1
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Engbrecht M, Grundei D, Dilger A, Wiedemann H, Aust AK, Baumgärtner S, Helfrich S, Kergl-Räpple F, Bürkle A, Mangerich A. Monitoring nucleolar-nucleoplasmic protein shuttling in living cells by high-content microscopy and automated image analysis. Nucleic Acids Res 2024; 52:e72. [PMID: 39036969 PMCID: PMC11347172 DOI: 10.1093/nar/gkae598] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2023] [Revised: 05/25/2024] [Accepted: 06/26/2024] [Indexed: 07/23/2024] Open
Abstract
The nucleolus has core functions in ribosome biosynthesis, but also acts as a regulatory hub in a plethora of non-canonical processes, including cellular stress. Upon DNA damage, several DNA repair factors shuttle between the nucleolus and the nucleoplasm. Yet, the molecular mechanisms underlying such spatio-temporal protein dynamics remain to be deciphered. Here, we present a novel imaging platform to investigate nucleolar-nucleoplasmic protein shuttling in living cells. For image acquisition, we used a commercially available automated fluorescence microscope and for image analysis, we developed a KNIME workflow with implementation of machine learning-based tools. We validated the method with different nucleolar proteins, i.e., PARP1, TARG1 and APE1, by monitoring their shuttling dynamics upon oxidative stress. As a paradigm, we analyzed PARP1 shuttling upon H2O2 treatment in combination with a range of pharmacological inhibitors in a novel reporter cell line. These experiments revealed that inhibition of SIRT7 results in a loss of nucleolar PARP1 localization. Finally, we unraveled specific differences in PARP1 shuttling dynamics after co-treatment with H2O2 and different clinical PARP inhibitors. Collectively, this work delineates a highly sensitive and versatile bioimaging platform to investigate swift nucleolar-nucleoplasmic protein shuttling in living cells, which can be employed for pharmacological screening and in-depth mechanistic analyses.
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Affiliation(s)
- Marina Engbrecht
- Molecular Toxicology, Department of Biology, University of Konstanz, 78457 Konstanz, Germany
| | - David Grundei
- Molecular Toxicology, Department of Biology, University of Konstanz, 78457 Konstanz, Germany
| | - Asisa M Dilger
- Nutritional Toxicology, Institute of Nutritional Science, University of Potsdam, 14469 Potsdam, Germany
| | - Hannah Wiedemann
- Molecular Toxicology, Department of Biology, University of Konstanz, 78457 Konstanz, Germany
| | - Ann-Kristin Aust
- Molecular Toxicology, Department of Biology, University of Konstanz, 78457 Konstanz, Germany
| | - Sarah Baumgärtner
- Molecular Toxicology, Department of Biology, University of Konstanz, 78457 Konstanz, Germany
| | | | | | - Alexander Bürkle
- Molecular Toxicology, Department of Biology, University of Konstanz, 78457 Konstanz, Germany
| | - Aswin Mangerich
- Molecular Toxicology, Department of Biology, University of Konstanz, 78457 Konstanz, Germany
- Nutritional Toxicology, Institute of Nutritional Science, University of Potsdam, 14469 Potsdam, Germany
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2
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Chakraborty S, Mishra J, Roy A, Niharika, Manna S, Baral T, Nandi P, Patra S, Patra SK. Liquid-liquid phase separation in subcellular assemblages and signaling pathways: Chromatin modifications induced gene regulation for cellular physiology and functions including carcinogenesis. Biochimie 2024; 223:74-97. [PMID: 38723938 DOI: 10.1016/j.biochi.2024.05.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2023] [Revised: 03/08/2024] [Accepted: 05/04/2024] [Indexed: 05/24/2024]
Abstract
Liquid-liquid phase separation (LLPS) describes many biochemical processes, including hydrogel formation, in the integrity of macromolecular assemblages and existence of membraneless organelles, including ribosome, nucleolus, nuclear speckles, paraspeckles, promyelocytic leukemia (PML) bodies, Cajal bodies (all exert crucial roles in cellular physiology), and evidence are emerging day by day. Also, phase separation is well documented in generation of plasma membrane subdomains and interplay between membranous and membraneless organelles. Intrinsically disordered regions (IDRs) of biopolymers/proteins are the most critical sticking regions that aggravate the formation of such condensates. Remarkably, phase separated condensates are also involved in epigenetic regulation of gene expression, chromatin remodeling, and heterochromatinization. Epigenetic marks on DNA and histones cooperate with RNA-binding proteins through their IDRs to trigger LLPS for facilitating transcription. How phase separation coalesces mutant oncoproteins, orchestrate tumor suppressor genes expression, and facilitated cancer-associated signaling pathways are unravelling. That autophagosome formation and DYRK3-mediated cancer stem cell modification also depend on phase separation is deciphered in part. In view of this, and to linchpin insight into the subcellular membraneless organelle assembly, gene activation and biological reactions catalyzed by enzymes, and the downstream physiological functions, and how all these events are precisely facilitated by LLPS inducing organelle function, epigenetic modulation of gene expression in this scenario, and how it goes awry in cancer progression are summarized and presented in this article.
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Affiliation(s)
- Subhajit Chakraborty
- Epigenetics and Cancer Research Laboratory, Biochemistry and Molecular Biology Group, Department of Life Science, National Institute of Technology, Rourkela, India
| | - Jagdish Mishra
- Epigenetics and Cancer Research Laboratory, Biochemistry and Molecular Biology Group, Department of Life Science, National Institute of Technology, Rourkela, India
| | - Ankan Roy
- Epigenetics and Cancer Research Laboratory, Biochemistry and Molecular Biology Group, Department of Life Science, National Institute of Technology, Rourkela, India
| | - Niharika
- Epigenetics and Cancer Research Laboratory, Biochemistry and Molecular Biology Group, Department of Life Science, National Institute of Technology, Rourkela, India
| | - Soumen Manna
- Epigenetics and Cancer Research Laboratory, Biochemistry and Molecular Biology Group, Department of Life Science, National Institute of Technology, Rourkela, India
| | - Tirthankar Baral
- Epigenetics and Cancer Research Laboratory, Biochemistry and Molecular Biology Group, Department of Life Science, National Institute of Technology, Rourkela, India
| | - Piyasa Nandi
- Epigenetics and Cancer Research Laboratory, Biochemistry and Molecular Biology Group, Department of Life Science, National Institute of Technology, Rourkela, India
| | - Subhajit Patra
- Department of Chemical Engineering, Maulana Azad National Institute of Technology, Bhopal, India
| | - Samir Kumar Patra
- Epigenetics and Cancer Research Laboratory, Biochemistry and Molecular Biology Group, Department of Life Science, National Institute of Technology, Rourkela, India.
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3
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Cockrell AJ, Lange JJ, Wood C, Mattingly M, McCroskey SM, Bradford WD, Conkright-Fincham J, Weems L, Guo MS, Gerton JL. Regulators of rDNA array morphology in fission yeast. PLoS Genet 2024; 20:e1011331. [PMID: 38968290 PMCID: PMC11253961 DOI: 10.1371/journal.pgen.1011331] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2023] [Revised: 07/17/2024] [Accepted: 06/04/2024] [Indexed: 07/07/2024] Open
Abstract
Nucleolar morphology is a well-established indicator of ribosome biogenesis activity that has served as the foundation of many screens investigating ribosome production. Missing from this field of study is a broad-scale investigation of the regulation of ribosomal DNA morphology, despite the essential role of rRNA gene transcription in modulating ribosome output. We hypothesized that the morphology of rDNA arrays reflects ribosome biogenesis activity. We established GapR-GFP, a prokaryotic DNA-binding protein that recognizes transcriptionally-induced overtwisted DNA, as a live visual fluorescent marker for quantitative analysis of rDNA organization in Schizosaccharomyces pombe. We found that the morphology-which we refer to as spatial organization-of the rDNA arrays is dynamic throughout the cell cycle, under glucose starvation, RNA pol I inhibition, and TOR activation. Screening the haploid S. pombe Bioneer deletion collection for spatial organization phenotypes revealed large ribosomal protein (RPL) gene deletions that alter rDNA organization. Further work revealed RPL gene deletion mutants with altered rDNA organization also demonstrate resistance to the TOR inhibitor Torin1. A genetic analysis of signaling pathways essential for this resistance phenotype implicated many factors including a conserved MAPK, Pmk1, previously linked to extracellular stress responses. We propose RPL gene deletion triggers altered rDNA morphology due to compensatory changes in ribosome biogenesis via multiple signaling pathways, and we further suggest compensatory responses may contribute to human diseases such as ribosomopathies. Altogether, GapR-GFP is a powerful tool for live visual reporting on rDNA morphology under myriad conditions.
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Affiliation(s)
- Alexandria J. Cockrell
- Stowers Institute for Medical Research, Kansas City, Missouri, United States of America
- Department of Biochemistry and Molecular Biology, University of Kansas Medical Center, Kansas City, Kansas, United States of America
| | - Jeffrey J. Lange
- Stowers Institute for Medical Research, Kansas City, Missouri, United States of America
| | - Christopher Wood
- Stowers Institute for Medical Research, Kansas City, Missouri, United States of America
| | - Mark Mattingly
- Stowers Institute for Medical Research, Kansas City, Missouri, United States of America
| | - Scott M. McCroskey
- Stowers Institute for Medical Research, Kansas City, Missouri, United States of America
| | - William D. Bradford
- Stowers Institute for Medical Research, Kansas City, Missouri, United States of America
| | - Juliana Conkright-Fincham
- Stowers Institute for Medical Research, Kansas City, Missouri, United States of America
- Promega Corporation, Madison, Wisconsin, United States of America
| | - Lauren Weems
- Stowers Institute for Medical Research, Kansas City, Missouri, United States of America
| | - Monica S. Guo
- Department of Microbiology, University of Washington School of Medicine, Seattle, state of Washington, United States of America
| | - Jennifer L. Gerton
- Stowers Institute for Medical Research, Kansas City, Missouri, United States of America
- Department of Biochemistry and Molecular Biology, University of Kansas Medical Center, Kansas City, Kansas, United States of America
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4
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Sartsanga C, Phengchat R, Wako T, Fukui K, Ohmido N. Localization and quantitative distribution of a chromatin structural protein Topoisomerase II on plant chromosome using HVTEM and UHVTEM. Micron 2024; 179:103596. [PMID: 38359615 DOI: 10.1016/j.micron.2024.103596] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2023] [Revised: 01/29/2024] [Accepted: 01/29/2024] [Indexed: 02/17/2024]
Abstract
Topoisomerase II (TopoII) is an essential structural protein of the metaphase chromosome. It maintains the axial compaction of chromosomes during metaphase. It is localized at the axial region of chromosomes and accumulates at the centromeric region in metaphase chromosomes. However, little is known about TopoII localization and distribution in plant chromosomes, except for several publications. We used high voltage transmission electron microscopy (HVTEM) and ultra-high voltage transmission electron microscopy (UHVTEM) in conjunction with immunogold labeling and visualization techniques to detect TopoII and investigate its localization, alignment, and density on the barley chromosome at 1.4 nm scale. We found that HVTEM and UHVTEM combined with immunogold labeling is suitable for the detection of structural proteins, including a single molecule of TopoII. This is because the average size of the gold particles for TopoII visualization after silver enhancement is 8.9 ± 3.9 nm, which is well detected. We found that 31,005 TopoII molecules are distributed along the barley chromosomes in an unspecific pattern at the chromosome arms and accumulate specifically at the nucleolus organizer regions (NORs) and centromeric region. The TopoII density were 1.32-fold, 1.58-fold, and 1.36-fold at the terminal region, at the NORs, and the centromeric region, respectively. The findings of TopoII localization in this study support the multiple reported functions of TopoII in the barley metaphase chromosome.
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Affiliation(s)
- Channarong Sartsanga
- Graduate School of Human Development and Environment, Kobe University, Tsurukabuto 3-11, Nada-ku, 657-8501, Kobe, Japan
| | - Rinyaporn Phengchat
- Nanotechnology Research Centre, National Research of Council, 11421 Saskatchewan Drive, T6G 2M9 Edmonton, Alberta, Canada
| | - Toshiyuki Wako
- Institute of Crop Sciences, National Agriculture and Food Research Organization, 2-1-1 Kannondai, Tsukuba, Ibaraki 305-8518, Japan
| | - Kiichi Fukui
- Graduate School of Pharmaceutical Sciences, Osaka University, Yamadaoka 1-6, Suita, Osaka 565-0871, Japan
| | - Nobuko Ohmido
- Graduate School of Human Development and Environment, Kobe University, Tsurukabuto 3-11, Nada-ku, 657-8501, Kobe, Japan.
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5
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Potapova TA, Unruh JR, Conkright-Fincham J, Banks CAS, Florens L, Schneider DA, Gerton JL. Distinct states of nucleolar stress induced by anticancer drugs. eLife 2023; 12:RP88799. [PMID: 38099650 PMCID: PMC10723795 DOI: 10.7554/elife.88799] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2023] Open
Abstract
Ribosome biogenesis is a vital and highly energy-consuming cellular function occurring primarily in the nucleolus. Cancer cells have an elevated demand for ribosomes to sustain continuous proliferation. This study evaluated the impact of existing anticancer drugs on the nucleolus by screening a library of anticancer compounds for drugs that induce nucleolar stress. For a readout, a novel parameter termed 'nucleolar normality score' was developed that measures the ratio of the fibrillar center and granular component proteins in the nucleolus and nucleoplasm. Multiple classes of drugs were found to induce nucleolar stress, including DNA intercalators, inhibitors of mTOR/PI3K, heat shock proteins, proteasome, and cyclin-dependent kinases (CDKs). Each class of drugs induced morphologically and molecularly distinct states of nucleolar stress accompanied by changes in nucleolar biophysical properties. In-depth characterization focused on the nucleolar stress induced by inhibition of transcriptional CDKs, particularly CDK9, the main CDK that regulates RNA Pol II. Multiple CDK substrates were identified in the nucleolus, including RNA Pol I- recruiting protein Treacle, which was phosphorylated by CDK9 in vitro. These results revealed a concerted regulation of RNA Pol I and Pol II by transcriptional CDKs. Our findings exposed many classes of chemotherapy compounds that are capable of inducing nucleolar stress, and we recommend considering this in anticancer drug development.
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Affiliation(s)
| | - Jay R Unruh
- Stowers Institute for Medical ResearchKansas CityUnited States
| | | | | | | | - David Alan Schneider
- Department of Biochemistry and Molecular Genetics, University of Alabama at BirminghamBirminghamUnited States
| | - Jennifer L Gerton
- Stowers Institute for Medical ResearchKansas CityUnited States
- Department of Biochemistry and Molecular Biology, University of Kansas Medical CenterKansas CityUnited States
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6
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Abstract
The p-arms of the five human acrocentric chromosomes bear nucleolar organizer regions (NORs) comprising ribosomal gene (rDNA) repeats that are organized in a homogeneous tandem array and transcribed in a telomere-to-centromere direction. Precursor ribosomal RNA transcripts are processed and assembled into ribosomal subunits, the nucleolus being the physical manifestation of this process. I review current understanding of nucleolar chromosome biology and describe current exploration into a role for the NOR chromosomal context. Full DNA sequences for acrocentric p-arms are now emerging, aided by the current revolution in long-read sequencing and genome assembly. Acrocentric p-arms vary from 10.1 to 16.7 Mb, accounting for ∼2.2% of the genome. Bordering rDNA arrays, distal junctions, and proximal junctions are shared among the p-arms, with distal junctions showing evidence of functionality. The remaining p-arm sequences comprise multiple satellite DNA classes and segmental duplications that facilitate recombination between heterologous chromosomes, which is likely also involved in Robertsonian translocations.
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Affiliation(s)
- Brian McStay
- Centre for Chromosome Biology, College of Science and Engineering, University of Galway, Galway, Ireland;
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7
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Liskovykh M, Petrov NS, Noskov VN, Masumoto H, Earnshaw WC, Schlessinger D, Shabalina SA, Larionov V, Kouprina N. Actively transcribed rDNA and distal junction (DJ) sequence are involved in association of NORs with nucleoli. Cell Mol Life Sci 2023; 80:121. [PMID: 37043028 PMCID: PMC10097779 DOI: 10.1007/s00018-023-04770-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2022] [Revised: 03/27/2023] [Accepted: 03/28/2023] [Indexed: 04/13/2023]
Abstract
Although they are organelles without a limiting membrane, nucleoli have an exclusive structure, built upon the rDNA-rich acrocentric short arms of five human chromosomes (nucleolar organizer regions or NORs). This has raised the question: what are the structural features of a chromosome required for its inclusion in a nucleolus? Previous work has suggested that sequences adjacent to the tandemly repeated rDNA repeat units (DJ, distal junction sequence) may be involved, and we have extended such studies by addressing several issues related to the requirements for the association of NORs with nucleoli. We exploited both a set of somatic cell hybrids containing individual human acrocentric chromosomes and a set of Human Artificial Chromosomes (HACs) carrying different parts of a NOR, including an rDNA unit or DJ or PJ (proximal junction) sequence. Association of NORs with nucleoli was increased when constituent rDNA was transcribed and may be also affected by the status of heterochromatin blocks formed next to the rDNA arrays. Furthermore, our data suggest that a relatively small size DJ region, highly conserved in evolution, is also involved, along with the rDNA repeats, in the localization of p-arms of acrocentric chromosomes in nucleoli. Thus, we infer a cooperative action of rDNA sequence-stimulated by its activity-and sequences distal to rDNA contributing to incorporation into nucleoli. Analysis of NOR sequences also identified LncRNA_038958 in the DJ, a candidate transcript with the region of the suggested promoter that is located close to the DJ/rDNA boundary and contains CTCF binding sites. This LncRNA may affect RNA Polymerase I and/or nucleolar activity. Our findings provide the basis for future studies to determine which RNAs and proteins interact critically with NOR sequences to organize the higher-order structure of nucleoli and their function in normal cells and pathological states.
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Affiliation(s)
- Mikhail Liskovykh
- Developmental Therapeutics Branch, National Cancer Institute, NIH, Bethesda, MD, 20892, USA.
| | - Nikolai S Petrov
- Developmental Therapeutics Branch, National Cancer Institute, NIH, Bethesda, MD, 20892, USA
| | - Vladimir N Noskov
- Developmental Therapeutics Branch, National Cancer Institute, NIH, Bethesda, MD, 20892, USA
| | - Hiroshi Masumoto
- Laboratory of Chromosome Engineering, Department of Frontier Research and Development, Kazusa DNA Research Institute, Kisarazu, Chiba, 292-0818, Japan
| | - William C Earnshaw
- Wellcome Centre for Cell Biology, University of Edinburgh, Edinburgh, EH9 3JR, Scotland, UK
| | - David Schlessinger
- National Institute on Aging, Laboratory of Genetics and Genomics, NIH, Baltimore, MD, 21224, USA
| | - Svetlana A Shabalina
- National Center for Biotechnology Information, National Library of Medicine, NIH, Bethesda, MD, 20892, USA
| | - Vladimir Larionov
- Developmental Therapeutics Branch, National Cancer Institute, NIH, Bethesda, MD, 20892, USA.
| | - Natalay Kouprina
- Developmental Therapeutics Branch, National Cancer Institute, NIH, Bethesda, MD, 20892, USA.
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8
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Li X, An Z, Zhang W, Li F. Phase Separation: Direct and Indirect Driving Force for High-Order Chromatin Organization. Genes (Basel) 2023; 14:499. [PMID: 36833426 PMCID: PMC9956262 DOI: 10.3390/genes14020499] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2023] [Revised: 02/09/2023] [Accepted: 02/14/2023] [Indexed: 02/18/2023] Open
Abstract
The multi-level spatial chromatin organization in the nucleus is closely related to chromatin activity. The mechanism of chromatin organization and remodeling attract much attention. Phase separation describes the biomolecular condensation which is the basis for membraneless compartments in cells. Recent research shows that phase separation is a key aspect to drive high-order chromatin structure and remodeling. In addition, chromatin functional compartmentalization in the nucleus which is formed by phase separation also plays an important role in overall chromatin structure. In this review, we summarized the latest work about the role of phase separation in spatial chromatin organization, focusing on direct and indirect effects of phase separation on 3D chromatin organization and its impact on transcription regulation.
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Affiliation(s)
- Xiaoli Li
- Division of Cell, Developmental and Integrative Biology, School of Medicine, South China University of Technology, Guangzhou 510006, China
- Department of Cell Biology and Genetics, Core Facility of Developmental Biology, Chongqing Medical University, Chongqing 400016, China
| | - Ziyang An
- State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-Sen University, Guangzhou 510275, China
| | - Wenqing Zhang
- Division of Cell, Developmental and Integrative Biology, School of Medicine, South China University of Technology, Guangzhou 510006, China
| | - Feifei Li
- Division of Cell, Developmental and Integrative Biology, School of Medicine, South China University of Technology, Guangzhou 510006, China
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9
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Alemasova EE, Lavrik OI. A sePARate phase? Poly(ADP-ribose) versus RNA in the organization of biomolecular condensates. Nucleic Acids Res 2022; 50:10817-10838. [PMID: 36243979 DOI: 10.1093/nar/gkac866] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2022] [Revised: 09/14/2022] [Accepted: 10/09/2022] [Indexed: 11/13/2022] Open
Abstract
Condensates are biomolecular assemblies that concentrate biomolecules without the help of membranes. They are morphologically highly versatile and may emerge via distinct mechanisms. Nucleic acids-DNA, RNA and poly(ADP-ribose) (PAR) play special roles in the process of condensate organization. These polymeric scaffolds provide multiple specific and nonspecific interactions during nucleation and 'development' of macromolecular assemblages. In this review, we focus on condensates formed with PAR. We discuss to what extent the literature supports the phase separation origin of these structures. Special attention is paid to similarities and differences between PAR and RNA in the process of dynamic restructuring of condensates during their functioning.
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Affiliation(s)
- Elizaveta E Alemasova
- Institute of Chemical Biology and Fundamental Medicine, SB RAS, Novosibirsk 630090, Russia
| | - Olga I Lavrik
- Institute of Chemical Biology and Fundamental Medicine, SB RAS, Novosibirsk 630090, Russia.,Novosibirsk State University, Novosibirsk 630090, Russia
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10
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Karyka E, Berrueta Ramirez N, Webster CP, Marchi PM, Graves EJ, Godena VK, Marrone L, Bhargava A, Ray S, Ning K, Crane H, Hautbergue GM, El-Khamisy SF, Azzouz M. SMN-deficient cells exhibit increased ribosomal DNA damage. Life Sci Alliance 2022; 5:e202101145. [PMID: 35440492 PMCID: PMC9018017 DOI: 10.26508/lsa.202101145] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2021] [Revised: 04/04/2022] [Accepted: 04/04/2022] [Indexed: 12/26/2022] Open
Abstract
Spinal muscular atrophy, the leading genetic cause of infant mortality, is a motor neuron disease caused by low levels of survival motor neuron (SMN) protein. SMN is a multifunctional protein that is implicated in numerous cytoplasmic and nuclear processes. Recently, increasing attention is being paid to the role of SMN in the maintenance of DNA integrity. DNA damage and genome instability have been linked to a range of neurodegenerative diseases. The ribosomal DNA (rDNA) represents a particularly unstable locus undergoing frequent breakage. Instability in rDNA has been associated with cancer, premature ageing syndromes, and a number of neurodegenerative disorders. Here, we report that SMN-deficient cells exhibit increased rDNA damage leading to impaired ribosomal RNA synthesis and translation. We also unravel an interaction between SMN and RNA polymerase I. Moreover, we uncover an spinal muscular atrophy motor neuron-specific deficiency of DDX21 protein, which is required for resolving R-loops in the nucleolus. Taken together, our findings suggest a new role of SMN in rDNA integrity.
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Affiliation(s)
- Evangelia Karyka
- The Healthy Lifespan Institute and Neuroscience Institute, Neurodegeneration and Genome Stability Group, University of Sheffield, Sheffield, UK
- Sheffield Institute for Translational Neuroscience, University of Sheffield, Sheffield, UK
| | - Nelly Berrueta Ramirez
- The Healthy Lifespan Institute and Neuroscience Institute, Neurodegeneration and Genome Stability Group, University of Sheffield, Sheffield, UK
- Department of Molecular Biology and Biotechnology, The Institute of Neuroscience and the Healthy Lifespan Institute, School of Bioscience, Firth Court, University of Sheffield, Sheffield, UK
| | - Christopher P Webster
- The Healthy Lifespan Institute and Neuroscience Institute, Neurodegeneration and Genome Stability Group, University of Sheffield, Sheffield, UK
- Sheffield Institute for Translational Neuroscience, University of Sheffield, Sheffield, UK
| | - Paolo M Marchi
- The Healthy Lifespan Institute and Neuroscience Institute, Neurodegeneration and Genome Stability Group, University of Sheffield, Sheffield, UK
- Sheffield Institute for Translational Neuroscience, University of Sheffield, Sheffield, UK
| | - Emily J Graves
- The Healthy Lifespan Institute and Neuroscience Institute, Neurodegeneration and Genome Stability Group, University of Sheffield, Sheffield, UK
- Sheffield Institute for Translational Neuroscience, University of Sheffield, Sheffield, UK
| | - Vinay K Godena
- Sheffield Institute for Translational Neuroscience, University of Sheffield, Sheffield, UK
| | - Lara Marrone
- Sheffield Institute for Translational Neuroscience, University of Sheffield, Sheffield, UK
| | - Anushka Bhargava
- Sheffield Institute for Translational Neuroscience, University of Sheffield, Sheffield, UK
| | - Swagat Ray
- Department of Molecular Biology and Biotechnology, The Institute of Neuroscience and the Healthy Lifespan Institute, School of Bioscience, Firth Court, University of Sheffield, Sheffield, UK
- Department of Life Sciences, School of Life and Environmental Sciences, University of Lincoln, Lincoln, UK
| | - Ke Ning
- The Healthy Lifespan Institute and Neuroscience Institute, Neurodegeneration and Genome Stability Group, University of Sheffield, Sheffield, UK
- Sheffield Institute for Translational Neuroscience, University of Sheffield, Sheffield, UK
| | - Hannah Crane
- Department of Molecular Biology and Biotechnology, The Institute of Neuroscience and the Healthy Lifespan Institute, School of Bioscience, Firth Court, University of Sheffield, Sheffield, UK
| | - Guillaume M Hautbergue
- The Healthy Lifespan Institute and Neuroscience Institute, Neurodegeneration and Genome Stability Group, University of Sheffield, Sheffield, UK
- Sheffield Institute for Translational Neuroscience, University of Sheffield, Sheffield, UK
| | - Sherif F El-Khamisy
- The Healthy Lifespan Institute and Neuroscience Institute, Neurodegeneration and Genome Stability Group, University of Sheffield, Sheffield, UK
- Department of Molecular Biology and Biotechnology, The Institute of Neuroscience and the Healthy Lifespan Institute, School of Bioscience, Firth Court, University of Sheffield, Sheffield, UK
- The Institute of Cancer Therapeutics, University of Bradford, Bradford, UK
| | - Mimoun Azzouz
- The Healthy Lifespan Institute and Neuroscience Institute, Neurodegeneration and Genome Stability Group, University of Sheffield, Sheffield, UK
- Sheffield Institute for Translational Neuroscience, University of Sheffield, Sheffield, UK
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11
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Ide S, Tamura S, Maeshima K. Chromatin behavior in living cells: Lessons from single‐nucleosome imaging and tracking. Bioessays 2022; 44:e2200043. [DOI: 10.1002/bies.202200043] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2022] [Revised: 04/24/2022] [Accepted: 04/26/2022] [Indexed: 11/05/2022]
Affiliation(s)
- Satoru Ide
- Genome Dynamics Laboratory National Institute of Genetics, ROIS Mishima Shizuoka Japan
- Department of Genetics School of Life Science SOKENDAI Mishima Shizuoka Japan
| | - Sachiko Tamura
- Genome Dynamics Laboratory National Institute of Genetics, ROIS Mishima Shizuoka Japan
| | - Kazuhiro Maeshima
- Genome Dynamics Laboratory National Institute of Genetics, ROIS Mishima Shizuoka Japan
- Department of Genetics School of Life Science SOKENDAI Mishima Shizuoka Japan
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12
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Gál Z, Nieto B, Boukoura S, Rasmussen AV, Larsen DH. Treacle Sticks the Nucleolar Responses to DNA Damage Together. Front Cell Dev Biol 2022; 10:892006. [PMID: 35646927 PMCID: PMC9133508 DOI: 10.3389/fcell.2022.892006] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2022] [Accepted: 04/21/2022] [Indexed: 01/05/2023] Open
Abstract
The importance of chromatin environment for DNA repair has gained increasing recognition in recent years. The nucleolus is the largest sub-compartment within the nucleus: it has distinct biophysical properties, selective protein retention, and houses the specialized ribosomal RNA genes (collectively referred to as rDNA) with a unique chromatin composition. These genes have high transcriptional activity and a repetitive nature, making them susceptible to DNA damage and resulting in the highest frequency of rearrangements across the genome. A distinct DNA damage response (DDR) secures the fidelity of this genomic region, the so-called nucleolar DDR (n-DDR). The composition of the n-DDR reflects the characteristics of nucleolar chromatin with the nucleolar protein Treacle (also referred to as TCOF1) as a central coordinator retaining several well-characterized DDR proteins in the nucleolus. In this review, we bring together data on the structure of Treacle, its known functions in ribosome biogenesis, and its involvement in multiple branches of the n-DDR to discuss their interconnection. Furthermore, we discuss how the functions of Treacle in ribosome biogenesis and in the n-DDR may contribute to Treacher Collins Syndrome, a disease caused by mutations in Treacle. Finally, we outline outstanding questions that need to be addressed for a more comprehensive understanding of Treacle, the n-DDR, and the coordination of ribosome biogenesis and DNA repair.
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Abstract
In eukaryotic cells, protein and RNA factors involved in genome activities like transcription, RNA processing, DNA replication, and repair accumulate in self-organizing membraneless chromatin subcompartments. These structures contribute to efficiently conduct chromatin-mediated reactions and to establish specific cellular programs. However, the underlying mechanisms for their formation are only partly understood. Recent studies invoke liquid-liquid phase separation (LLPS) of proteins and RNAs in the establishment of chromatin activity patterns. At the same time, the folding of chromatin in the nucleus can drive genome partitioning into spatially distinct domains. Here, the interplay between chromatin organization, chromatin binding, and LLPS is discussed by comparing and contrasting three prototypical chromatin subcompartments: the nucleolus, clusters of active RNA polymerase II, and pericentric heterochromatin domains. It is discussed how the different ways of chromatin compartmentalization are linked to transcription regulation, the targeting of soluble factors to certain parts of the genome, and to disease-causing genetic aberrations.
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Affiliation(s)
- Karsten Rippe
- Division of Chromatin Networks, German Cancer Research Center (DKFZ) and Bioquant, 69120 Heidelberg, Germany
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14
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Chebrout M, Koné MC, Jan HU, Cournut M, Letheule M, Fleurot R, Aguirre-Lavin T, Peynot N, Jouneau A, Beaujean N, Bonnet-Garnier A. Transcription of rRNA in early mouse embryos promotes chromatin reorganization and expression of major satellite repeats. J Cell Sci 2022; 135:274059. [DOI: 10.1242/jcs.258798] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2021] [Accepted: 01/09/2022] [Indexed: 11/20/2022] Open
Abstract
During the first cell cycles of the early development, the chromatin of the embryo is highly reprogrammed alongside that embryonic genome starts its own transcription. The spatial organization of the genome is a major process that contributes to regulating gene transcription in time and space, however, it is poorly studied in the context of early embryos. To study the cause and effect link between transcription and spatial organization in embryos, we focused on the ribosomal genes, that are first silent and begin to transcribe during the 2-cell stage in the mouse. We demonstrated that ribosomal sequences and early unprocessed rRNAs are spatially organized in a very peculiar manner from the 2-cell to the 16-cell. Using drugs interfering with ribosomal DNA transcription, we show that this organization, totally different from somatic cells, depends on an active transcription of ribosomal genes and induces a unique chromatin environment that favors transcription of major satellite sequences after the 4-cell stage.
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Affiliation(s)
- Martine Chebrout
- Université Paris-Saclay, UVSQ, INRAE, BREED, 78350, Jouy-en-Josas, France
- Ecole Nationale Vétérinaire d'Alfort, BREED, 94700, Maisons-Alfort, France
| | - Maïmouna Coura Koné
- Université Paris-Saclay, UVSQ, INRAE, BREED, 78350, Jouy-en-Josas, France
- Ecole Nationale Vétérinaire d'Alfort, BREED, 94700, Maisons-Alfort, France
| | - Habib U. Jan
- Université Paris-Saclay, UVSQ, INRAE, BREED, 78350, Jouy-en-Josas, France
- Ecole Nationale Vétérinaire d'Alfort, BREED, 94700, Maisons-Alfort, France
| | - Marie Cournut
- Université Paris-Saclay, UVSQ, INRAE, BREED, 78350, Jouy-en-Josas, France
- Ecole Nationale Vétérinaire d'Alfort, BREED, 94700, Maisons-Alfort, France
| | - Martine Letheule
- Université Paris-Saclay, UVSQ, INRAE, BREED, 78350, Jouy-en-Josas, France
- Ecole Nationale Vétérinaire d'Alfort, BREED, 94700, Maisons-Alfort, France
| | - Renaud Fleurot
- Université Paris-Saclay, UVSQ, INRAE, BREED, 78350, Jouy-en-Josas, France
- Ecole Nationale Vétérinaire d'Alfort, BREED, 94700, Maisons-Alfort, France
| | - Tiphaine Aguirre-Lavin
- Université Paris-Saclay, UVSQ, INRAE, BREED, 78350, Jouy-en-Josas, France
- Ecole Nationale Vétérinaire d'Alfort, BREED, 94700, Maisons-Alfort, France
| | - Nathalie Peynot
- Université Paris-Saclay, UVSQ, INRAE, BREED, 78350, Jouy-en-Josas, France
- Ecole Nationale Vétérinaire d'Alfort, BREED, 94700, Maisons-Alfort, France
| | - Alice Jouneau
- Université Paris-Saclay, UVSQ, INRAE, BREED, 78350, Jouy-en-Josas, France
- Ecole Nationale Vétérinaire d'Alfort, BREED, 94700, Maisons-Alfort, France
| | - Nathalie Beaujean
- Université Paris-Saclay, UVSQ, INRAE, BREED, 78350, Jouy-en-Josas, France
- Ecole Nationale Vétérinaire d'Alfort, BREED, 94700, Maisons-Alfort, France
| | - Amélie Bonnet-Garnier
- Université Paris-Saclay, UVSQ, INRAE, BREED, 78350, Jouy-en-Josas, France
- Ecole Nationale Vétérinaire d'Alfort, BREED, 94700, Maisons-Alfort, France
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15
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Batnasan E, Koivukoski S, Kärkkäinen M, Latonen L. Nuclear Organization in Response to Stress: A Special Focus on Nucleoli. Results Probl Cell Differ 2022; 70:469-494. [PMID: 36348119 DOI: 10.1007/978-3-031-06573-6_17] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
In this chapter, we discuss the nuclear organization and how it responds to different types of stress. A key component in these responses is molecular traffic between the different sub-nucleolar compartments, such as nucleoplasm, chromatin, nucleoli, and various speckle and body compartments. This allows specific repair and response activities in locations where they normally are not active and serve to halt sensitive functions until the stress insult passes and inflicted damage has been repaired. We focus on mammalian cells and their nuclear organization, especially describing the central role of the nucleolus in nuclear stress responses. We describe events after multiple stress types, including DNA damage, various drugs, and toxic compounds, and discuss the involvement of macromolecular traffic between dynamic, phase-separated nuclear organelles and foci. We delineate the key proteins and non-coding RNA in the formation of stress-responsive, non-membranous nuclear organelles, many of which are relevant to the formation of and utilization in cancer treatment.
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Affiliation(s)
- Enkhzaya Batnasan
- Institute of Biomedicine, University of Eastern Finland, Kuopio, Finland
| | - Sonja Koivukoski
- Institute of Biomedicine, University of Eastern Finland, Kuopio, Finland
| | - Minttu Kärkkäinen
- Institute of Biomedicine, University of Eastern Finland, Kuopio, Finland
| | - Leena Latonen
- Institute of Biomedicine, University of Eastern Finland, Kuopio, Finland.
- Foundation for the Finnish Cancer Institute, Helsinki, Finland.
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16
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Moraleva AA, Deryabin AS, Rubtsov YP, Rubtsova MP, Dontsova OA. Eukaryotic Ribosome Biogenesis: The 40S Subunit. Acta Naturae 2022; 14:14-30. [PMID: 35441050 PMCID: PMC9013438 DOI: 10.32607/actanaturae.11540] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2021] [Accepted: 02/02/2022] [Indexed: 11/29/2022] Open
Abstract
The formation of eukaryotic ribosomes is a sequential process of ribosomal precursors maturation in the nucleolus, nucleoplasm, and cytoplasm. Hundreds of ribosomal biogenesis factors ensure the accurate processing and formation of the ribosomal RNAs' tertiary structure, and they interact with ribosomal proteins. Most of what we know about the ribosome assembly has been derived from yeast cell studies, and the mechanisms of ribosome biogenesis in eukaryotes are considered quite conservative. Although the main stages of ribosome biogenesis are similar across different groups of eukaryotes, this process in humans is much more complicated owing to the larger size of the ribosomes and pre-ribosomes and the emergence of regulatory pathways that affect their assembly and function. Many of the factors involved in the biogenesis of human ribosomes have been identified using genome-wide screening based on RNA interference. This review addresses the key aspects of yeast and human ribosome biogenesis, using the 40S subunit as an example. The mechanisms underlying these differences are still not well understood, because, unlike yeast, there are no effective methods for characterizing pre-ribosomal complexes in humans. Understanding the mechanisms of human ribosome assembly would have an incidence on a growing number of genetic diseases (ribosomopathies) caused by mutations in the genes encoding ribosomal proteins and ribosome biogenesis factors. In addition, there is evidence that ribosome assembly is regulated by oncogenic signaling pathways, and that defects in the ribosome biogenesis are linked to the activation of tumor suppressors.
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Affiliation(s)
- A. A. Moraleva
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry of the Russian Academy of Sciences, Moscow, 117997 Russia
| | - A. S. Deryabin
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry of the Russian Academy of Sciences, Moscow, 117997 Russia
| | - Yu. P. Rubtsov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry of the Russian Academy of Sciences, Moscow, 117997 Russia
| | - M. P. Rubtsova
- Lomonosov Moscow State University, Faculty of Chemistry, Moscow, 119991 Russia
| | - O. A. Dontsova
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry of the Russian Academy of Sciences, Moscow, 117997 Russia
- Lomonosov Moscow State University, Faculty of Chemistry, Moscow, 119991 Russia
- Skolkovo Institute of Science and Technology, Moscow, 121205 Russia
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17
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Kasselimi E, Pefani DE, Taraviras S, Lygerou Z. Ribosomal DNA and the nucleolus at the heart of aging. Trends Biochem Sci 2022; 47:328-341. [DOI: 10.1016/j.tibs.2021.12.007] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2021] [Revised: 12/15/2021] [Accepted: 12/16/2021] [Indexed: 12/15/2022]
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18
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Fabian-Morales E, Vallejo-Escamilla D, Gudiño A, Rodríguez A, González-Barrios R, Rodríguez Torres YL, Castro Hernández C, de la Torre-Luján AH, Oliva-Rico DA, Ornelas Guzmán EC, López Saavedra A, Frias S, Herrera LA. Large-scale topological disruption of chromosome territories 9 and 22 is associated with nonresponse to treatment in CML. Int J Cancer 2021; 150:1455-1470. [PMID: 34913480 PMCID: PMC9303775 DOI: 10.1002/ijc.33903] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2021] [Revised: 11/07/2021] [Accepted: 12/09/2021] [Indexed: 11/29/2022]
Abstract
Chronic myeloid leukemia (CML) is a myeloproliferative neoplasm defined by the presence of t(9;22) translocation whose origin has been associated with the tridimensional genome organization. This rearrangement leads to the fusion of BCR and ABL1 genes giving rise to a chimeric protein with constitutive kinase activity. Imatinib, a tyrosine kinase inhibitor (TKI), is used as a first‐line treatment for CML, though ~40% of CML patients do not respond. Here, using structured illumination microscopy (SIM) and 3D reconstruction, we studied the 3D organization patterns of the ABL1 and BCR genes, and their chromosome territories (CTs) CT9 and CT22, in CD34+ cells from CML patients that responded or not to TKI. We found that TKI resistance in CML is associated with high levels of structural disruption of CT9 and CT22 in CD34+ cells, increased CT volumes (especially for CT22), intermingling between CT9 and CT22, and an open‐chromatin epigenetic mark in CT22. Altogether our results suggest that large‐scale disruption of CT9 and CT22 correlates with the clinical response of CML patients, which could be translated into a potential prognostic marker of response to treatment in this disease and provide novel insights into the mechanisms underlying resistance to TKI in CML.
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Affiliation(s)
- Eunice Fabian-Morales
- Doctorado en Ciencias Biomédicas, Universidad Nacional Autónoma de México (UNAM), Mexico City, Mexico.,Unidad de Aplicaciones Avanzadas en Microscopía (ADMiRA), Instituto Nacional de Cancerología (INCan), Red de Apoyo a la Investigación (RAI), Universidad Nacional Autónoma de México (UNAM), Mexico City, Mexico.,Unidad de Investigación Biomédica en Cáncer, Instituto Nacional de Cancerología (INCan), Mexico City, Mexico.,Departamento de Medicina Genómica y Toxicología Ambiental, Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, Ciudad Universitaria, Apartado Postal 70228, Mexico City, Mexico
| | - David Vallejo-Escamilla
- Unidad de Aplicaciones Avanzadas en Microscopía (ADMiRA), Instituto Nacional de Cancerología (INCan), Red de Apoyo a la Investigación (RAI), Universidad Nacional Autónoma de México (UNAM), Mexico City, Mexico.,Unidad de Investigación Biomédica en Cáncer, Instituto Nacional de Cancerología (INCan), Mexico City, Mexico.,Departamento de Medicina Genómica y Toxicología Ambiental, Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, Ciudad Universitaria, Apartado Postal 70228, Mexico City, Mexico
| | - Adriana Gudiño
- Unidad de Aplicaciones Avanzadas en Microscopía (ADMiRA), Instituto Nacional de Cancerología (INCan), Red de Apoyo a la Investigación (RAI), Universidad Nacional Autónoma de México (UNAM), Mexico City, Mexico.,Unidad de Investigación Biomédica en Cáncer, Instituto Nacional de Cancerología (INCan), Mexico City, Mexico
| | - Alfredo Rodríguez
- Departamento de Medicina Genómica y Toxicología Ambiental, Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, Ciudad Universitaria, Apartado Postal 70228, Mexico City, Mexico.,Instituto Nacional de Pediatría (INP), Mexico City, Mexico
| | - Rodrigo González-Barrios
- Unidad de Investigación Biomédica en Cáncer, Instituto Nacional de Cancerología (INCan), Mexico City, Mexico.,Departamento de Medicina Genómica y Toxicología Ambiental, Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, Ciudad Universitaria, Apartado Postal 70228, Mexico City, Mexico
| | - Yameli L Rodríguez Torres
- Unidad de Aplicaciones Avanzadas en Microscopía (ADMiRA), Instituto Nacional de Cancerología (INCan), Red de Apoyo a la Investigación (RAI), Universidad Nacional Autónoma de México (UNAM), Mexico City, Mexico.,Unidad de Investigación Biomédica en Cáncer, Instituto Nacional de Cancerología (INCan), Mexico City, Mexico
| | - Clementina Castro Hernández
- Unidad de Investigación Biomédica en Cáncer, Instituto Nacional de Cancerología (INCan), Mexico City, Mexico.,Departamento de Medicina Genómica y Toxicología Ambiental, Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, Ciudad Universitaria, Apartado Postal 70228, Mexico City, Mexico
| | | | - Diego A Oliva-Rico
- Unidad de Aplicaciones Avanzadas en Microscopía (ADMiRA), Instituto Nacional de Cancerología (INCan), Red de Apoyo a la Investigación (RAI), Universidad Nacional Autónoma de México (UNAM), Mexico City, Mexico.,Unidad de Investigación Biomédica en Cáncer, Instituto Nacional de Cancerología (INCan), Mexico City, Mexico.,Departamento de Medicina Genómica y Toxicología Ambiental, Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, Ciudad Universitaria, Apartado Postal 70228, Mexico City, Mexico
| | - Erandhi C Ornelas Guzmán
- Unidad de Aplicaciones Avanzadas en Microscopía (ADMiRA), Instituto Nacional de Cancerología (INCan), Red de Apoyo a la Investigación (RAI), Universidad Nacional Autónoma de México (UNAM), Mexico City, Mexico.,Unidad de Investigación Biomédica en Cáncer, Instituto Nacional de Cancerología (INCan), Mexico City, Mexico
| | - Alejandro López Saavedra
- Unidad de Aplicaciones Avanzadas en Microscopía (ADMiRA), Instituto Nacional de Cancerología (INCan), Red de Apoyo a la Investigación (RAI), Universidad Nacional Autónoma de México (UNAM), Mexico City, Mexico.,Unidad de Investigación Biomédica en Cáncer, Instituto Nacional de Cancerología (INCan), Mexico City, Mexico.,Departamento de Medicina Genómica y Toxicología Ambiental, Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, Ciudad Universitaria, Apartado Postal 70228, Mexico City, Mexico
| | - Sara Frias
- Departamento de Medicina Genómica y Toxicología Ambiental, Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, Ciudad Universitaria, Apartado Postal 70228, Mexico City, Mexico.,Laboratorio de Citogenética, Instituto Nacional de Pediatría (INP), Mexico City, Mexico
| | - Luis A Herrera
- Unidad de Investigación Biomédica en Cáncer, Instituto Nacional de Cancerología (INCan), Mexico City, Mexico.,Departamento de Medicina Genómica y Toxicología Ambiental, Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, Ciudad Universitaria, Apartado Postal 70228, Mexico City, Mexico.,Instituto Nacional de Medicina Genómica (INMEGEN), Mexico City, Mexico
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19
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Miyake T, McDermott JC. Nucleolar localization of c-Jun. FEBS J 2021; 289:748-765. [PMID: 34499807 DOI: 10.1111/febs.16187] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2021] [Revised: 08/09/2021] [Accepted: 09/06/2021] [Indexed: 01/20/2023]
Abstract
Nucleoli are well defined for their function in ribosome biogenesis, but only a small fraction of the nucleolar proteome has been characterized. Here, we report that the proto-oncogene, c-Jun, is targeted to the nucleolus. Using live cell imaging in myogenic cells, we document that the c-Jun basic domain contains a unique, evolutionarily conserved motif that determines nucleolar targeting. Fos family Jun dimer partners, such as Fra2, while nuclear, do not co-localize with c-Jun in the nucleolus. A point mutation in c-Jun that mimics Fra2 (M260E) in its Nucleolar Localization sequence (NoLS) results in loss of c-Jun nucleolar targeting while still preserving nuclear localization. Fra2 can sequester c-Jun in the nucleoplasm, indicating that the stoichiometric ratio of heterodimeric partners regulates c-Jun nucleolar targeting. Finally, nucleolar localization of c-Jun modulates nucleolar architecture and ribosomal RNA accumulation. These studies highlight a novel role for Jun family proteins in the nucleolus, having potential implications for a diverse array of AP-1-regulated cellular processes.
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Affiliation(s)
- Tetsuaki Miyake
- Department of Biology, York University, Toronto, ON, Canada.,Muscle Health Research Centre (MHRC), York University, Toronto, ON, Canada.,Centre for Research in Biomolecular Interactions (CRBI), York University, Toronto, ON, Canada
| | - John C McDermott
- Department of Biology, York University, Toronto, ON, Canada.,Muscle Health Research Centre (MHRC), York University, Toronto, ON, Canada.,Centre for Research in Biomolecular Interactions (CRBI), York University, Toronto, ON, Canada.,Centre for Research in Mass Spectrometry (CRMS), York University, Toronto, ON, Canada
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20
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Thoms HC, Stark LA. The NF-κB Nucleolar Stress Response Pathway. Biomedicines 2021; 9:biomedicines9091082. [PMID: 34572268 PMCID: PMC8471347 DOI: 10.3390/biomedicines9091082] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2021] [Revised: 08/09/2021] [Accepted: 08/20/2021] [Indexed: 12/20/2022] Open
Abstract
The nuclear organelle, the nucleolus, plays a critical role in stress response and the regulation of cellular homeostasis. P53 as a downstream effector of nucleolar stress is well defined. However, new data suggests that NF-κB also acts downstream of nucleolar stress to regulate cell growth and death. In this review, we will provide insight into the NF-κB nucleolar stress response pathway. We will discuss apoptosis mediated by nucleolar sequestration of RelA and new data demonstrating a role for p62 (sequestosome (SQSTM1)) in this process. We will also discuss activation of NF-κB signalling by degradation of the RNA polymerase I (PolI) complex component, transcription initiation factor-IA (TIF-IA (RRN3)), and contexts where TIF-IA-NF-κB signalling may be important. Finally, we will discuss how this pathway is targeted by aspirin to mediate apoptosis of colon cancer cells.
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21
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Yoneda M, Nakagawa T, Hattori N, Ito T. The nucleolus from a liquid droplet perspective. J Biochem 2021; 170:153-162. [PMID: 34358306 DOI: 10.1093/jb/mvab090] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2021] [Accepted: 07/27/2021] [Indexed: 11/14/2022] Open
Abstract
The nucleolus is a membrane-less organelle sequestered from the nucleus by liquid droplet formation through a liquid-liquid phase separation (LLPS). It plays important roles in cell homeostasis through its internal thermodynamic changes. Reversible nucleolar transitions between coalescence and dispersion are dependent on the concentrations, conformations, and interactions of its molecular liquid droplet-forming components, including DNA, RNA, and protein. The liquid droplet-like properties of the nucleolus enable its diverse dynamic roles. The liquid droplet formation mechanism, by which the nucleolus is sequestered from the nucleoplasm despite the absence of a membrane, explains a number of complex nucleolar functions.
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Affiliation(s)
- Mitsuhiro Yoneda
- Department of Biochemistry, Nagasaki University School of Medicine, Nagasaki, 852-8523, JAPAN.,Nagasaki University Graduate School of Biomedical Sciences, Nagasaki, 852-8523, JAPAN
| | - Takeya Nakagawa
- Department of Biochemistry, Nagasaki University School of Medicine, Nagasaki, 852-8523, JAPAN.,Nagasaki University Graduate School of Biomedical Sciences, Nagasaki, 852-8523, JAPAN
| | - Naoko Hattori
- Department of Biochemistry, Nagasaki University School of Medicine, Nagasaki, 852-8523, JAPAN.,Nagasaki University Graduate School of Biomedical Sciences, Nagasaki, 852-8523, JAPAN
| | - Takashi Ito
- Department of Biochemistry, Nagasaki University School of Medicine, Nagasaki, 852-8523, JAPAN.,Nagasaki University Graduate School of Biomedical Sciences, Nagasaki, 852-8523, JAPAN
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22
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Antagonising Chromatin Remodelling Activities in the Regulation of Mammalian Ribosomal Transcription. Genes (Basel) 2021; 12:genes12070961. [PMID: 34202617 PMCID: PMC8303148 DOI: 10.3390/genes12070961] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2021] [Revised: 06/16/2021] [Accepted: 06/19/2021] [Indexed: 12/29/2022] Open
Abstract
Ribosomal transcription constitutes the major energy consuming process in cells and is regulated in response to proliferation, differentiation and metabolic conditions by several signalling pathways. These act on the transcription machinery but also on chromatin factors and ncRNA. The many ribosomal gene repeats are organised in a number of different chromatin states; active, poised, pseudosilent and repressed gene repeats. Some of these chromatin states are unique to the 47rRNA gene repeat and do not occur at other locations in the genome, such as the active state organised with the HMG protein UBF whereas other chromatin state are nucleosomal, harbouring both active and inactive histone marks. The number of repeats in a certain state varies on developmental stage and cell type; embryonic cells have more rRNA gene repeats organised in an open chromatin state, which is replaced by heterochromatin during differentiation, establishing different states depending on cell type. The 47S rRNA gene transcription is regulated in different ways depending on stimulus and chromatin state of individual gene repeats. This review will discuss the present knowledge about factors involved, such as chromatin remodelling factors NuRD, NoRC, CSB, B-WICH, histone modifying enzymes and histone chaperones, in altering gene expression and switching chromatin states in proliferation, differentiation, metabolic changes and stress responses.
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23
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Mutual dependency between lncRNA LETN and protein NPM1 in controlling the nucleolar structure and functions sustaining cell proliferation. Cell Res 2021; 31:664-683. [PMID: 33432115 PMCID: PMC8169757 DOI: 10.1038/s41422-020-00458-6] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2020] [Accepted: 11/30/2020] [Indexed: 02/06/2023] Open
Abstract
Fundamental processes such as ribosomal RNA synthesis and chromatin remodeling take place in the nucleolus, which is hyperactive in fast-proliferating cells. The sophisticated regulatory mechanism underlying the dynamic nucleolar structure and functions is yet to be fully explored. The present study uncovers the mutual functional dependency between a previously uncharacterized human long non-coding RNA, which we renamed LETN, and a key nucleolar protein, NPM1. Specifically, being upregulated in multiple types of cancer, LETN resides in the nucleolus via direct binding with NPM1. LETN plays a critical role in facilitating the formation of NPM1 pentamers, which are essential building blocks of the nucleolar granular component and control the nucleolar functions. Repression of LETN or NPM1 led to similar and profound changes of the nucleolar morphology and arrest of the nucleolar functions, which led to proliferation inhibition of human cancer cells and neural progenitor cells. Interestingly, this inter-dependency between LETN and NPM1 is associated with the evolutionarily new variations of NPM1 and the coincidental emergence of LETN in higher primates. We propose that this human-specific protein-lncRNA axis renders an additional yet critical layer of regulation with high physiological relevance in both cancerous and normal developmental processes that require hyperactive nucleoli.
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25
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Mangan H, McStay B. Human nucleoli comprise multiple constrained territories, tethered to individual chromosomes. Genes Dev 2021; 35:483-488. [PMID: 33664058 PMCID: PMC8015717 DOI: 10.1101/gad.348234.121] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2021] [Accepted: 02/01/2021] [Indexed: 11/24/2022]
Abstract
It is unknown how ribosomal gene (rDNA) arrays from multiple chromosomal nucleolar organizers (NORs) partition within human nucleoli. Exploration of this paradigm for chromosomal organization is complicated by the shared DNA sequence composition of five NOR-bearing acrocentric chromosome p-arms. Here, we devise a methodology for genetic manipulation of individual NORs. Efficient "scarless" genome editing of rDNA repeats is achieved on "poised" human NORs held within monochromosomal cell hybrids. Subsequent transfer to human cells introduces "active" NORs yielding readily discernible functional customized ribosomes. We reveal that ribosome biogenesis occurs entirely within constrained territories, tethered to individual NORs inside a larger nucleolus.
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Affiliation(s)
- Hazel Mangan
- Centre for Chromosome Biology, School of Natural Sciences, National University of Ireland Galway, Galway H91 W2TY, Ireland
| | - Brian McStay
- Centre for Chromosome Biology, School of Natural Sciences, National University of Ireland Galway, Galway H91 W2TY, Ireland
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Kim W, Kim DY, Lee KH. RNA-Binding Proteins and the Complex Pathophysiology of ALS. Int J Mol Sci 2021; 22:ijms22052598. [PMID: 33807542 PMCID: PMC7961459 DOI: 10.3390/ijms22052598] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2021] [Revised: 02/26/2021] [Accepted: 03/01/2021] [Indexed: 12/21/2022] Open
Abstract
Genetic analyses of patients with amyotrophic lateral sclerosis (ALS) have identified disease-causing mutations and accelerated the unveiling of complex molecular pathogenic mechanisms, which may be important for understanding the disease and developing therapeutic strategies. Many disease-related genes encode RNA-binding proteins, and most of the disease-causing RNA or proteins encoded by these genes form aggregates and disrupt cellular function related to RNA metabolism. Disease-related RNA or proteins interact or sequester other RNA-binding proteins. Eventually, many disease-causing mutations lead to the dysregulation of nucleocytoplasmic shuttling, the dysfunction of stress granules, and the altered dynamic function of the nucleolus as well as other membrane-less organelles. As RNA-binding proteins are usually components of several RNA-binding protein complexes that have other roles, the dysregulation of RNA-binding proteins tends to cause diverse forms of cellular dysfunction. Therefore, understanding the role of RNA-binding proteins will help elucidate the complex pathophysiology of ALS. Here, we summarize the current knowledge regarding the function of disease-associated RNA-binding proteins and their role in the dysfunction of membrane-less organelles.
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Affiliation(s)
- Wanil Kim
- Division of Cosmetic Science and Technology, Daegu Haany University, Hanuidae-ro 1, Gyeongsan, Gyeongbuk 38610, Korea;
| | - Do-Yeon Kim
- Department of Pharmacology, School of Dentistry, Kyungpook National University, Daegu 41940, Korea
- Correspondence: (D.-Y.K.); (K.-H.L.); Tel.: +82-53-660-6880 (D.-Y.K.); +82-53-819-7743 (K.-H.L.)
| | - Kyung-Ha Lee
- Division of Cosmetic Science and Technology, Daegu Haany University, Hanuidae-ro 1, Gyeongsan, Gyeongbuk 38610, Korea;
- Correspondence: (D.-Y.K.); (K.-H.L.); Tel.: +82-53-660-6880 (D.-Y.K.); +82-53-819-7743 (K.-H.L.)
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Poot M, Hochstenbach R. Prevalence and Phenotypic Impact of Robertsonian Translocations. Mol Syndromol 2021; 12:1-11. [PMID: 33776621 PMCID: PMC7983559 DOI: 10.1159/000512676] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2020] [Accepted: 10/26/2020] [Indexed: 12/11/2022] Open
Abstract
Robertsonian translocations (RTs) result from fusion of 2 acrocentric chromosomes (e.g., 13, 14, 15, 21, 22) and consequential losses of segments of the p arms containing 47S rDNA clusters and transcription factor binding sites. Depending on the position of the breakpoints, the size of these losses vary considerably between types of RTs. The prevalence of RTs in the general population is estimated to be around 1 per 800 individuals, making RTs the most common chromosomal rearrangement in healthy individuals. Based on their prevalence, RTs are classified as "common," rob(13;14) and rob(14;21), or "rare" (the 8 remaining nonhomologous combinations). Carriers of RTs are at an increased risk for offspring with chromosomal imbalances or with uniparental disomy. RTs are generally regarded as phenotypically neutral, although, due to RTs formation, 2 of the 10 ribosomal rDNA gene clusters, several long noncoding RNAs, and in the case of RTs involving chromosome 21, several mRNA encoding genes are lost. Nevertheless, recent evidence indicates that RTs may have a significant phenotypic impact. In particular, rob(13;14) carriers have a significantly elevated risk for breast cancer. While RTs are easily spotted by routine karyotyping, they may go unnoticed if only array-CGH and NextGen sequencing methods are applied. This review first discusses possible molecular mechanisms underlying the particularly high rates of RT formation and their incidence in the general population, and second, likely causes for the elevated cancer risk of some RTs will be examined.
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Affiliation(s)
- Martin Poot
- Department of Human Genetics, University of Würzburg, Würzburg, Germany
| | - Ron Hochstenbach
- Department of Clinical Genetics, Amsterdam UMC, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
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Huo CY, Chang ML, Cheng H, Ma TT, Fu Y, Wang Y, Wang YY, Kan YC, Li DD. Small nucleolar RNA of silkworm can translocate from the nucleolus to the cytoplasm under abiotic stress. Cell Biol Int 2021; 45:1091-1097. [PMID: 33501699 DOI: 10.1002/cbin.11555] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2020] [Accepted: 01/24/2021] [Indexed: 12/19/2022]
Abstract
Small nucleolar RNAs (snoRNAs) are thought to be exclusively nuclear and guide nucleotide modifications of ribosomal RNAs. Recently, more and more evidence has suggested that the nucleolus is a stress sensor for changes in growth status and that snoRNAs may orchestrate the response to environmental stress through molecular interactions outside of the nucleus. We previously showed that a box C/D snoRNA Bm-15 had both nuclear and cytoplasmic location in BmN4 cell line of the silkworm, Bombyx mori. To further study the functional roles of Bm-15, changes in expression level and cellular location of Bm-15 were examined in BmN4 cells subjected to serum starvation and ultraviolet (UV) ray radiation. Results indicated that total RNA level of Bm-15 was unchanged after 24 h serum starvation, but exhibited 3-fold increases in the cytoplasm, and the nuclear-to-cytosolic distribution ratio was reduced from 5:1 to 2:1. Moreover, UV radiation also causes rapid decline in nuclear Bm-15 and progressive cytoplasmic accumulation with a percentage of 22% and 57% after 6 and 24 h UV radiation. UV treatment results in a dramatic decrease in Bm-15 nuclear-to-cytosolic ratio from 7:1 to 2:1 and 2:1 to 1:20 after 6 and 24 h UV radiation, respectively. We show here for the first time that box C/D snoRNAs can translocate from the nucleus to the cytoplasm under the abiotic stress of nutritional deficiency and UV radiation. The rapid translocation of snoRNAs from nucleus to cytoplasm may slow down the maturation of rRNAs and synthesis of ribosomes to enhance the stress resistance of cells.
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Affiliation(s)
- Chun-Yue Huo
- China-UK-NYNU-RRes Joint Laboratory of Insect Biology, Henan Key Laboratory of Insect Biology in Funiu Mountain, Nanyang Normal University, 1638 Wolong Road, Nanyang, Henan, 473061, China
| | - Mei-Ling Chang
- China-UK-NYNU-RRes Joint Laboratory of Insect Biology, Henan Key Laboratory of Insect Biology in Funiu Mountain, Nanyang Normal University, 1638 Wolong Road, Nanyang, Henan, 473061, China
| | - Hao Cheng
- China-UK-NYNU-RRes Joint Laboratory of Insect Biology, Henan Key Laboratory of Insect Biology in Funiu Mountain, Nanyang Normal University, 1638 Wolong Road, Nanyang, Henan, 473061, China
| | - Tian-Tian Ma
- China-UK-NYNU-RRes Joint Laboratory of Insect Biology, Henan Key Laboratory of Insect Biology in Funiu Mountain, Nanyang Normal University, 1638 Wolong Road, Nanyang, Henan, 473061, China
| | - Yu Fu
- China-UK-NYNU-RRes Joint Laboratory of Insect Biology, Henan Key Laboratory of Insect Biology in Funiu Mountain, Nanyang Normal University, 1638 Wolong Road, Nanyang, Henan, 473061, China
| | - Yi Wang
- China-UK-NYNU-RRes Joint Laboratory of Insect Biology, Henan Key Laboratory of Insect Biology in Funiu Mountain, Nanyang Normal University, 1638 Wolong Road, Nanyang, Henan, 473061, China
| | - Yan-Yan Wang
- China-UK-NYNU-RRes Joint Laboratory of Insect Biology, Henan Key Laboratory of Insect Biology in Funiu Mountain, Nanyang Normal University, 1638 Wolong Road, Nanyang, Henan, 473061, China
| | - Yun-Chao Kan
- China-UK-NYNU-RRes Joint Laboratory of Insect Biology, Henan Key Laboratory of Insect Biology in Funiu Mountain, Nanyang Normal University, 1638 Wolong Road, Nanyang, Henan, 473061, China
- School of Life Science, Henan University, Jin Ming Avenue, Kaifeng, Henan, 475004, China
| | - Dan-Dan Li
- China-UK-NYNU-RRes Joint Laboratory of Insect Biology, Henan Key Laboratory of Insect Biology in Funiu Mountain, Nanyang Normal University, 1638 Wolong Road, Nanyang, Henan, 473061, China
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29
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Korsholm LM, Gál Z, Nieto B, Quevedo O, Boukoura S, Lund CC, Larsen DH. Recent advances in the nucleolar responses to DNA double-strand breaks. Nucleic Acids Res 2020; 48:9449-9461. [PMID: 32857853 PMCID: PMC7515731 DOI: 10.1093/nar/gkaa713] [Citation(s) in RCA: 35] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2020] [Revised: 08/13/2020] [Accepted: 08/26/2020] [Indexed: 12/15/2022] Open
Abstract
DNA damage poses a serious threat to human health and cells therefore continuously monitor and repair DNA lesions across the genome. Ribosomal DNA is a genomic domain that represents a particular challenge due to repetitive sequences, high transcriptional activity and its localization in the nucleolus, where the accessibility of DNA repair factors is limited. Recent discoveries have significantly extended our understanding of how cells respond to DNA double-strand breaks (DSBs) in the nucleolus, and new kinases and multiple down-stream targets have been identified. Restructuring of the nucleolus can occur as a consequence of DSBs and new data point to an active regulation of this process, challenging previous views. Furthermore, new insights into coordination of cell cycle phases and ribosomal DNA repair argue against existing concepts. In addition, the importance of nucleolar-DNA damage response (n-DDR) mechanisms for maintenance of genome stability and the potential of such factors as anti-cancer targets is becoming apparent. This review will provide a detailed discussion of recent findings and their implications for our understanding of the n-DDR. The n-DDR shares features with the DNA damage response (DDR) elsewhere in the genome but is also emerging as an independent response unique to ribosomal DNA and the nucleolus.
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Affiliation(s)
| | | | - Blanca Nieto
- Danish Cancer Society Research Center, Nucleolar Stress and Disease Group, Strandboulevarden 49, 2100 Copenhagen, Denmark
| | - Oliver Quevedo
- Danish Cancer Society Research Center, Nucleolar Stress and Disease Group, Strandboulevarden 49, 2100 Copenhagen, Denmark
| | - Stavroula Boukoura
- Danish Cancer Society Research Center, Nucleolar Stress and Disease Group, Strandboulevarden 49, 2100 Copenhagen, Denmark
| | - Casper Carstens Lund
- Danish Cancer Society Research Center, Nucleolar Stress and Disease Group, Strandboulevarden 49, 2100 Copenhagen, Denmark
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Kadam R, Harish M, Dalvi K, Teni T. Novel nucleolar localization of clusterin and its associated functions in human oral cancers: An in vitro and in silico analysis. Cell Biochem Funct 2020; 39:380-391. [PMID: 33155695 DOI: 10.1002/cbf.3600] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2020] [Revised: 09/25/2020] [Accepted: 10/05/2020] [Indexed: 02/05/2023]
Abstract
Clusterin (CLU), a multifunctional chaperonic glycoprotein associated with diverse cellular functions has been shown to act as an oncogene or tumour suppressor gene in different cancers, implying a dual role in tumorigenesis. Here, we investigated the expression of CLU isoforms, their subcellular localization and functional significance in oral cancer cells. Significant downregulation of secretory CLU (sCLU) transcripts was observed in oral cancer cell lines and tumours versus normal cells while the nuclear CLU (nCLU) transcripts were undetectable. We demonstrated for the first time the nucleolar localization of sCLU, its response to different nucleolar stresses and association with cajal bodies post nucleolar stress. Functionally, knockdown of CLU revealed its negative association with ribosome biogenesis implying a possible tumour suppressor like role in oral cancers. Further, loss of sCLU in these cells also resulted in altered nuclear morphology and shrunken tubulin filaments. In addition, the levels of nucleolar Nucleophosmin 1(NPM1) and Fibrillarin, known to regulate nuclear morphology were downregulated indicating a possible role of sCLU in their stabilization. Further, an in silico docking approach to gain insights into the interaction of sCLU with nucleolar proteins NPM1, Fibrillarin, UBF and Nucleolin, revealed the involvement of a conserved region comprising of amino acid residues 140-155 of sCLU β-chain, specifically via the Phe152 residue in hydrophobic interactions with these client nucleolar proteins indicating a possible stabilizing or regulatory role of sCLU. SIGNIFICANCE OF THE STUDY: This is the first study to demonstrate the nucleolar localization of sCLU and its associated functions in oral cancer cells. Downregulation of sCLU in oral cancer tissues and cell lines, and its negative association with ribogenesis suggest its tumour suppressor like role in oral cancers. The possible role of sCLU in stabilization or regulation of different nucleolar proteins thereby impacting their functions is also implicated.
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Affiliation(s)
- Rajashree Kadam
- Teni Laboratory, Advanced Centre for Treatment, Research and Education in Cancer (ACTREC), Tata Memorial Centre TMC, Navi Mumbai, India.,Homi Bhabha National Institute, Training School Complex, Mumbai, India
| | - Mahalakshmi Harish
- Protein Interactome Lab for Structural and Functional Biology, Advanced Centre for Treatment, Research and Education in Cancer (ACTREC), Tata Memorial Centre TMC, Navi Mumbai, India.,Homi Bhabha National Institute, Training School Complex, Mumbai, India
| | - Kajal Dalvi
- Teni Laboratory, Advanced Centre for Treatment, Research and Education in Cancer (ACTREC), Tata Memorial Centre TMC, Navi Mumbai, India
| | - Tanuja Teni
- Teni Laboratory, Advanced Centre for Treatment, Research and Education in Cancer (ACTREC), Tata Memorial Centre TMC, Navi Mumbai, India.,Homi Bhabha National Institute, Training School Complex, Mumbai, India
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31
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Houston R, Sekine S, Calderon MJ, Seifuddin F, Wang G, Kawagishi H, Malide DA, Li Y, Gucek M, Pirooznia M, Nelson AJ, Stokes MP, Stewart-Ornstein J, Mullett SJ, Wendell SG, Watkins SC, Finkel T, Sekine Y. Acetylation-mediated remodeling of the nucleolus regulates cellular acetyl-CoA responses. PLoS Biol 2020; 18:e3000981. [PMID: 33253182 PMCID: PMC7728262 DOI: 10.1371/journal.pbio.3000981] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2020] [Revised: 12/10/2020] [Accepted: 10/29/2020] [Indexed: 12/14/2022] Open
Abstract
The metabolite acetyl-coenzyme A (acetyl-CoA) serves as an essential element for a wide range of cellular functions including adenosine triphosphate (ATP) production, lipid synthesis, and protein acetylation. Intracellular acetyl-CoA concentrations are associated with nutrient availability, but the mechanisms by which a cell responds to fluctuations in acetyl-CoA levels remain elusive. Here, we generate a cell system to selectively manipulate the nucleo-cytoplasmic levels of acetyl-CoA using clustered regularly interspaced short palindromic repeat (CRISPR)-mediated gene editing and acetate supplementation of the culture media. Using this system and quantitative omics analyses, we demonstrate that acetyl-CoA depletion alters the integrity of the nucleolus, impairing ribosomal RNA synthesis and evoking the ribosomal protein-dependent activation of p53. This nucleolar remodeling appears to be mediated through the class IIa histone deacetylases (HDACs). Our findings highlight acetylation-mediated control of the nucleolus as an important hub linking acetyl-CoA fluctuations to cellular stress responses.
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Affiliation(s)
- Ryan Houston
- Aging Institute, Department of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
| | - Shiori Sekine
- Aging Institute, Department of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
- Division of Cardiology, Department of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
| | - Michael J. Calderon
- Department of Cell Biology, Center for Biologic Imaging, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
| | - Fayaz Seifuddin
- National Heart, Lung, and Blood Institute, NIH, Bethesda, Maryland, United States of America
| | - Guanghui Wang
- National Heart, Lung, and Blood Institute, NIH, Bethesda, Maryland, United States of America
| | - Hiroyuki Kawagishi
- National Heart, Lung, and Blood Institute, NIH, Bethesda, Maryland, United States of America
| | - Daniela A. Malide
- National Heart, Lung, and Blood Institute, NIH, Bethesda, Maryland, United States of America
| | - Yuesheng Li
- National Heart, Lung, and Blood Institute, NIH, Bethesda, Maryland, United States of America
| | - Marjan Gucek
- National Heart, Lung, and Blood Institute, NIH, Bethesda, Maryland, United States of America
| | - Mehdi Pirooznia
- National Heart, Lung, and Blood Institute, NIH, Bethesda, Maryland, United States of America
| | - Alissa J. Nelson
- Cell Signaling Technology, INC., Danvers, Massachusetts, United States of America
| | - Matthew P. Stokes
- Cell Signaling Technology, INC., Danvers, Massachusetts, United States of America
| | - Jacob Stewart-Ornstein
- Department of Computational and Systems Biology, University of Pittsburgh and Hillman Cancer Center, Pittsburgh, Pennsylvania, United States of America
| | - Steven J. Mullett
- Department of Pharmacology and Chemical Biology, the Health Sciences Metabolomics and Lipidomics Core, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
| | - Stacy G. Wendell
- Department of Pharmacology and Chemical Biology, the Health Sciences Metabolomics and Lipidomics Core, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
| | - Simon C. Watkins
- Department of Cell Biology, Center for Biologic Imaging, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
| | - Toren Finkel
- Aging Institute, Department of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
- Division of Cardiology, Department of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
- National Heart, Lung, and Blood Institute, NIH, Bethesda, Maryland, United States of America
| | - Yusuke Sekine
- Aging Institute, Department of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
- National Heart, Lung, and Blood Institute, NIH, Bethesda, Maryland, United States of America
- Division of Endocrinology and Metabolism, Department of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
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Ide S, Imai R, Ochi H, Maeshima K. Transcriptional suppression of ribosomal DNA with phase separation. SCIENCE ADVANCES 2020; 6:6/42/eabb5953. [PMID: 33055158 PMCID: PMC7556839 DOI: 10.1126/sciadv.abb5953] [Citation(s) in RCA: 43] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/13/2020] [Accepted: 08/25/2020] [Indexed: 05/21/2023]
Abstract
The nucleolus is a nuclear body with multiphase liquid droplets for ribosomal RNA (rRNA) transcription. How rRNA transcription is regulated in the droplets remains unclear. Here, using single-molecule tracking of RNA polymerase I (Pol I) and chromatin-bound upstream binding factor (UBF), we reveal suppression of transcription with phase separation. For transcription, active Pol I formed small clusters/condensates that constrained rDNA chromatin in the nucleolus fibrillar center (FC). Treatment with a transcription inhibitor induced Pol I to dissociate from rDNA chromatin and to move like a liquid within the nucleolar cap that transformed from the FC. Expression of a Pol I mutant associated with a craniofacial disorder inhibited transcription by competing with wild-type Pol I clusters and transforming the FC into the nucleolar cap. The cap droplet excluded an initiation factor, ensuring robust silencing. Our findings suggest a mechanism of rRNA transcription suppression via phase separation of intranucleolar molecules governed by Pol I.
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Affiliation(s)
- Satoru Ide
- Genome Dynamics Laboratory, National Institute of Genetics, Mishima, Shizuoka 411-8540, Japan.
- Department of Genetics, Sokendai (Graduate University for Advanced Studies), Shizuoka 411-8540, Japan
| | - Ryosuke Imai
- Genome Dynamics Laboratory, National Institute of Genetics, Mishima, Shizuoka 411-8540, Japan
- Department of Genetics, Sokendai (Graduate University for Advanced Studies), Shizuoka 411-8540, Japan
| | - Hiroko Ochi
- Genome Dynamics Laboratory, National Institute of Genetics, Mishima, Shizuoka 411-8540, Japan
| | - Kazuhiro Maeshima
- Genome Dynamics Laboratory, National Institute of Genetics, Mishima, Shizuoka 411-8540, Japan.
- Department of Genetics, Sokendai (Graduate University for Advanced Studies), Shizuoka 411-8540, Japan
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Engbrecht M, Mangerich A. The Nucleolus and PARP1 in Cancer Biology. Cancers (Basel) 2020; 12:cancers12071813. [PMID: 32640701 PMCID: PMC7408768 DOI: 10.3390/cancers12071813] [Citation(s) in RCA: 35] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2020] [Revised: 06/26/2020] [Accepted: 07/01/2020] [Indexed: 12/13/2022] Open
Abstract
The nucleolus has been known for a long time to fulfill crucial functions in ribosome biogenesis, of which cancer cells can become addicted to in order to produce sufficient amounts of proteins for cell proliferation. Recently, the nucleolus has emerged as a central regulatory hub in many other cancer-relevant processes, including stress sensing, DNA damage response, cell cycle control, and proteostasis. This fostered the idea that nucleolar processes can be exploited in cancer therapy. Interestingly, a significant proportion of poly(ADP-ribose) polymerase 1 (PARP1) molecules are localized in the nucleolus and PARP1 also plays crucial roles in many processes that are important in cancer biology, including genome maintenance, replication, transcription, and chromatin remodeling. Furthermore, during the last years, PARP1 came into focus in oncology since it represents a promising target of pharmacological PARP inhibitors in various types of cancers. Here, we provide an overview of our current understanding on the role of PARP1 in nucleolar functions and discuss potential implications in cancer biology and therapy.
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Frank L, Rippe K. Repetitive RNAs as Regulators of Chromatin-Associated Subcompartment Formation by Phase Separation. J Mol Biol 2020; 432:4270-4286. [DOI: 10.1016/j.jmb.2020.04.015] [Citation(s) in RCA: 37] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2019] [Revised: 04/14/2020] [Accepted: 04/14/2020] [Indexed: 12/21/2022]
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Vydzhak O, Luke B, Schindler N. Non-coding RNAs at the Eukaryotic rDNA Locus: RNA-DNA Hybrids and Beyond. J Mol Biol 2020; 432:4287-4304. [PMID: 32446803 DOI: 10.1016/j.jmb.2020.05.011] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2019] [Revised: 05/14/2020] [Accepted: 05/15/2020] [Indexed: 12/12/2022]
Abstract
The human ribosomal DNA (rDNA) locus encodes a variety of long non-coding RNAs (lncRNAs). Among them, the canonical ribosomal RNAs that are the catalytic components of the ribosomes, as well as regulatory lncRNAs including promoter-associated RNAs (pRNA), stress-induced promoter and pre-rRNA antisense RNAs (PAPAS), and different intergenic spacer derived lncRNA species (IGSRNA). In addition, externally encoded lncRNAs are imported into the nucleolus, which orchestrate the complex regulation of the nucleolar state in normal and stress conditions via a plethora of molecular mechanisms. This review focuses on the triplex and R-loop formation aspects of lncRNAs at the rDNA locus in yeast and human cells. We discuss the protein players that regulate R-loops at rDNA and how their misregulation contributes to DNA damage and disease. Furthermore, we speculate how DNA lesions such as rNMPs or 8-oxo-dG might affect RNA-DNA hybrid formation. The transcription of lncRNA from rDNA has been observed in yeast, plants, flies, worms, mouse and human cells. This evolutionary conservation highlights the importance of lncRNAs in rDNA function and maintenance.
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Affiliation(s)
- Olga Vydzhak
- Institute of Molecular Biology (IMB), Johannes Gutenberg-University Mainz, Ackermannweg 4, 55128 Mainz, Germany
| | - Brian Luke
- Institute of Molecular Biology (IMB), Johannes Gutenberg-University Mainz, Ackermannweg 4, 55128 Mainz, Germany; Institute of Developmental Biology and Neurobiology (IDN), Johannes Gutenberg-University Mainz, 55128 Mainz, Germany
| | - Natalie Schindler
- Institute of Developmental Biology and Neurobiology (IDN), Johannes Gutenberg-University Mainz, 55128 Mainz, Germany.
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NORs on human acrocentric chromosome p-arms are active by default and can associate with nucleoli independently of rDNA. Proc Natl Acad Sci U S A 2020; 117:10368-10377. [PMID: 32332163 PMCID: PMC7229746 DOI: 10.1073/pnas.2001812117] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022] Open
Abstract
A detailed description of how the genome is organized within the human nucleus is a major research goal. Nucleolar organizer regions (NORs) comprising ribosomal DNA (rDNA) arrays are located on the p-arms of the five human acrocentric chromosomes. Here we characterize the rules of engagement between NORs and nucleoli. We reveal variation in rDNA distribution, with some primary cell lines containing as many as four acrocentrics devoid of rDNA. We establish the default status of NORs as active and show that acrocentric p-arms devoid of rDNA retain nucleolar association potential. Based on our data, we propose that in diploid human cells, all 10 acrocentric chromosomes are nucleolar-associated, with involvement of non-rDNA sequences buffering against variable rDNA distribution. Nucleoli, the sites of ribosome biogenesis and the largest structures in human nuclei, form around nucleolar organizer regions (NORs) comprising ribosomal DNA (rDNA) arrays. NORs are located on the p-arms of the five human acrocentric chromosomes. Defining the rules of engagement between these p-arms and nucleoli takes on added significance as describing the three-dimensional organization of the human genome represents a major research goal. Here we used fluorescent in situ hybridization (FISH) and immuno-FISH on metaphase chromosomes from karyotypically normal primary and hTERT-immortalized human cell lines to catalog NORs in terms of their relative rDNA content and activity status. We demonstrate that a proportion of acrocentric p-arms in cell lines and from normal human donors have no detectable rDNA. Surprisingly, we found that all NORs with detectable rDNA are active, as defined by upstream binding factor loading. We determined the nucleolar association status of all NORs during interphase, and found that nucleolar association of acrocentric p-arms can occur independently of rDNA content, suggesting that sequences elsewhere on these chromosome arms drive nucleolar association. In established cancer lines, we characterize a variety of chromosomal rearrangements involving acrocentric p-arms and observe silent, rDNA-containing NORs that are dissociated from nucleoli. In conclusion, our findings indicate that within human nuclei, positioning of all 10 acrocentric chromosomes is dictated by nucleolar association. Furthermore, these nucleolar associations are buffered against interindividual variation in the distribution of rDNA.
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uL3 Mediated Nucleolar Stress Pathway as a New Mechanism of Action of Antiproliferative G-quadruplex TBA Derivatives in Colon Cancer Cells. Biomolecules 2020; 10:biom10040583. [PMID: 32290083 PMCID: PMC7226491 DOI: 10.3390/biom10040583] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2020] [Revised: 03/28/2020] [Accepted: 04/05/2020] [Indexed: 12/29/2022] Open
Abstract
The antiproliferative G-quadruplex aptamers are a promising and challenging subject in the framework of the anticancer therapeutic oligonucleotides research field. Although several antiproliferative G-quadruplex aptamers have been identified and proven to be effective on different cancer cell lines, their mechanism of action is still unexplored. We have recently described the antiproliferative activity of a heterochiral thrombin binding aptamer (TBA) derivative, namely, LQ1. Here, we investigate the molecular mechanisms of LQ1 activity and the structural and antiproliferative properties of two further TBA derivatives, differing from LQ1 only by the small loop base-compositions. We demonstrate that in p53 deleted colon cancer cells, LQ1 causes nucleolar stress, impairs ribosomal RNA processing, leading to the accumulation of pre-ribosomal RNAs, arrests cells in the G2/M phase and induces early apoptosis. Importantly, the depletion of uL3 abrogates all these effects, indicating that uL3 is a crucial player in the mechanism of action of LQ1. Taken together, our findings identify p53-independent and uL3-dependent nucleolar stress as a novel stress response pathway activated by a specific G-quadruplex TBA derivative. To the best of our knowledge, this investigation reveals, for the first time, the involvement of the nucleolar stress pathway in the mechanism of action of antiproliferative G-quadruplex aptamers.
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38
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Sun M, Wang R, Zhang H, Jiang Y, He J, Li S, Liu R. Molecular cytogenetic characterization of small supernumerary marker 15 in infertile male: A case report. Exp Ther Med 2020; 19:2927-2932. [PMID: 32256778 PMCID: PMC7086184 DOI: 10.3892/etm.2020.8542] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2019] [Accepted: 01/06/2020] [Indexed: 02/06/2023] Open
Abstract
Small supernumerary marker chromosomes (sSMCs) are defined as structurally abnormal chromosomes that may be detected pre- or postnataly in patients with developmental and/or mental retardation or infertility. sSMC on chromosome 15 accounts for the highest proportion of all sSMCs and may be detected in subfertile individuals. The present study reports the case of a male patient with oligoasthenoteratozoospermia and an sSMC. The sSMC was identified and characterized according to G-banding analysis, chromosomal microarray analysis (CMA) and fluorescence in situ hybridization (FISH) analysis. Chromosomal karyotype analysis suggested that the patient presented with 47,XY,+mar. CMA was used to characterize the sSMC, which revealed a 0.44-Mb microduplication in 6q25.3q26. Subsequently, FISH using centromere-specific probes for chromosomes 13/21, 14/22 and 15 was applied to identify the origin of the sSMC, which was finally determined to be inverted duplicated(15)(q11.2). It was hypothesized that heterochromatin in the sSMC is responsible for the patient's fertility problem. The presence of heterochromatin may disrupt regular meiosis, thereby affecting normal spermatogenesis. Impaired spermatogenesis in infertile males with an sSMC derived from chromosome 15 was also reviewed by searching published literature and the sSMC database (http://ssmc-tl.com/sSMC.html). For patients with low sperm parameters and complete absence of spermatozoa in the ejaculate, including infertile males with an sSMC with spermatozoa, intracytoplasmic sperm injection is considered as an effective assisted reproductive technique. It may be concluded that molecular cytogenetic techniques are critical tools for delineating sSMCs in infertile males and may be beneficial in identifying sSMC carriers to ensure they receive clinical genetic counseling.
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Affiliation(s)
- Meiling Sun
- Center for Reproductive Medicine and Center for Prenatal Diagnosis, The First Hospital, Jilin University, Changchun, Jilin 130021, P.R. China.,Jilin Engineering Research Center for Reproductive Medicine and Genetics, Jilin University, Changchun, Jilin 130021, P.R. China
| | - Ruixue Wang
- Center for Reproductive Medicine and Center for Prenatal Diagnosis, The First Hospital, Jilin University, Changchun, Jilin 130021, P.R. China.,Jilin Engineering Research Center for Reproductive Medicine and Genetics, Jilin University, Changchun, Jilin 130021, P.R. China
| | - Hongguo Zhang
- Center for Reproductive Medicine and Center for Prenatal Diagnosis, The First Hospital, Jilin University, Changchun, Jilin 130021, P.R. China.,Jilin Engineering Research Center for Reproductive Medicine and Genetics, Jilin University, Changchun, Jilin 130021, P.R. China
| | - Yuting Jiang
- Center for Reproductive Medicine and Center for Prenatal Diagnosis, The First Hospital, Jilin University, Changchun, Jilin 130021, P.R. China.,Jilin Engineering Research Center for Reproductive Medicine and Genetics, Jilin University, Changchun, Jilin 130021, P.R. China
| | - Jing He
- Center for Reproductive Medicine and Center for Prenatal Diagnosis, The First Hospital, Jilin University, Changchun, Jilin 130021, P.R. China.,Jilin Engineering Research Center for Reproductive Medicine and Genetics, Jilin University, Changchun, Jilin 130021, P.R. China
| | - Shibo Li
- Department of Pediatrics, University of Oklahoma Health Sciences Center, Oklahoma, OK 73104, USA
| | - Ruizhi Liu
- Center for Reproductive Medicine and Center for Prenatal Diagnosis, The First Hospital, Jilin University, Changchun, Jilin 130021, P.R. China.,Jilin Engineering Research Center for Reproductive Medicine and Genetics, Jilin University, Changchun, Jilin 130021, P.R. China
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39
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Zhou H, Li L, Wang Q, Hu Y, Zhao W, Gautam M, Li L. H3K9 Demethylation-Induced R-Loop Accumulation Is Linked to Disorganized Nucleoli. Front Genet 2020; 11:43. [PMID: 32117455 PMCID: PMC7025566 DOI: 10.3389/fgene.2020.00043] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2019] [Accepted: 01/15/2020] [Indexed: 11/24/2022] Open
Abstract
The nucleolar structure and integrity are important for a range of cellular functions of the nucleoli. It has been shown that cells lacking histone H3 Lysine 9 (H3K9) methylation form fragmented nucleoli. However, the molecular mechanism involved remains poorly understood. Here, we present evidence suggesting that loss of H3K9 dimethylation (H3K9me2) triggers R-loop accumulation at the rDNA locus, which further leads to the multilobed nucleoli. We reveal that suppression of H3K9 methyltransferase G9a by the inhibitor BIX 01294 causes R-loop accumulation at the rDNA region as well as inducing formation of multiple nucleoli. SiRNA-mediated knockdown of RNase H1 which can hydrolyze the RNA chain in R-loops causes an increase in R-loop formation, which in turn results in multiple nucleoli in one nucleus, whereas H3K9me2 levels are not affected by R-loop accumulation. Inhibition of RNA polymerase I transcription elongation by small molecule inhibitors induces a substantial decrease in H3K9me2 levels, accumulation of R-loops at rDNA sites, and nucleolus fragmentation. These results provide a mechanistic insight into the role of H3K9me2 in the structural integrity and organization of nucleoli via regulating R-loop accumulation.
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Affiliation(s)
- Hong Zhou
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan, China
| | - Le Li
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan, China
| | - Qing Wang
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan, China
| | - Yan Hu
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan, China
| | - Weiwei Zhao
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan, China
| | - Mayank Gautam
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan, China
| | - Lijia Li
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan, China
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Mooser C, Symeonidou IE, Leimbacher PA, Ribeiro A, Shorrocks AMK, Jungmichel S, Larsen SC, Knechtle K, Jasrotia A, Zurbriggen D, Jeanrenaud A, Leikauf C, Fink D, Nielsen ML, Blackford AN, Stucki M. Treacle controls the nucleolar response to rDNA breaks via TOPBP1 recruitment and ATR activation. Nat Commun 2020; 11:123. [PMID: 31913317 PMCID: PMC6949271 DOI: 10.1038/s41467-019-13981-x] [Citation(s) in RCA: 45] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2019] [Accepted: 12/10/2019] [Indexed: 01/10/2023] Open
Abstract
Induction of DNA double-strand breaks (DSBs) in ribosomal DNA (rDNA) repeats is associated with ATM-dependent repression of ribosomal RNA synthesis and large-scale reorganization of nucleolar architecture, but the signaling events that regulate these responses are largely elusive. Here we show that the nucleolar response to rDNA breaks is dependent on both ATM and ATR activity. We further demonstrate that ATM- and NBS1-dependent recruitment of TOPBP1 in the nucleoli is required for inhibition of ribosomal RNA synthesis and nucleolar segregation in response to rDNA breaks. Mechanistically, TOPBP1 recruitment is mediated by phosphorylation-dependent interactions between three of its BRCT domains and conserved phosphorylated Ser/Thr residues at the C-terminus of the nucleolar phosphoprotein Treacle. Our data thus reveal an important cooperation between TOPBP1 and Treacle in the signaling cascade that triggers transcriptional inhibition and nucleolar segregation in response to rDNA breaks.
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Affiliation(s)
- Clémence Mooser
- Department of Gynecology, University of Zurich, Wagistrasse 14, CH-8952, Schlieren, Switzerland
| | - Ioanna-Eleni Symeonidou
- Department of Gynecology, University of Zurich, Wagistrasse 14, CH-8952, Schlieren, Switzerland
| | - Pia-Amata Leimbacher
- Department of Gynecology, University of Zurich, Wagistrasse 14, CH-8952, Schlieren, Switzerland
| | - Alison Ribeiro
- Department of Gynecology, University of Zurich, Wagistrasse 14, CH-8952, Schlieren, Switzerland
| | - Ann-Marie K Shorrocks
- Department of Oncology, Medical Research Council Weatherall Institute of Molecular Medicine, University of Oxford, John Radcliffe Hospital, Oxford, OX3 9DS, UK
- Cancer Research UK/Medical Research Council Oxford Institute for Radiation Oncology, University of Oxford, Oxford, OX3 7DQ, UK
| | - Stephanie Jungmichel
- The Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, Faculty of Health and Medical Sciences, Bledgamsvej 3B DK-2200, Copenhagen, Denmark
| | - Sara C Larsen
- The Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, Faculty of Health and Medical Sciences, Bledgamsvej 3B DK-2200, Copenhagen, Denmark
| | - Katja Knechtle
- Department of Gynecology, University of Zurich, Wagistrasse 14, CH-8952, Schlieren, Switzerland
| | - Arti Jasrotia
- Department of Gynecology, University of Zurich, Wagistrasse 14, CH-8952, Schlieren, Switzerland
| | - Diana Zurbriggen
- Department of Gynecology, University of Zurich, Wagistrasse 14, CH-8952, Schlieren, Switzerland
| | - Alain Jeanrenaud
- Department of Gynecology, University of Zurich, Wagistrasse 14, CH-8952, Schlieren, Switzerland
| | - Colin Leikauf
- Department of Gynecology, University of Zurich, Wagistrasse 14, CH-8952, Schlieren, Switzerland
| | - Daniel Fink
- Department of Gynecology, University of Zurich, Wagistrasse 14, CH-8952, Schlieren, Switzerland
| | - Michael L Nielsen
- The Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, Faculty of Health and Medical Sciences, Bledgamsvej 3B DK-2200, Copenhagen, Denmark
| | - Andrew N Blackford
- Department of Oncology, Medical Research Council Weatherall Institute of Molecular Medicine, University of Oxford, John Radcliffe Hospital, Oxford, OX3 9DS, UK
- Cancer Research UK/Medical Research Council Oxford Institute for Radiation Oncology, University of Oxford, Oxford, OX3 7DQ, UK
| | - Manuel Stucki
- Department of Gynecology, University of Zurich, Wagistrasse 14, CH-8952, Schlieren, Switzerland.
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Abstract
In the past 25 years, genetic and biochemical analyses of ribosome assembly in yeast have identified most of the factors that participate in this complex pathway and have generated models for the mechanisms driving the assembly. More recently, the publication of numerous cryo-electron microscopy structures of yeast ribosome assembly intermediates has provided near-atomic resolution snapshots of ribosome precursor particles. Satisfyingly, these structural data support the genetic and biochemical models and provide additional mechanistic insight into ribosome assembly. In this Review, we discuss the mechanisms of assembly of the yeast small ribosomal subunit and large ribosomal subunit in the nucleolus, nucleus and cytoplasm. Particular emphasis is placed on concepts such as the mechanisms of RNA compaction, the functions of molecular switches and molecular mimicry, the irreversibility of assembly checkpoints and the roles of structural and functional proofreading of pre-ribosomal particles.
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42
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van Sluis M, Gailín MÓ, McCarter JGW, Mangan H, Grob A, McStay B. Human NORs, comprising rDNA arrays and functionally conserved distal elements, are located within dynamic chromosomal regions. Genes Dev 2019; 33:1688-1701. [PMID: 31727772 PMCID: PMC6942050 DOI: 10.1101/gad.331892.119] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2019] [Accepted: 10/23/2019] [Indexed: 01/09/2023]
Abstract
In this study, van Sluis et al. investigated the role of chromosomal context in nuclear organizer regions (NORs)/ribosomal gene (rDNA) in nucleolar formation and function. The analyses combined sequence capture and long-read sequencing to characterize the regions distal to rDNA arrays (DJ) on isolated acrocentric chromosomes, and their findings provide direct evidence for exchanges between heterologous human acrocentric p-arms, and uncover extensive structural variation between chromosomes and among individuals. Human nucleolar organizer regions (NORs), containing ribosomal gene (rDNA) arrays, are located on the p-arms of acrocentric chromosomes (HSA13–15, 21, and 22). Absence of these p-arms from genome references has hampered research on nucleolar formation. Previously, we assembled a distal junction (DJ) DNA sequence contig that abuts rDNA arrays on their telomeric side, revealing that it is shared among the acrocentrics and impacts nucleolar organization. To facilitate inclusion into genome references, we describe sequencing the DJ from all acrocentrics, including three versions of HSA21, ∼3 Mb of novel sequence. This was achieved by exploiting monochromosomal somatic cell hybrids containing single human acrocentric chromosomes with NORs that retain functional potential. Analyses revealed remarkable DJ sequence and functional conservation among human acrocentrics. Exploring chimpanzee acrocentrics, we show that “DJ-like” sequences and abutting rDNA arrays are inverted as a unit in comparison to humans. Thus, rDNA arrays and linked DJs represent a conserved functional locus. We provide direct evidence for exchanges between heterologous human acrocentric p-arms, and uncover extensive structural variation between chromosomes and among individuals. These findings lead us to revaluate the molecular definition of NORs, identify novel genomic structural variation, and provide a rationale for the distinctive chromosomal organization of NORs.
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Affiliation(s)
- Marjolein van Sluis
- Centre for Chromosome Biology, School of Natural Sciences, National University of Ireland Galway, Galway, Ireland
| | - Michael Ó Gailín
- Centre for Chromosome Biology, School of Natural Sciences, National University of Ireland Galway, Galway, Ireland
| | - Joseph G W McCarter
- Centre for Chromosome Biology, School of Natural Sciences, National University of Ireland Galway, Galway, Ireland
| | - Hazel Mangan
- Centre for Chromosome Biology, School of Natural Sciences, National University of Ireland Galway, Galway, Ireland
| | - Alice Grob
- Centre for Chromosome Biology, School of Natural Sciences, National University of Ireland Galway, Galway, Ireland
| | - Brian McStay
- Centre for Chromosome Biology, School of Natural Sciences, National University of Ireland Galway, Galway, Ireland
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43
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Siebenwirth C, Greubel C, Drexler GA, Reindl J, Walsh DWM, Schwarz B, Sammer M, Baur I, Pospiech H, Schmid TE, Dollinger G, Friedl AA. Local inhibition of rRNA transcription without nucleolar segregation after targeted ion irradiation of the nucleolus. J Cell Sci 2019; 132:jcs.232181. [PMID: 31492757 PMCID: PMC6803363 DOI: 10.1242/jcs.232181] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2019] [Accepted: 08/29/2019] [Indexed: 12/18/2022] Open
Abstract
Nucleoli have attracted interest for their role as cellular stress sensors and as potential targets for cancer treatment. The effect of DNA double-strand breaks (DSBs) in nucleoli on rRNA transcription and nucleolar organisation appears to depend on the agent used to introduce DSBs, DSB frequency and the presence (or not) of DSBs outside the nucleoli. To address the controversy, we targeted nucleoli with carbon ions at the ion microbeam SNAKE. Localized ion irradiation with 1-100 carbon ions per point (about 0.3-30 Gy per nucleus) did not lead to overall reduced ribonucleotide incorporation in the targeted nucleolus or other nucleoli of the same cell. However, both 5-ethynyluridine incorporation and Parp1 protein levels were locally decreased at the damaged nucleolar chromatin regions marked by γH2AX, suggesting localized inhibition of rRNA transcription. This locally restricted transcriptional inhibition was not accompanied by nucleolar segregation, a structural reorganisation observed after inhibition of rRNA transcription by treatment with actinomycin D or UV irradiation. The presented data indicate that even multiple complex DSBs do not lead to a pan-nucleolar response if they affect only a subnucleolar region.
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Affiliation(s)
- Christian Siebenwirth
- Bundeswehr Institute of Radiobiology, 80937 Munich, Germany .,Institute for Applied Physics and Metrology, Universität der Bundeswehr München, 85577 Neubiberg, Germany.,Department of Radiation Therapy and Radiooncology, Technical University of Munich, 81675 Munich, Germany
| | - Christoph Greubel
- Institute for Applied Physics and Metrology, Universität der Bundeswehr München, 85577 Neubiberg, Germany
| | - Guido A Drexler
- Department of Radiation Oncology, University Hospital, Ludwig Maximilians University of Munich, 81377 Munich, Germany
| | - Judith Reindl
- Institute for Applied Physics and Metrology, Universität der Bundeswehr München, 85577 Neubiberg, Germany
| | - Dietrich W M Walsh
- Institute for Applied Physics and Metrology, Universität der Bundeswehr München, 85577 Neubiberg, Germany
| | - Benjamin Schwarz
- Institute for Applied Physics and Metrology, Universität der Bundeswehr München, 85577 Neubiberg, Germany
| | - Matthias Sammer
- Institute for Applied Physics and Metrology, Universität der Bundeswehr München, 85577 Neubiberg, Germany
| | - Iris Baur
- Department of Radiation Oncology, University Hospital, Ludwig Maximilians University of Munich, 81377 Munich, Germany
| | - Helmut Pospiech
- Leibniz Institute for Age Research - Fritz Lipmann Institute (FLI), 07745 Jena, Germany
| | - Thomas E Schmid
- Department of Radiation Therapy and Radiooncology, Technical University of Munich, 81675 Munich, Germany
| | - Günther Dollinger
- Institute for Applied Physics and Metrology, Universität der Bundeswehr München, 85577 Neubiberg, Germany
| | - Anna A Friedl
- Department of Radiation Oncology, University Hospital, Ludwig Maximilians University of Munich, 81377 Munich, Germany
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44
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Gunduz M, Okan MA, Sengil AZ, Temel H, Comert M, Okur M. The relationship of argyrophilic proteins of the nuclear‐organized regions and atopic dermatitis in children. Exp Dermatol 2019; 28:1309-1312. [DOI: 10.1111/exd.14031] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2019] [Revised: 08/20/2019] [Accepted: 09/03/2019] [Indexed: 12/20/2022]
Affiliation(s)
- Mehmet Gunduz
- Department of Pediatrics Istanbul Medipol University Faculty of Medicine Istanbul Turkey
| | - Meliha A. Okan
- Department of Pediatrics Istanbul Medipol University Faculty of Medicine Istanbul Turkey
| | - Ahmet Z. Sengil
- Department of Genetics Istanbul Medipol University Faculty of Medicine Istanbul Turkey
| | - Hayrettin Temel
- Department of Pediatrics Istanbul Medipol University Faculty of Medicine Istanbul Turkey
| | - Murat Comert
- Department of Pediatrics Istanbul Medipol University Faculty of Medicine Istanbul Turkey
| | - Mesut Okur
- Department of Pediatrics Istanbul Medipol University Faculty of Medicine Istanbul Turkey
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45
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Bartholomé O, Franck C, Piscicelli P, Lalun N, Defourny J, Renauld J, Thelen N, Lamaye F, Ploton D, Thiry M. Relationships between the structural and functional organization of the turtle cell nucleolus. J Struct Biol 2019; 208:107398. [PMID: 31585176 DOI: 10.1016/j.jsb.2019.09.015] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2019] [Revised: 09/21/2019] [Accepted: 09/27/2019] [Indexed: 12/30/2022]
Abstract
The nucleolus is a multifunctional structure of the eukaryotic cell nucleus. However, its primary role is ribosome formation. Although the factors and mechanisms involved in ribogenesis are well conserved in eukaryotes, two types of nucleoli have been observed under the electron microscope: a tricompartmentalized nucleolus in amniotes and a bicompartmentalized nucleolus in other species. A recent study has also revealed that turtles, although belonging to amniotes, displayed a nucleolus with bipartite organization, suggesting that this reptile group may have carried out a reversion phenomenon during evolution. In this study, we examine in great detail the functional organization of the turtle nucleolus. In liver and spleen cells cultured in vitro, we confirm that the turtle nucleolus is mainly formed by two components: a fibrillar zone surrounded by a granular zone. We further show that the fibrillar zone includes densely-contrasted strands, which are positive after silver-stained Nucleolar Organizer Region (Ag-NOR) staining and DNA labelling. We also reveal that the dense strands condensed into a very compact mass within the fibrillar zone after a treatment with actinomycin D or 5,6-dichlorobenzimidazole riboside. Finally, by using pulse-chase experiments with BrUTP, three-dimensional image reconstructions of confocal optical sections, and electron microscopy analysis of ultrathin sections, we show that the topological and spatial dynamics of rRNA within the nucleolus extend from upstream binding factor (UBF)-positive sites in the fibrillar zone to the granular zone, without ever releasing the positive sites for the UBF. Together, these results seem to clearly indicate that the compartmentalization of the turtle nucleolus into two main components reflects a less orderly organization of ribosome formation.
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Affiliation(s)
- Odile Bartholomé
- Unit of Cell Biology, GIGA-Neurosciences, University of Liege, CHU Sart-Tilman, B36, 4000 Liege, Belgium
| | - Claire Franck
- Unit of Cell Biology, GIGA-Neurosciences, University of Liege, CHU Sart-Tilman, B36, 4000 Liege, Belgium
| | - Patricia Piscicelli
- Unit of Cell Biology, GIGA-Neurosciences, University of Liege, CHU Sart-Tilman, B36, 4000 Liege, Belgium
| | - Nathalie Lalun
- UMRCNRS 6237, Université de Reims Champagne-Ardenne, 51 rue Cognacq-Jay, 51095 Reims Cedex, France
| | - Jean Defourny
- Unit of Cell Biology, GIGA-Neurosciences, University of Liege, CHU Sart-Tilman, B36, 4000 Liege, Belgium
| | - Justine Renauld
- Unit of Cell Biology, GIGA-Neurosciences, University of Liege, CHU Sart-Tilman, B36, 4000 Liege, Belgium
| | - Nicolas Thelen
- Unit of Cell Biology, GIGA-Neurosciences, University of Liege, CHU Sart-Tilman, B36, 4000 Liege, Belgium
| | - Françoise Lamaye
- Unit of Cell Biology, GIGA-Neurosciences, University of Liege, CHU Sart-Tilman, B36, 4000 Liege, Belgium
| | - Dominique Ploton
- UMRCNRS 6237, Université de Reims Champagne-Ardenne, 51 rue Cognacq-Jay, 51095 Reims Cedex, France
| | - Marc Thiry
- Unit of Cell Biology, GIGA-Neurosciences, University of Liege, CHU Sart-Tilman, B36, 4000 Liege, Belgium.
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Korsholm LM, Gál Z, Lin L, Quevedo O, Ahmad DA, Dulina E, Luo Y, Bartek J, Larsen DH. Double-strand breaks in ribosomal RNA genes activate a distinct signaling and chromatin response to facilitate nucleolar restructuring and repair. Nucleic Acids Res 2019; 47:8019-8035. [PMID: 31184714 PMCID: PMC6735822 DOI: 10.1093/nar/gkz518] [Citation(s) in RCA: 50] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2018] [Revised: 05/29/2019] [Accepted: 06/03/2019] [Indexed: 12/21/2022] Open
Abstract
The nucleolus is a nuclear sub-domain containing the most highly transcribed genes in the genome. Hundreds of human ribosomal RNA (rRNA) genes, located in the nucleolus, rely on constant maintenance. DNA double-strand breaks (DSBs) in rRNA genes activate the ATM kinase, repress rRNA transcription and induce nucleolar cap formation. Yet how ribosomal-DNA (rDNA) lesions are detected and processed remains elusive. Here, we use CRISPR/Cas9-mediated induction of DSBs and report a chromatin response unique to rDNA depending on ATM-phosphorylation of the nucleolar protein TCOF1 and recruitment of the MRE11-RAD50-NBS1 (MRN) complex via the NBS1-subunit. NBS1- and MRE11-depleted cells fail to suppress rRNA transcription and to translocate rDNA into nucleolar caps. Furthermore, the DNA damage response (DDR) kinase ATR operates downstream of the ATM-TCOF1-MRN interplay and is required to fully suppress rRNA transcription and complete DSB-induced nucleolar restructuring. Unexpectedly, we find that DSBs in rDNA neither activate checkpoint kinases CHK1/CHK2 nor halt cell-cycle progression, yet the nucleolar-DDR protects against genomic aberrations and cell death. Our data highlight the concept of a specialized nucleolar DNA damage response (n-DDR) with a distinct protein composition, spatial organization and checkpoint communication. The n-DDR maintains integrity of ribosomal RNA genes, with implications for cell physiology and disease.
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Affiliation(s)
- Lea M Korsholm
- Nucleolar Stress and Disease Group, Danish Cancer Society Research Center, Danish Cancer Society, Strandboulevarden 49, DK-2100 Copenhagen, Denmark
- Genome Integrity Unit, Danish Cancer Society Research Center, Danish Cancer Society, Strandboulevarden 49, DK-2100 Copenhagen, Denmark
| | - Zita Gál
- Nucleolar Stress and Disease Group, Danish Cancer Society Research Center, Danish Cancer Society, Strandboulevarden 49, DK-2100 Copenhagen, Denmark
- Genome Integrity Unit, Danish Cancer Society Research Center, Danish Cancer Society, Strandboulevarden 49, DK-2100 Copenhagen, Denmark
| | - Lin Lin
- Department of Biomedicine, Aarhus University, 8000 Aarhus, Denmark
- China National GeneBank, BGI-Shenzhen, 518083 Shenzhen, China
| | - Oliver Quevedo
- Nucleolar Stress and Disease Group, Danish Cancer Society Research Center, Danish Cancer Society, Strandboulevarden 49, DK-2100 Copenhagen, Denmark
- Genome Integrity Unit, Danish Cancer Society Research Center, Danish Cancer Society, Strandboulevarden 49, DK-2100 Copenhagen, Denmark
| | - Diana A Ahmad
- Nucleolar Stress and Disease Group, Danish Cancer Society Research Center, Danish Cancer Society, Strandboulevarden 49, DK-2100 Copenhagen, Denmark
- Genome Integrity Unit, Danish Cancer Society Research Center, Danish Cancer Society, Strandboulevarden 49, DK-2100 Copenhagen, Denmark
| | - Ekaterina Dulina
- Nucleolar Stress and Disease Group, Danish Cancer Society Research Center, Danish Cancer Society, Strandboulevarden 49, DK-2100 Copenhagen, Denmark
- Genome Integrity Unit, Danish Cancer Society Research Center, Danish Cancer Society, Strandboulevarden 49, DK-2100 Copenhagen, Denmark
| | - Yonglun Luo
- Department of Biomedicine, Aarhus University, 8000 Aarhus, Denmark
- China National GeneBank, BGI-Shenzhen, 518083 Shenzhen, China
- Lars Bolund Institute of Regenerative Medicine, BGI-Qingdao, 266555 Qingdao, China
| | - Jiri Bartek
- Genome Integrity Unit, Danish Cancer Society Research Center, Danish Cancer Society, Strandboulevarden 49, DK-2100 Copenhagen, Denmark
- Department of Medical Biochemistry and Biophysics, Science for Life Laboratory, Division of Genome Biology, Karolinska Institutet, SE-171 65 Solna, Sweden
| | - Dorthe H Larsen
- Nucleolar Stress and Disease Group, Danish Cancer Society Research Center, Danish Cancer Society, Strandboulevarden 49, DK-2100 Copenhagen, Denmark
- Genome Integrity Unit, Danish Cancer Society Research Center, Danish Cancer Society, Strandboulevarden 49, DK-2100 Copenhagen, Denmark
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47
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Tchelidze P, Kaplan H, Terryn C, Lalun N, Ploton D, Thiry M. Electron tomography reveals changes in spatial distribution of UBTF1 and UBTF2 isoforms within nucleolar components during rRNA synthesis inhibition. J Struct Biol 2019; 208:191-204. [PMID: 31479756 DOI: 10.1016/j.jsb.2019.08.014] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2019] [Revised: 08/29/2019] [Accepted: 08/30/2019] [Indexed: 12/01/2022]
Abstract
Upstream binding transcription factor (UBTF) is a co-regulator of RNA polymerase I by constituting an initiation complex on rRNA genes. UBTF plays a role in rDNA bending and its maintenance in "open" state. It exists as two splicing variants, UBTF1 and UBTF2, which cannot be discerned with antibodies raised against UBTF. We investigated the ultrastructural localization of each variant in cells synthesizing GFP-tagged UBTF1 or UBTF2 by using anti-GFP antibodies and pre-embedding nanogold strategy. Detailed 3D distribution of UBTF1 and 2 was also studied by electron tomography. In control cells, the two isoforms are very abundant within fibrillar centers, but their repartition strongly differs. Electron tomography shows that UBTF1 is disposed as fibrils that are folded in coils whereas UBTF2 is localized homogenously, preferentially at their cortical area. As UBTF is a useful marker to trace rDNA genes, we used these data to improve our previous model of 3D organization of active transcribing rDNA gene within fibrillar centers. Finally, when rRNA synthesis is inhibited during actinomycin D treatment or entry in mitosis, UBTF1 and UBTF2 show a similar distribution along extended 3D loop-like structures. Altogether these data suggest new roles for UBTF1 and UBTF2 isoforms in the organization of active and inactive rDNA genes.
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Affiliation(s)
- Pavel Tchelidze
- Faculty of Health, Eastern European University, Tbilisi, Georgia
| | - Hervé Kaplan
- Université de Reims Champagne Ardenne, Reims, France
| | - Christine Terryn
- Platform of Cellular and Tissular Imaging (PICT), Université de Reims Champagne Ardenne, Reims, France
| | - Nathalie Lalun
- UMR-S 1250 INSERM, Université de Reims Champagne Ardenne, France
| | - Dominique Ploton
- BioSpecT, EA 7506, Université de Reims Champagne Ardenne, France
| | - Marc Thiry
- Unit of Cell and Tissue Biology, GIGA-Neurosciences, University of Liège, Liège, Belgium.
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Chen J, Stark LA. Insights into the Relationship between Nucleolar Stress and the NF-κB Pathway. Trends Genet 2019; 35:768-780. [PMID: 31434627 DOI: 10.1016/j.tig.2019.07.009] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2019] [Revised: 07/22/2019] [Accepted: 07/24/2019] [Indexed: 02/06/2023]
Abstract
The nuclear organelle the nucleolus and the transcription factor nuclear factor of κ-light-chain-enhancer of activated B cells (NF-κB) are both central to the control of cellular homeostasis, dysregulated in common diseases and implicated in the ageing process. Until recently, it was believed that they acted independently to regulate homeostasis in health and disease. However, there is an emerging body of evidence suggesting that nucleoli and NF-κB signalling converge at multiple levels. Here we will review current understanding of this crosstalk. We will discuss activation of the NF-κB pathway by nucleolar stress and induction of apoptosis by nucleolar sequestration of NF-κB/RelA. We will also discuss the role of TIF-IA, COMMD1, and nucleophosmin, which are key players in this crosstalk, and the therapeutic relevance, particularly with respect to the antitumour effects of aspirin.
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Affiliation(s)
- Jingyu Chen
- University of Edinburgh Cancer Research Centre, Institute of Genetics and Molecular Medicine, Western General Hospital, Crewe Road, Edinburgh, Scotland EH4 2XU, UK
| | - Lesley A Stark
- University of Edinburgh Cancer Research Centre, Institute of Genetics and Molecular Medicine, Western General Hospital, Crewe Road, Edinburgh, Scotland EH4 2XU, UK.
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Correll CC, Bartek J, Dundr M. The Nucleolus: A Multiphase Condensate Balancing Ribosome Synthesis and Translational Capacity in Health, Aging and Ribosomopathies. Cells 2019; 8:cells8080869. [PMID: 31405125 PMCID: PMC6721831 DOI: 10.3390/cells8080869] [Citation(s) in RCA: 68] [Impact Index Per Article: 13.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2019] [Revised: 07/31/2019] [Accepted: 08/06/2019] [Indexed: 12/21/2022] Open
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.
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Affiliation(s)
- Carl C Correll
- Center for Proteomics and Molecular Therapeutics, Rosalind Franklin University of Medicine & Science, North Chicago, IL 60064, USA.
| | - Jiri Bartek
- Danish Cancer Society Research Center, Genome Integrity Unit, DK-2100 Copenhagen, Denmark
- Division of Genome Biology, Department of Medical Biochemistry and Biophysics, Science for Life Laboratory, Karolinska Institute, SE-171 77 Stockholm, Sweden
| | - Miroslav Dundr
- Center for Cancer Cell Biology Immunology and Infection, Rosalind Franklin University of Medicine & Science, North Chicago, IL 60064, USA.
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50
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Nucleolar DNA Double-Strand Break Responses Underpinning rDNA Genomic Stability. Trends Genet 2019; 35:743-753. [PMID: 31353047 DOI: 10.1016/j.tig.2019.07.001] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2019] [Revised: 06/28/2019] [Accepted: 07/01/2019] [Indexed: 12/12/2022]
Abstract
Nucleoli, the sites of ribosome biogenesis, form around ribosomal gene (rDNA) arrays termed nucleolar organiser regions (NORs). These are the most transcriptionally active regions of the human genome and specialised responses have evolved to ensure their genomic stability. This review focuses on nucleolar responses to DNA double-strand breaks (DSBs) introduced into rDNA arrays using sequence-specific endonucleases, including CRISPR/Cas9. Repair of rDNA DSBs is predominantly carried out by the homology-directed repair (HDR) pathway that is facilitated by inhibition of transcription by RNA polymerase-I (Pol-I) and ensuing dramatic nucleolar reorganisation. Additionally, we review evidence that nucleoli can sense and respond to DSBs elsewhere in the genome.
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