Cell Biology and Anatomy Discipline

Center for Cancer Cell Biology, Immunology, and Infection

Research

Awarded to:
Mirek Dundr

https://www.youtube.com/watch?v=K7OP3AAHWBE

The mammalian cell nucleus is a highly organized organelle, which reflects the complex regulation of its multiple activities. The nucleus contains an ever-growing number of specialized compartments, many of which contain disease gene products such as spinal muscular atrophy, Xeroderma Pigmentosum, Werner syndrome, amongst others.

Biological compartmentalization is a foundation of cellular function for all living systems. Distribution of functionally linked components into shared spaces maximizes efficiency, limits biological noise, and reduces waste. Within the nucleus, a number of functionally critical structures composed of proteins and nucleic acids, known as membraneless biomolecular condensates (MBCs), exist. Recent advances have implicated liquid-liquid phase transition as the governing organizational principle of these structures. Important questions remain concerning how MBC formation is initiated and orchestrated, and how MBCs are structurally organized in the liquid-like state to perform multiple functions.

One of the most important questions in modern cell biology is how gene expression is organized in the cell nucleus. Recent discoveries suggest that the nuclear interior is highly organized and nuclear processes may depend on the dynamics of nuclear components and compartments. Fundamental questions concerning the understanding of the dynamic organization of gene expression have not been answered: How are nuclear compartments maintained in the membrane-less interior of the nucleus? How are transcription and RNA processing complexes regulated within the nucleus? What are the molecular mechanisms that coordinate the functions of these complexes in the highly dynamic nuclear environment? I would like to address these aspects of gene expression and nuclear function using in vivo imaging combined with molecular biology/biochemical approaches.

The role of Cajal bodies in 3D organization of the genome

In humans, about two meters of DNA must be tightly packed to fit into the limited space of the cell nucleus. This must occur, however, whilst still allowing the cell to function properly. One way that this is achieved is by dividing the cell nucleus into a variety of structural domains called nuclear bodies. Despite their prominence in the nucleus, the function of nuclear bodies is still unclear. A prime example is the Cajal body, which is present in cancer cells but absent in healthy cells. The Cajal body plays a key role in processing of RNAs (which ultimately produce proteins) by helping to assemble a specialized set of molecules called spliceosomal snRNAs. Currently, we do not know with what genes Cajal bodies are most physically associated with, or the implications of their loss for cancer cell function.

To answer the questions, we studied the active grouping of genes around Cajal bodies in cancer. Using a newly-developed microscopy method to study five genes at the same time with a Cajal body, we established that Cajal bodies and are often situated where several different chromosomes interact. By performing a gene-interaction mapping analysis called 4C-seq we identified all the genes that physically associate with the Cajal body. Excitingly, Cajal bodies simultaneously interact with multiple chromosomes and spliceosomal snRNA genes to form clusters. These clusters are not present in healthy normal cells lacking Cajal bodies. We also discovered that chromosome 1, the largest human chromosome, could be reorganized into a rosette that engulfed a single Cajal body by grouping genes which are very far away from each other. To confirm our data, we pioneered a new analysis that can accurately determine whether genes physically cluster around a Cajal body using a technique known as deep imaging. Here, we could automatically count overlapping genes and Cajal bodies from 1000s of cancer cells. Removal of Cajal bodies from cancer cells by reducing the levels of an essential Cajal body protein reduced the number of these specific gene clusters and decreased target gene activity. Ultimately, without Cajal bodies, cells could not accurately process RNAs, which has serious implications for cancer biology.

Our work shows that Cajal bodies form at sites of high gene activity where they help to further stimulate these genes. By looking at the effect of Cajal bodies on all RNAs in the cell, we also discovered that these structures have wide-reaching effects on RNA processing in cancer cells. These observations suggest that Cajal bodies change the 3D organization of the human genome in cancer and may help researchers to further understand how our cells change during disease.

Publications

• Schmit JD, Feric M, and Dundr M (2021) How hierarchical interactions make membraneless organelles tick like clockwork. Trends in Biochemical Sciences, 46(7):525-534.
• Correll, CC, Bartek J, Dundr M (2019) The Nucleolus: A Multiphase Condensate Balancing Ribosome Synthesis and Translational Capacity in Health, Aging and Ribosomopathies. Cells. 8(8). doi: 10.3390/cells8080869
• Bártová E, Legartová S., Suchánková S., Dundr M., Krejci J. (2018) A role of the 53BP1 protein in genome protection: structural and functional characteristics of 53BP1-dependent DNA repair. Aging. doi: 10.18632/aging.101917
• Sawyer, I.A., Bartek, J., Dundr, M. (2018). Phase separated microenvironments inside the cell nucleus are linked to disease and regulate epigenetic state, transcription and RNA processing. Seminars in Cell Dev. Biol. doi: 10.1016/j.semcdb.2018.07.001
• Sawyer IA, Sturgill D, Dundr M.  Membraneless nuclear organelles and the search for phases within phases.  Wiley Interdiscip Rev RNA. 2019 Mar;10(2):e1514. doi: 10.1002/wrna.1514. Epub 2018 Oct 25. Review. (PubMed)
• Sawyer IA, Bartek J, Dundr M. Phase separated microenvironments inside the nucleus are linked to disease and regulate epigenetic state, transcription and RNA processing. Semin Cell Dev Biol. 2018 Jul 11. pii: S1084-9521(18)30120-4. doi: 10.1016/j.semcdb.2018.07.001. [Epub ahead of print] Review. (PubMed)
• Albrecht TR, Shevtsov SP, Wu Y, Mascibroda LG, Peart NJ, Huang KL, Sawyer IA, Tong L, Dundr M, Wagner EJ.  Integrator subunit 4 is a 'Symplekin-like' scaffold that associates with INTS9/11 to form the Integrator cleavage module.  Nucleic Acids Res. 2018 May 4;46(8):4241-4255. doi: 10.1093/nar/gky100.  (PubMed)
• Sawyer I.A., Dundr M. (2017) Nuclear bodies. Chapter 11. Nuclear Architecture and Dynamics (Lavelle C. and Victor, J-M, editors). Translational Epigenetics Series. Elsevier. 235–256. doi.org/10.1016/B978-0-12-803480-4.00010-7
• Sawyer IA, Dundr M.  Chromatin loops and causality loops: the influence of RNA upon spatial nuclear architecture.  Chromosoma. 2017 Oct;126(5):541-557. doi: 10.1007/s00412-017-0632-y. Epub 2017 Jun 7.  (PubMed)
• Sawyer IA, Sturgill D, Sung M-H, Hager GL, Dundr M. (2016). Cajal body function in genome organization and transcriptome diversity. BioEssays 38: 1197-1208.  (PubMed)
• Sawyer IA, Hager GL, Dundr M. (2016) Specific genomic cues regulate Cajal body assembly. RNA Biology. DOI:10.1080/15476286.2016.1243648  (PubMed)
• Sawyer IA, Dundr M. (2016) Nuclear bodies: built to boost. J Cell Biol. 213:509-11.  (PubMed)
• Sawyer IA, Shevtsov SP, Dundr M. (2016). Spectral imaging to visualize higher-order genomic organization. Nucleus. 7:325-38.  (PubMed)
• Wang Q, Sawyer IA, Sung MH, Sturgill D, Shevtsov SP, Pegoraro G, Hakim O, Baek S, Hager GL, Dundr M. (2016) Cajal bodies are linked to genome conformation. Nature Communications. DOI: 10.1038/ncomms10966.  (PubMed)
• Salomon-Kent R, Marom R, John S, Dundr M., Schiltz LR, Gutierrez J, Workman J, Benayahu D, Hager GL (2015) New face for Chromatin-Related Mesenchymal Modulator: n-CHD9 localizes to nucleoli and interacts with ribosomal genes. J Cell Physiol 230:2270-80.  (PubMed)
• Olson, MOJ and Dundr, M. (2014) Nucleolus: Structure and Function. eLS, 10.1002/9780470015902.a0005975.pub3. 
• Case, AM, Sawyer, IA, Dundr, M., Hastings ML (2014) Pre-mRNA Splicing: Function and Dysfunction. Encyclopedia of Cell Biology, 503-511. 
• Dundr, M. Nucleation of nuclear bodies by RNA. (2013). Methods Mol. Biol. 1042: 351-64.  (PubMed)
• Ko, N.L., Taylor, J.M., Bellon, M., Pratt, G., Rechsteiner, M., Shevtsov, S.P., Dundr, M., Nicot, C. (2013) HTLV-I p30 Recruits the Proteasome Activator PA28g to Suppress Virus Replication. Blood 121: 791-800.
• Tripathi V, Song DY, Zong X, Shevtsov SP, Hearn S, Fu X-D, Dundr M., Prasanth KV (2012) SRSF1 modulates the organization of splicing factors in nuclear speckles and regulates transcription. Mol. Biol. Cell. 23: 3694-3706.  (PubMed)
• Poh YC, Shevtsov SP, Chowdhury F, Wu DC, Na S, Dundr M.*, Wang N (2012) Dynamic force-induced direct dissociation of protein complexes in a nuclear body in living cells. Nat. Commun. 3:866. doi: 10.1038/ncomms1873. *co-corresponding author.  (PubMed)
• Kamieniarz K, Izzo A, Dundr M., Tropberger P, Ozretic L, Kirfel J, Scheer E, Tropel P, Wisniewski JR, Tora L, Viville S, Buettner R, Schneider R. (2012) A dual role of linker histone H1.4 Lys 34 acetylation in transcriptional activation. Genes Dev. 26: 797-802.  (PubMed)
• Dundr M. (2012) Nuclear bodies: multifunctional companions of the genome. Curr Opin Cell Biol. 24: Apr 25.  (PubMed)
• Dundr, M. (2011) Seed and grow: a two-step model for nuclear body biogenesis. J. Cell Biol. 193: 605-6.  (PubMed)
• Hergeth, S.P., Dundr, M., Tropberger, P., Zee, B.M., Garcia, B.A., Daujat, S., Schneider, R. (2011) Isoform specific phosphorylation of human linker histone H1.4 in mitosis by Aurora B kinase. J. Cell Sci. 124: 1623-8.  (PubMed)
• Liu, J., Chung, H-J., He, L., Malide D., Dundr, M., Levens, D. (2011) Synergetic action of JTV1 and FBP induces USP29 transcription to stabilize p53. EMBO J. 30: 846-58.  (PubMed)
• Shevtsov, S.P., Dundr, M. (2011) Nucleation of nuclear bodies by RNA. Nature Cell Biol. 13: 167-73.  (PubMed)
• Dundr, M.*, Misteli T. (2010). Biogenesis of nuclear bodies. The Nucleus. (Spector, D.L., Misteli, T., eds.) Cold Spring Harbor Press. *contributed equally, co-corresponding author. Cold Spring Harb. Perspect. Biol. 2:a000711. 
• Vogler, C., Huber, C., Waldmann, T., Braun, L., Chassignet, I., Dundr, M., Längst, G., Schneider, R. Histone H2A C-terminus regulates chromatin dynamics, remodeling and histone H1 binding and cellular stress response. PLoS Genet. 6:e1001234.  (PubMed)
• Weiss, T., Hergeth, S., Zeissler, U., Izzo, A., Tropberger, P., Zee, B.M., Dundr, M., Garcia, B.A., Daujat, S., Schneider, R. (2010) Histone H1 variant-specific lysine methylation by G9a/KMT1C and Glp1/KMT1D. Epigenetics Chromatin. 3: 7.  (PubMed)
• Shevtsov S, Dundr M. (2009).De novo formation of subnuclear bodies on their target genes. Chromosome Res. 17: 535-6.
• Kaiser TE, Intine RV, Dundr M. (2008). De novo formation of a subnuclear body. Science 322:1713-7.  (PubMed)
• Bierhoff H, Dundr M., Michels AA, Grummt I. (2008). Phosphorylation by casein kinase 2 facilitates rRNA gene transcription by promoting dissociation of TIF-IA from elongating RNA polymerase I. Mol Cell Biol. 28: 4988-98.  (PubMed)
• Dundr M., Ospina JK, Sung MH, John S, Upender M, Ried T, Hager GL, Matera AG. (2007). Actin-dependent intranuclear repositioning of an active gene locus in vivo. J. Cell Biol. 179: 1095-103 Corresponding author  (PubMed)
• Fukumoto R, Dundr M., Nicot C, Adams A, Valeri VW, Samelson LE, Franchini G. (2007). Inhibition of T-cell receptor signal transduction and viral expression by the linker for activation of T cells-interacting p12(I) protein of human T-cell leukemia/lymphoma virus type 1. J. Virol. : 81: 9088-99  (PubMed)
• Gorski. S.A., Dundr, M. *, Misteli, T. (2006). The road much traveled: trafficking in the cell nucleus. Curr. Opin. Cell Biol. 18: 284-90. *contributed equally.  (PubMed)
• Stavreva, D.A., Kawasaki, M., Dundr, M., Koberna, K., Mueller, W.G., Tsujimura-Takahashi, T., Komatsu, W., Hayno, T., Raska, I., Misteli, T., Takahashi, N., McNally, J.G. (2006). Potential roles for ubiquitin and the proteasome during ribosome biogenesis. Mol. Cell Biol. 26: 5131-45.  (PubMed)
• Ghorbel, S., Sinha-Datta, U., Dundr, M., Brown, M., Franchini, G., Nicot, C. (2006). Human T-cell leukemia virus type I p30 nuclear/nucleolar retention is mediated through interactions with RNA and a constituent of the 60S ribosomal subunit. J. Biol. Chem. 281(48): 37150-8.  (PubMed)
• Wagner, E.J., Ospina, JK, Hu, Y., Dundr, M., Matera, A.G., Marzluff, W.F. (2006). Conserved zinc fingers mediate multiple functions of ZFP100, a U7snRNP associated protein. RNA 12: 1206-18.  (PubMed)
• Chung, H.-J., Liu, J., Dundr, M., Nie, Z., Sanford, S., Levens, D. (2006). FBPs are calibrated molecular tools to adjust gene expression. Mol. Cell Biol. 26: 6584-97.  (PubMed)
• Jiao, W., Datta, J., Lin, H.-M., Dundr, M., Rane, S.G. (2006) Nucleocytoplasmic shuttling of the retinoblastoma tumor suppressor protein via Cdk phosphorylation-dependent nuclear export. J. Biol Chem. 281: 38098-108.  (PubMed)
• Olson, M.O.J., Dundr, M. (2005) The moving parts of the nucleolus. Histochem. Cell Biol. 123: 203-216.  (PubMed)
• Dundr, M., Ospina J.K., Sung M.H., John S., Upender M., Ried T., Hager G.L., Matera A.G. (2007) Actin-dependent intranuclear repositioning of an active gene locus in vivo. J. Cell Biol. 179:1095-103  (PubMed)
• Fukumoto R., Dundr, M., Nicot C., Adams A., Valeri V.W., Samelson L.E., Franchini G. (2007) Inhibition of T-cell receptor signal transduction and viral expression by the linker for activation of T cells-interacting p12(I) protein of human T-cell leukemia/lymphoma virus type 1. J. Virol. 81:9088-99.  (PubMed)
• Franchini, G., Fukumoto, R., Dundr, M. Valeri, V.W. (2005) HTLV-1 p12I and p30II proteins in viral persistence and pathogenesis. Braz. J. Infect. Dis. 9: 447-9.
• Dundr, M., Misteli, T. (2004) Transcriptional complexity from dynamic interaction networks in vivo. Current Genomics. 5: 559-566. 
• Chen, D., Dundr, M. Wang, C., Leung, A., Lamond, A., Misteli, T., Huang, S. (2005) Condensed mitotic chromatin is accessible to the transcription machinery and chromatin structural proteins. J. Cell Biol. 168: 41-54.  (PubMed)
• Younis, I., Khair, L., Dundr, M., Lairmore, M., Franchini, G., Green, P.L. (2004) Repression of human T-cell leukemia virus type 1 and 2 replication by a novel postranscriptional regulator. J. Virol. 78: 11077-11083.  (PubMed)
• Dundr, M., Hebert, M.D., Hongzi Xu, H., Stanek, D., Karpova, T.S., Neugebauer, K, M.D., Matera, A.G., Misteli, T. (2004) In vivo kinetics of Cajal body components. J. Cell Biol. 164: 831-842.  (PubMed)
• Intine, R., Dundr, M., Vasssilev, A., Schwartz, E., Zhou Y., DePamphilis, M.L., Maraia, R.J. (2004) Nonphosphorylated human La accumulates at nucleolar sites involved in rRNA biogenesis and interacts with nucleolin. Mol. Cell. Biol. 24: 10894-10904.  (PubMed)
• Nicot, C, Dundr, M., Johnson, J.M., Fullen, J.R., Fukumoto, R., Misteli, T., Franchini, G. (2004) A novel post-transcriptional mechanism for retroviral latency. Nature Med. 10: 197-201.
• Dundr, M., Misteli T. (2003) Gene expression dynamics. Biomed Pharmacother. 57: 180.
• Cheutin, T, Misteli T, Dundr, M. (2004) Dynamics of Nucleolar Components. In The Nucleolus. M. Olson ed., Landes Bioscience. Kluwer Academic/Klenum Publ., pp. 29-40.
• Parada L., Elbi C., Dundr, M. and Misteli T. (2003) Gene expression. In Essential Cell Biology: Volume 2: Cell Function (Davey J and Lord M, ed). Oxford University Press. 47-77.
• Dundr, M., Hoffmann-Rohrer U., Hu Q., Grummt I., Rothblum L.I., Phair R.D. Misteli T. (2002) A kinetic framework for RNA polymerase in vivo. Science 298: 1623-1626.  (PubMed)
• Dundr, M., McNally J.G., Cohen J, Misteli T. (2002). Quantitation of GFP fusion proteins in single living cells. J. Struct Biol. 140: 92-99.  (PubMed)
• Dundr, M., Misteli T. (2003) Measuring dynamics of nuclear proteins by photobleaching. Current Protocols in Cell Biology, Unit 13.5 (1-18), Supplement 18.  (PubMed)
• Cavanaugh A., Hirschler-Laszkiewicz I., Hu Q., Dundr, M., Smink T., Misteli T., Rothblum L.I. (2002) Rrn3 phosphorylation is a regulatory switch for ribosome biogenesis: cycloheximide inhibits the phosphorylation of Rrn3 and the interaction between Rrn3 and RPA43. J. Biol. Chem. 277: 27423-27432.  (PubMed)
• Intine R.V., Dundr, M., Misteli T., Maraia R.J. (2002) Aberrant nuclear trafficking of La protein leads to disordered processing of associated precursor tRNAs. Mol. Cell 9: 1113-1123.  (PubMed)
• Dundr, M. and Misteli T. (2002) Nucleolomics: An inventory of the nucleolus. Mol. Cell 9: 5-7.  (PubMed)
• Dundr, M. and Misteli T. (2001) Functional architecture in the cell nucleus. Biochem. J. 356: 297-310.  (PubMed)
• Dundr, M., Misteli T., Olson M.O.J. (2000). The dynamics of postmitotic reassembly of the nucleolus. J. Cell Biol. 150: 433-446.  (PubMed)
• Olson M.O.J, Dundr, M., Szebeni A. (2000). The nucleolus: an old factory with unexpected capabilities. Trends Cell Biol. 10: 189-196.  (PubMed)