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Article ; Online: Keeping membraneless organelles apart.

Schmit, Jeremy D / Dundr, Miroslav

2023 Volume 25, Issue 11, Page(s) 1566–1567

Language	English
Publishing date	2023-11-06
Publishing country	England
Document type	Journal Article
ZDB-ID	1474722-4
ISSN	1476-4679 ; 1465-7392
ISSN (online)	1476-4679
ISSN	1465-7392
DOI	10.1038/s41556-023-01265-y
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Zs.A 5169: Show issues			Location: Je nach Verfügbarkeit (siehe Angabe bei Bestand) bis Jg. 1994: Bestellungen von Artikeln über das Online-Bestellformular Jg. 1995 - 2021: Lesesall (2.OG) ab Jg. 2022: Lesesaal (EG)
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Article: How Hierarchical Interactions Make Membraneless Organelles Tick Like Clockwork.

Schmit, Jeremy D / Feric, Marina / Dundr, Miroslav

Trends in biochemical sciences

2021 Volume 46, Issue 7, Page(s) 525–534

Abstract: Biomolecular condensates appear throughout the cell, serving many different biochemical functions. We argue that condensate functionality is optimized when the interactions driving condensation vary widely in affinity. Strong interactions provide ... ...

Abstract	Biomolecular condensates appear throughout the cell, serving many different biochemical functions. We argue that condensate functionality is optimized when the interactions driving condensation vary widely in affinity. Strong interactions provide structural specificity needed to encode functional properties but carry the risk of kinetic arrest, while weak interactions allow the system to remain dynamic but do not restrict the conformational ensemble enough to sustain specific functional features. To support our opinion, we describe illustrative examples of the interplay of strong and weak interactions that are found in the nucleolus, SPOP/DAXX condensates, polySUMO/polySIM condensates, chromatin, and stress granules. The common feature of these systems is a hierarchical assembly motif in which weak, transient interactions condense structurally defined functional units.
MeSH term(s)	Animals ; Chromatin ; Kinetics ; Organelles ; Ticks
Chemical Substances	Chromatin
Language	English
Publishing date	2021-01-20
Publishing country	England
Document type	Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't ; Review
ZDB-ID	194216-5
ISSN	1362-4326 ; 0968-0004 ; 0376-5067
ISSN (online)	1362-4326
ISSN	0968-0004 ; 0376-5067
DOI	10.1016/j.tibs.2020.12.011
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Zs.A 1207: Show issues

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Article ; Online: Nucleation of nuclear bodies.

Dundr, Miroslav

Methods in molecular biology (Clifton, N.J.)

2013 Volume 1042, Page(s) 351–364

Abstract: The nucleus is a complex organelle containing numerous highly dynamic, structurally stable domains and bodies, harboring functions that have only begun to be defined. However, the molecular mechanisms for their formation are still poorly understood. ... ...

Abstract	The nucleus is a complex organelle containing numerous highly dynamic, structurally stable domains and bodies, harboring functions that have only begun to be defined. However, the molecular mechanisms for their formation are still poorly understood. Recently it has been shown that a nuclear body can form de novo by self-organization. But little is known regarding what triggers the formation of a nuclear body and how subsequent assembly steps are orchestrated. Nuclear bodies are frequently associated with specific active gene loci that directly contribute to their formation. Both coding and noncoding RNAs can initiate the assembly of nuclear bodies with which they are physiologically associated. Thus, the formation of nuclear bodies occurs via recruitment and consequent accumulation of resident proteins in the nuclear bodies by nucleating RNA acting as a seeder. In this chapter I describe how to set up an experimental cell system to probe de novo biogenesis of a nuclear body by nucleating RNA and nuclear body components tethered on chromatin.
MeSH term(s)	Cell Line, Tumor ; Cell Nucleus/genetics ; Cell Nucleus/metabolism ; Cloning, Molecular/methods ; Coiled Bodies/genetics ; Coiled Bodies/metabolism ; Green Fluorescent Proteins/genetics ; HeLa Cells ; Histones/genetics ; Humans ; In Situ Hybridization, Fluorescence/methods ; Lac Operon/genetics ; Lac Repressors/genetics ; Nuclear Proteins/genetics ; Transcription, Genetic
Chemical Substances	Histones ; Lac Repressors ; Nuclear Proteins ; Green Fluorescent Proteins (147336-22-9)
Language	English
Publishing date	2013-08-25
Publishing country	United States
Document type	Journal Article ; Research Support, N.I.H., Extramural
ISSN	1940-6029
ISSN (online)	1940-6029
DOI	10.1007/978-1-62703-526-2_23
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Article ; Online: Nuclear bodies: multifunctional companions of the genome.

Dundr, Miroslav

Current opinion in cell biology

2012 Volume 24, Issue 3, Page(s) 415–422

Abstract: It has become increasingly apparent that gene expression is regulated by the functional interplay between spatial genome organization and nuclear architecture. Within the nuclear environment a variety of distinct nuclear bodies exist. They are dynamic, ... ...

Abstract	It has become increasingly apparent that gene expression is regulated by the functional interplay between spatial genome organization and nuclear architecture. Within the nuclear environment a variety of distinct nuclear bodies exist. They are dynamic, self-organizing structures that do not assemble as pre-formed entities but rather emerge as a direct reflection of specific activities associated with gene expression and genome maintenance. Here I summarize recent findings on functions of some of the most prominent nuclear bodies, including the nucleolus, Cajal body, PML nuclear body, Polycomb group body and the 53BP1 nuclear body. The emerging view is that their organization is orchestrated by similar principles, and they function in fundamental cellular processes involved in homeostasis, differentiation, development and disease.
MeSH term(s)	Cell Nucleolus/genetics ; Cell Nucleolus/metabolism ; Cell Nucleus/genetics ; Cell Nucleus/metabolism ; Cell Nucleus/physiology ; Coiled Bodies/genetics ; Coiled Bodies/metabolism ; Genome ; Humans
Language	English
Publishing date	2012-04-25
Publishing country	England
Document type	Journal Article ; Research Support, N.I.H., Extramural ; Review
ZDB-ID	1026381-0
ISSN	1879-0410 ; 0955-0674
ISSN (online)	1879-0410
ISSN	0955-0674
DOI	10.1016/j.ceb.2012.03.010
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Zs.A 2963: Show issues

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Article ; Online: Seed and grow: a two-step model for nuclear body biogenesis.

Dundr, Miroslav

The Journal of cell biology

2011 Volume 193, Issue 4, Page(s) 605–606

Abstract: Nuclear bodies are dynamic structures that form at sites of specific activities associated with gene expression and genome maintenance. A paper in this issue (White et al. 2011. J. Cell Biol. doi: 10.1083/jcb.201012077) highlights key features of nuclear ...

Abstract	Nuclear bodies are dynamic structures that form at sites of specific activities associated with gene expression and genome maintenance. A paper in this issue (White et al. 2011. J. Cell Biol. doi: 10.1083/jcb.201012077) highlights key features of nuclear body biogenesis and suggests a unifying model in which formation of nuclear bodies is driven by nonrandom, biologically determined initial seeding events followed by stochastic self-assembly.
MeSH term(s)	Animals ; Apoptosis Regulatory Proteins/metabolism ; Cell Nucleus Structures/metabolism ; Drosophila Proteins/genetics ; Drosophila Proteins/metabolism ; Drosophila melanogaster/embryology ; Drosophila melanogaster/genetics ; Drosophila melanogaster/metabolism ; Forkhead Transcription Factors/metabolism ; Gene Expression Regulation ; Histones/genetics ; Histones/metabolism ; Mitosis ; Models, Biological ; Peptide Elongation Factors/metabolism ; Phosphoproteins/metabolism ; Polycomb-Group Proteins ; RNA Precursors/metabolism ; RNA Processing, Post-Transcriptional ; RNA, Messenger/metabolism ; Repressor Proteins/metabolism ; Ribonucleoprotein, U7 Small Nuclear/metabolism
Chemical Substances	Apoptosis Regulatory Proteins ; Drosophila Proteins ; Forkhead Transcription Factors ; Histones ; Peptide Elongation Factors ; Phosphoproteins ; Polycomb-Group Proteins ; RNA Precursors ; RNA, Messenger ; Repressor Proteins ; Ribonucleoprotein, U7 Small Nuclear ; Spt6 protein, Drosophila
Language	English
Publishing date	2011-05-16
Publishing country	United States
Document type	Journal Article
ZDB-ID	218154-x
ISSN	1540-8140 ; 0021-9525
ISSN (online)	1540-8140
ISSN	0021-9525
DOI	10.1083/jcb.201104087
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Article: How Hierarchical Interactions Make Membraneless Organelles Tick Like Clockwork

Schmit, Jeremy D / Feric, Marina / Dundr, Miroslav

Elsevier Ltd Trends in biochemical sciences. 2021 July, v. 46, no. 7

2021

Abstract	Biomolecular condensates appear throughout the cell, serving many different biochemical functions. We argue that condensate functionality is optimized when the interactions driving condensation vary widely in affinity. Strong interactions provide structural specificity needed to encode functional properties but carry the risk of kinetic arrest, while weak interactions allow the system to remain dynamic but do not restrict the conformational ensemble enough to sustain specific functional features. To support our opinion, we describe illustrative examples of the interplay of strong and weak interactions that are found in the nucleolus, SPOP/DAXX condensates, polySUMO/polySIM condensates, chromatin, and stress granules. The common feature of these systems is a hierarchical assembly motif in which weak, transient interactions condense structurally defined functional units.
Keywords	cell nucleolus ; chromatin ; condensates ; organelles ; risk ; ticks
Language	English
Dates of publication	2021-07
Size	p. 525-534.
Publishing place	Elsevier Ltd
Document type	Article
Note	NAL-AP-2-clean
ZDB-ID	194220-7
ISSN	0968-0004 ; 0376-5067
ISSN	0968-0004 ; 0376-5067
DOI	10.1016/j.tibs.2020.12.011
Database	NAL-Catalogue (AGRICOLA)

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Z 78/716: Show issues

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Article ; Online: Chromatin loops and causality loops: the influence of RNA upon spatial nuclear architecture.

Sawyer, Iain A / Dundr, Miroslav

Chromosoma

2017 Volume 126, Issue 5, Page(s) 541–557

Abstract: An intrinsic and essential trait exhibited by cells is the properly coordinated and integrated regulation of an astoundingly large number of simultaneous molecular decisions and reactions to maintain biochemical homeostasis. This is especially true ... ...

Abstract	An intrinsic and essential trait exhibited by cells is the properly coordinated and integrated regulation of an astoundingly large number of simultaneous molecular decisions and reactions to maintain biochemical homeostasis. This is especially true inside the cell nucleus, where the recognition of DNA and RNA by a vast range of nucleic acid-interacting proteins organizes gene expression patterns. However, this dynamic system is not regulated by simple "on" or "off" signals. Instead, transcription factor and RNA polymerase recruitment to DNA are influenced by the local chromatin and epigenetic environment, a gene's relative position within the nucleus and the action of noncoding RNAs. In addition, major phase-separated structural features of the nucleus, such as nucleoli and paraspeckles, assemble in direct response to specific transcriptional activities and, in turn, influence global genomic function. Currently, the interpretation of these data is trapped in a causality dilemma reminiscent of the "chicken and the egg" paradox as it is unclear whether changes in nuclear architecture promote RNA function or vice versa. Here, we review recent advances that suggest a complex and interdependent interaction network between gene expression, chromatin topology, and noncoding RNA function. We also discuss the functional links between these essential nuclear processes from the nanoscale (gene looping) to the macroscale (sub-nuclear gene positioning and nuclear body function) and briefly highlight some of the challenges that researchers may encounter when studying these phenomena.
MeSH term(s)	Animals ; Cell Nucleus/metabolism ; Chromatin/metabolism ; DNA/metabolism ; Epigenesis, Genetic ; Gene Expression Regulation ; Humans ; RNA, Long Noncoding/metabolism ; Spatial Analysis
Chemical Substances	Chromatin ; RNA, Long Noncoding ; DNA (9007-49-2)
Language	English
Publishing date	2017-06-07
Publishing country	Austria
Document type	Journal Article ; Review
ZDB-ID	203083-4
ISSN	1432-0886 ; 0009-5915
ISSN (online)	1432-0886
ISSN	0009-5915
DOI	10.1007/s00412-017-0632-y
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Article ; Online: A role of the 53BP1 protein in genome protection: structural and functional characteristics of 53BP1-dependent DNA repair.

Bártová, Eva / Legartová, Soňa / Dundr, Miroslav / Suchánková, Jana

Aging

2019 Volume 11, Issue 8, Page(s) 2488–2511

Abstract: Nuclear architecture plays a significant role in DNA repair mechanisms. It is evident that proteins involved in DNA repair are compartmentalized in not only spontaneously occurring DNA lesions or ionizing radiation-induced foci (IRIF), but a specific ... ...

Abstract	Nuclear architecture plays a significant role in DNA repair mechanisms. It is evident that proteins involved in DNA repair are compartmentalized in not only spontaneously occurring DNA lesions or ionizing radiation-induced foci (IRIF), but a specific clustering of these proteins can also be observed within the whole cell nucleus. For example, 53BP1-positive and BRCA1-positive DNA repair foci decorate chromocenters and can appear close to nuclear speckles. Both 53BP1 and BRCA1 are well-described factors that play an essential role in double-strand break (DSB) repair. These proteins are members of two protein complexes: 53BP1-RIF1-PTIP and BRCA1-CtIP, which make a "decision" determining whether canonical nonhomologous end joining (NHEJ) or homology-directed repair (HDR) is activated. It is generally accepted that 53BP1 mediates the NHEJ mechanism, while HDR is activated via a BRCA1-dependent signaling pathway. Interestingly, the 53BP1 protein appears relatively quickly at DSB sites, while BRCA1 is functional at later stages of DNA repair, as soon as the Mre11-Rad50-Nbs1 complex is recruited to the DNA lesions. A function of the 53BP1 protein is also linked to a specific histone signature, including phosphorylation of histone H2AX (γH2AX) or methylation of histone H4 at the lysine 20 position (H4K20me); therefore, we also discuss an epigenetic landscape of 53BP1-positive DNA lesions.
MeSH term(s)	Cell Nucleus/genetics ; Cell Nucleus/metabolism ; DNA Repair ; Humans ; Phosphorylation ; Tumor Suppressor p53-Binding Protein 1/genetics ; Tumor Suppressor p53-Binding Protein 1/metabolism
Chemical Substances	Tumor Suppressor p53-Binding Protein 1
Language	English
Publishing date	2019-04-18
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't ; Review
ISSN	1945-4589
ISSN (online)	1945-4589
DOI	10.18632/aging.101917
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Article ; Online: The Nucleolus: A Multiphase Condensate Balancing Ribosome Synthesis and Translational Capacity in Health, Aging and Ribosomopathies.

Correll, Carl C / Bartek, Jiri / Dundr, Miroslav

Cells

2019 Volume 8, Issue 8

Abstract: The nucleolus is the largest membrane-less structure in the eukaryotic nucleus. It is involved in the biogenesis of ribosomes, essential macromolecular machines responsible for synthesizing all proteins required by the cell. The assembly of ribosomes is ... ...

Abstract	The nucleolus is the largest membrane-less structure in the eukaryotic nucleus. It is involved in the biogenesis of ribosomes, essential macromolecular machines responsible for synthesizing all proteins required by the cell. The assembly of ribosomes is evolutionarily conserved and is the most energy-consuming cellular process needed for cell growth, proliferation, and homeostasis. Despite the significance of this process, the intricate pathophysiological relationship between the nucleolus and protein synthesis has only recently begun to emerge. Here, we provide perspective on new principles governing nucleolar formation and the resulting multiphase organization driven by liquid-liquid phase separation. With recent advances in the structural analysis of ribosome formation, we highlight the current understanding of the step-wise assembly of pre-ribosomal subunits and the quality control required for proper function. Finally, we address how aging affects ribosome genesis and how genetic defects in ribosome formation cause ribosomopathies, complex diseases with a predisposition to cancer.
MeSH term(s)	Aging/genetics ; Aging/metabolism ; Cell Cycle ; Cell Line, Tumor ; Cell Nucleolus/genetics ; Cell Nucleolus/metabolism ; DNA, Ribosomal/genetics ; DNA, Ribosomal/metabolism ; Eukaryotic Cells/cytology ; Eukaryotic Cells/metabolism ; Eukaryotic Cells/pathology ; Humans ; Mutation ; Neoplasms/genetics ; Neoplasms/metabolism ; Protein Biosynthesis ; Ribosomes/genetics ; Ribosomes/metabolism
Chemical Substances	DNA, Ribosomal
Language	English
Publishing date	2019-08-10
Publishing country	Switzerland
Document type	Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't ; Review
ZDB-ID	2661518-6
ISSN	2073-4409 ; 2073-4409
ISSN (online)	2073-4409
ISSN	2073-4409
DOI	10.3390/cells8080869
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Article ; Online: Nuclear bodies: Built to boost.

Sawyer, Iain A / Dundr, Miroslav

The Journal of cell biology

2016 Volume 213, Issue 5, Page(s) 509–511

Abstract: The classic archetypal function of nuclear bodies is to accelerate specific reactions within their crowded space. In this issue, Tatomer et al. (2016. J. Cell Biol http://dx.doi.org/10.1083/jcb.201504043) provide the first direct evidence that the ... ...

Abstract	The classic archetypal function of nuclear bodies is to accelerate specific reactions within their crowded space. In this issue, Tatomer et al. (2016. J. Cell Biol http://dx.doi.org/10.1083/jcb.201504043) provide the first direct evidence that the histone locus body acts to concentrate key factors required for the proper processing of histone pre-mRNAs.
MeSH term(s)	Animals ; Drosophila melanogaster/metabolism ; Histones/metabolism ; Humans ; Intranuclear Inclusion Bodies/metabolism ; Models, Biological ; RNA/metabolism ; Ribonucleoprotein, U7 Small Nuclear/metabolism
Chemical Substances	Histones ; Ribonucleoprotein, U7 Small Nuclear ; RNA (63231-63-0)
Language	English
Publishing date	2016-06-06
Publishing country	United States
Document type	Journal Article
ZDB-ID	218154-x
ISSN	1540-8140 ; 0021-9525
ISSN (online)	1540-8140
ISSN	0021-9525
DOI	10.1083/jcb.201605049
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