al. An approach to spatiotemporally resolve protein interaction networks in living cells. Cell 169, 350–360.e312 (2017).
Brangwynne, C. P. et al. Germline P granules are liquid droplets that localize by controlled dissolution/condensation. Science 324, 1729–1732 (2009).
Feric, M. et al. Coexisting liquid phases underlie nucleolar subcompartments. Cell 165, 1686–1697 (2016).
Frottin, F. et al. The nucleolus functions as a phase-separated protein quality control compartment. Science 365, 342–347 (2019).
Brangwynne, C. P., Mitchison, T. J. & Hyman, A. A. Active liquid-like behavior of nucleoli determines their size and shape in Xenopus laevis oocytes. Proc. Natl Acad. Sci. USA 108, 4334–4339 (2011).
Patel, A. et al. A liquid-to-solid phase transition of the ALS protein FUS accelerated by disease mutation. Cell 162, 1066–1077 (2015).
Shin, Y. et al. Liquid nuclear condensates mechanically sense and restructure the genome. Cell 175, 1481–1491.e1413 (2018).
Alberti, S., Gladfelter, A. & Mittag, T. Considerations and challenges in studying liquid-liquid phase separation and biomolecular condensates. Cell 176, 419–434 (2019).
McSwiggen, D. T., Mir, M., Darzacq, X. & Tjian, R. Evaluating phase separation in live cells: diagnosis, caveats, and functional consequences. Genes. Dev. 33, 1619–1634 (2019).
Lyon, A. S., Peeples, W. B. & Rosen, M. K. A framework for understanding the functions of biomolecular condensates across scales. Nat. Rev. Mol. Cell Biol. 22, 215–235 (2021).
Yang, J. et al. MYC phase separation selectively modulates the transcriptome. Nat. Struct. Mol. Biol. 31, 1567–1579 (2024).
Acknowledgements
We thank all members of the Di Stefano lab for stimulating discussions. We also thank R. Stadhouders, J. Lee, G. K. Datar and J. A. Riback for their insightful comments on the manuscript. B.D.S. is a Cancer Prevention and Research Institute of Texas (CPRIT) Scholar in Cancer Research. B.D.S. is supported by the CPRIT Recruitment of First-Time, Tenure-Track Faculty Member Award RR200079, the American Society of Hematology (ASH) Scholar Award, the Andrew McDonough B+ Foundation (AMBF), the Worldwide Cancer Research (WCR) Foundation, the Milky Way Research Foundation Investigator Award and the NIH National Institute of General Medical Sciences Maximizing Investigators’ Research Award 1R35GM147126-01. S.K. is supported by NIH National Cancer Institute 1F32CA288043-01. C.M.S. is supported by NIH grant T32DK060445.
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Kodali, S., Sands, C.M., Guo, L. et al. Biomolecular condensates in immune cell fate. Nat Rev Immunol 25, 445–459 (2025). https://doi.org/10.1038/s41577-025-01130-z
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DOI: https://doi.org/10.1038/s41577-025-01130-z