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Sibai DS, Tremblay MG, Lessard F, Tav C, Sabourin-Félix M, Robinson M, Moss T. TTF1 control of LncRNA synthesis delineates a tumor suppressor pathway directly regulating the ribosomal RNA genes. J Cell Physiol 2024; 239:e31303. [PMID: 38764354 DOI: 10.1002/jcp.31303] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2024] [Revised: 04/29/2024] [Accepted: 05/02/2024] [Indexed: 05/21/2024]
Abstract
The tumor suppressor p14/19ARF regulates ribosomal RNA (rRNA) synthesis by controlling the nucleolar localization of Transcription Termination Factor 1 (TTF1). However, the role played by TTF1 in regulating the rRNA genes and in potentially controlling growth has remained unclear. We now show that TTF1 expression regulates cell growth by determining the cellular complement of ribosomes. Unexpectedly, it achieves this by acting as a "roadblock" to synthesis of the noncoding LncRNA and pRNA that we show are generated from the "Spacer Promoter" duplications present upstream of the 47S pre-rRNA promoter on the mouse and human ribosomal RNA genes. Unexpectedly, the endogenous generation of these noncoding RNAs does not induce CpG methylation or gene silencing. Rather, it acts in cis to suppress 47S preinitiation complex formation and hence de novo pre-rRNA synthesis by a mechanism reminiscent of promoter interference or occlusion. Taken together, our data delineate a pathway from p19ARF to cell growth suppression via the regulation of ribosome biogenesis by noncoding RNAs and validate a key cellular growth law in mammalian cells.
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Affiliation(s)
- Dany S Sibai
- St-Patrick Research Group in Basic Oncology, Cancer Division of the Quebec University Hospital Research Centre, Laval University, Quebec City, Quebec, Canada
- Department of Molecular Biology, Medical Biochemistry and Pathology, Faculty of Medicine, Laval University, Quebec City, Quebec, Canada
- Cancer Research Centre, Laval University, Quebec City, Quebec, Canada
| | - Michel G Tremblay
- St-Patrick Research Group in Basic Oncology, Cancer Division of the Quebec University Hospital Research Centre, Laval University, Quebec City, Quebec, Canada
| | - Frédéric Lessard
- St-Patrick Research Group in Basic Oncology, Cancer Division of the Quebec University Hospital Research Centre, Laval University, Quebec City, Quebec, Canada
| | - Christophe Tav
- St-Patrick Research Group in Basic Oncology, Cancer Division of the Quebec University Hospital Research Centre, Laval University, Quebec City, Quebec, Canada
- Department of Molecular Biology, Medical Biochemistry and Pathology, Faculty of Medicine, Laval University, Quebec City, Quebec, Canada
- Cancer Research Centre, Laval University, Quebec City, Quebec, Canada
| | - Marianne Sabourin-Félix
- St-Patrick Research Group in Basic Oncology, Cancer Division of the Quebec University Hospital Research Centre, Laval University, Quebec City, Quebec, Canada
| | - Mark Robinson
- Department of Molecular Life Sciences, University of Zurich, Zurich, Switzerland
| | - Tom Moss
- St-Patrick Research Group in Basic Oncology, Cancer Division of the Quebec University Hospital Research Centre, Laval University, Quebec City, Quebec, Canada
- Department of Molecular Biology, Medical Biochemistry and Pathology, Faculty of Medicine, Laval University, Quebec City, Quebec, Canada
- Cancer Research Centre, Laval University, Quebec City, Quebec, Canada
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2
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Klushevskaya ES, Alembekov IR, Kravatsky YV, Tchurikov NA. Homeotic DUX4 Genes Shape Dynamic Inter-Chromosomal Contacts with Nucleoli in Human Cells. DOKL BIOCHEM BIOPHYS 2024; 517:259-263. [PMID: 39002012 DOI: 10.1134/s1607672924700935] [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: 03/25/2024] [Revised: 04/15/2024] [Accepted: 04/16/2024] [Indexed: 07/15/2024]
Abstract
Nucleoli form interchromosomal contacts with genes controlling differentiation and carcinogenesis. DUX4 genes specify transcription factor possessing two homeodomains. Previously, using Circular Chromosome Conformation Capture (4С) approach on population of cells, it was demonstrated that DUX4 gene clusters form frequent contacts with nucleoli. It was found also that these contacts are almost completely abolished after heat shock treatment. 4C approach as all ligation-mediated methods is capable to detect rather close interactions between chromatin loops in nuclei. In order to independently confirm the formation and the frequency of the contacts in single cells we used FISH approach. Here, we show that DUX genes in single cells form stable contacts in all tested HEK293T cells. During heat shock, DUX4 genes reversibly move 1-3 µm away from the nuclei. We conclude that interchromosomal contacts formed by nucleoli are strong, dynamic, and reversible, providing both the initiation and maintenance of a differentiated state.
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Affiliation(s)
- E S Klushevskaya
- Engelhardt Institute of Molecular Biology Russian Academy of Sciences, Moscow, Russia
| | - I R Alembekov
- Engelhardt Institute of Molecular Biology Russian Academy of Sciences, Moscow, Russia
| | - Y V Kravatsky
- Engelhardt Institute of Molecular Biology Russian Academy of Sciences, Moscow, Russia
| | - N A Tchurikov
- Engelhardt Institute of Molecular Biology Russian Academy of Sciences, Moscow, Russia.
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3
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Lerra L, Panatta M, Bär D, Zanini I, Tan JY, Pisano A, Mungo C, Baroux C, Panse VG, Marques AC, Santoro R. An RNA-dependent and phase-separated active subnuclear compartment safeguards repressive chromatin domains. Mol Cell 2024; 84:1667-1683.e10. [PMID: 38599210 PMCID: PMC11065421 DOI: 10.1016/j.molcel.2024.03.015] [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: 02/23/2023] [Revised: 10/19/2023] [Accepted: 03/16/2024] [Indexed: 04/12/2024]
Abstract
The nucleus is composed of functionally distinct membraneless compartments that undergo phase separation (PS). However, whether different subnuclear compartments are connected remains elusive. We identified a type of nuclear body with PS features composed of BAZ2A that associates with active chromatin. BAZ2A bodies depend on RNA transcription and BAZ2A non-disordered RNA-binding TAM domain. Although BAZ2A and H3K27me3 occupancies anticorrelate in the linear genome, in the nuclear space, BAZ2A bodies contact H3K27me3 bodies. BAZ2A-body disruption promotes BAZ2A invasion into H3K27me3 domains, causing H3K27me3-body loss and gene upregulation. Weak BAZ2A-RNA interactions, such as with nascent transcripts, promote BAZ2A bodies, whereas the strong binder long non-coding RNA (lncRNA) Malat1 impairs them while mediating BAZ2A association to chromatin at nuclear speckles. In addition to unraveling a direct connection between nuclear active and repressive compartments through PS mechanisms, the results also showed that the strength of RNA-protein interactions regulates this process, contributing to nuclear organization and the regulation of chromatin and gene expression.
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Affiliation(s)
- Luigi Lerra
- Department of Molecular Mechanisms of Disease (DMMD), University of Zurich, Zurich 8057, Switzerland; RNA Biology Program, Life Science Zurich Graduate School, University of Zurich, Zurich 8057, Switzerland
| | - Martina Panatta
- Department of Molecular Mechanisms of Disease (DMMD), University of Zurich, Zurich 8057, Switzerland; RNA Biology Program, Life Science Zurich Graduate School, University of Zurich, Zurich 8057, Switzerland
| | - Dominik Bär
- Department of Molecular Mechanisms of Disease (DMMD), University of Zurich, Zurich 8057, Switzerland
| | - Isabella Zanini
- Department of Molecular Mechanisms of Disease (DMMD), University of Zurich, Zurich 8057, Switzerland
| | - Jennifer Yihong Tan
- Department of Computational Biology, University of Lausanne, Lausanne 1015, Switzerland
| | - Agnese Pisano
- Institute of Medical Microbiology, University of Zurich, Zurich 8057, Switzerland
| | - Chiara Mungo
- Department of Molecular Mechanisms of Disease (DMMD), University of Zurich, Zurich 8057, Switzerland; Molecular Life Science Program, Life Science Zurich Graduate School, University of Zurich, Zurich 8057, Switzerland
| | - Célia Baroux
- Department of Plant and Microbial Biology and Zurich-Basel Plant Science Center, University of Zurich, Zurich 8057, Switzerland
| | - Vikram Govind Panse
- Institute of Medical Microbiology, University of Zurich, Zurich 8057, Switzerland
| | - Ana C Marques
- Department of Computational Biology, University of Lausanne, Lausanne 1015, Switzerland
| | - Raffaella Santoro
- Department of Molecular Mechanisms of Disease (DMMD), University of Zurich, Zurich 8057, Switzerland.
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4
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Kumari A, Vertii A. Perspective: "Current understanding of NADs dynamics and mechanisms of Disease". Gene 2024; 894:147960. [PMID: 37923094 DOI: 10.1016/j.gene.2023.147960] [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: 07/27/2023] [Revised: 10/09/2023] [Accepted: 10/31/2023] [Indexed: 11/07/2023]
Abstract
Chromatin architecture is essential for gene regulation, and multiple levels of the 3D chromatin organization exhibit dynamic changes during organismal development and cell differentiation. Heterochromatin, termed compartment B in Hi-C datasets, is a phase-separating gene-silencing form of chromatin, preferentially located at the two nuclear sites, nuclear (lamina-associate chromatin domains, LADs) and nucleoli (nucleoli-associated chromatin domains, NADs) peripheries. LADs and NADs contain both interchangeable and location-specific chromatin domains. Recent studies suggest striking dynamics in LADs and NADs during the differentiation of embryonic stem cells into neural progenitors and neurons. Here we discuss recent advances in understanding NADs changes during neuronal differentiation and future questions on how NADs integrity can contribute to healthy neurodevelopment and neurodevelopment diseases.
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Affiliation(s)
- Amrita Kumari
- Department of Molecular, Cellular and Cancer Biology, University of Massachusetts Medical School, Worcester, MA 1605, US
| | - Anastassiia Vertii
- Department of Molecular, Cellular and Cancer Biology, University of Massachusetts Medical School, Worcester, MA 1605, US.
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5
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Parra AS, Johnston CA. Phase Separation as a Driver of Stem Cell Organization and Function during Development. J Dev Biol 2023; 11:45. [PMID: 38132713 PMCID: PMC10743522 DOI: 10.3390/jdb11040045] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2023] [Revised: 12/04/2023] [Accepted: 12/08/2023] [Indexed: 12/23/2023] Open
Abstract
A properly organized subcellular composition is essential to cell function. The canonical organizing principle within eukaryotic cells involves membrane-bound organelles; yet, such structures do not fully explain cellular complexity. Furthermore, discrete non-membrane-bound structures have been known for over a century. Liquid-liquid phase separation (LLPS) has emerged as a ubiquitous mode of cellular organization without the need for formal lipid membranes, with an ever-expanding and diverse list of cellular functions that appear to be regulated by this process. In comparison to traditional organelles, LLPS can occur across wider spatial and temporal scales and involves more distinct protein and RNA complexes. In this review, we discuss the impacts of LLPS on the organization of stem cells and their function during development. Specifically, the roles of LLPS in developmental signaling pathways, chromatin organization, and gene expression will be detailed, as well as its impacts on essential processes of asymmetric cell division. We will also discuss how the dynamic and regulated nature of LLPS may afford stem cells an adaptable mode of organization throughout the developmental time to control cell fate. Finally, we will discuss how aberrant LLPS in these processes may contribute to developmental defects and disease.
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6
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Smirnov E, Molínová P, Chmúrčiaková N, Vacík T, Cmarko D. Non-canonical DNA structures in the human ribosomal DNA. Histochem Cell Biol 2023; 160:499-515. [PMID: 37750997 DOI: 10.1007/s00418-023-02233-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/15/2023] [Indexed: 09/27/2023]
Abstract
Non-canonical structures (NCS) refer to the various forms of DNA that differ from the B-conformation described by Watson and Crick. It has been found that these structures are usual components of the genome, actively participating in its essential functions. The present review is focused on the nine kinds of NCS appearing or likely to appear in human ribosomal DNA (rDNA): supercoiling structures, R-loops, G-quadruplexes, i-motifs, DNA triplexes, cruciform structures, DNA bubbles, and A and Z DNA conformations. We discuss the conditions of their generation, including their sequence specificity, distribution within the locus, dynamics, and beneficial and detrimental role in the cell.
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Affiliation(s)
- Evgeny Smirnov
- Laboratory of Cell Biology, Institute of Biology and Medical Genetics, First Faculty of Medicine, Charles University and General University Hospital in Prague, 128 00, Prague, Czech Republic.
| | - Pavla Molínová
- Laboratory of Cell Biology, Institute of Biology and Medical Genetics, First Faculty of Medicine, Charles University and General University Hospital in Prague, 128 00, Prague, Czech Republic
| | - Nikola Chmúrčiaková
- Laboratory of Cell Biology, Institute of Biology and Medical Genetics, First Faculty of Medicine, Charles University and General University Hospital in Prague, 128 00, Prague, Czech Republic
| | - Tomáš Vacík
- Laboratory of Cell Biology, Institute of Biology and Medical Genetics, First Faculty of Medicine, Charles University and General University Hospital in Prague, 128 00, Prague, Czech Republic
| | - Dušan Cmarko
- Laboratory of Cell Biology, Institute of Biology and Medical Genetics, First Faculty of Medicine, Charles University and General University Hospital in Prague, 128 00, Prague, Czech Republic
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7
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Miao J, Chen B, Xiao Y, Huang R, Xiao X, Lu S, Zhang L, Wang X, Ouyang Y, Chen X, Chen Q, Xiang Y, Guo X, Deng X, Wang L, Mai H, Zhao C. Long noncoding RNA LINC00173 induces radioresistance in nasopharyngeal carcinoma via inhibiting CHK2/P53 pathway. Cancer Gene Ther 2023; 30:1249-1259. [PMID: 37258811 DOI: 10.1038/s41417-023-00634-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2022] [Revised: 05/04/2023] [Accepted: 05/19/2023] [Indexed: 06/02/2023]
Abstract
Radiotherapy is the backbone of nasopharyngeal carcinoma (NPC), nearly 11-17% NPC patients suffered local relapse and 18-37% suffered distant metastasis mainly due to radioresistance. Therefore, the key of improving patients' survivals is to investigate the mechanism of radioresistance. In this study, we revealed that the expression level of long intergenic nonprotein coding RNA 173 (LINC00173) was significantly increased in the radioresistant NPC patients' tumour tissues compared with the radiosensitive patients by RNA-sequencing, which also predict poor prognosis in NPC. Overexpression of LINC00173 induced radioresistance of NPC cells in vitro and in vivo. Mechanistically, LINC00173 bound with checkpoint kinase 2 (CHK2) in nucleus, and impaired the irradiation-induced CHK2 phosphorylation, then suppressed the activation of P53 signalling pathway, which eventually inhibiting apoptosis and leading to radioresistance in NPC cells. In summary, LINC00173 decreases the occurrence of apoptosis through inhibiting the CHK2/P53 pathway, leads to NPC radioresistance and could be considered as a novel predictor and therapeutic target in NPC.
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Affiliation(s)
- Jingjing Miao
- Department of Nasopharyngeal Carcinoma, Sun Yat-sen University Cancer Center, State Key Laboratory of Oncology in South China, Guangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and Therapy, Guangzhou, 510060, China
| | - Boyu Chen
- Department of Experimental Research, Sun Yat-sen University Cancer Center, State Key Laboratory of Oncology in South China, Guangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and Therapy, Guangzhou, 510060, China
| | - Yunyun Xiao
- Department of Experimental Research, Sun Yat-sen University Cancer Center, State Key Laboratory of Oncology in South China, Guangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and Therapy, Guangzhou, 510060, China
| | - Runda Huang
- Department of Radiation Oncology, Sun Yat-sen University Cancer Center, State Key Laboratory of Oncology in South China, Guangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and Therapy, Guangzhou, 510060, China
| | - Xiao Xiao
- Department of Nasopharyngeal Carcinoma, Sun Yat-sen University Cancer Center, State Key Laboratory of Oncology in South China, Guangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and Therapy, Guangzhou, 510060, China
| | - Shunzhen Lu
- Department of Nasopharyngeal Carcinoma, Sun Yat-sen University Cancer Center, State Key Laboratory of Oncology in South China, Guangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and Therapy, Guangzhou, 510060, China
| | - Lu Zhang
- Department of Radiation Oncology, Sun Yat-sen University Cancer Center, State Key Laboratory of Oncology in South China, Guangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and Therapy, Guangzhou, 510060, China
| | - Xuguang Wang
- Department of Nasopharyngeal Carcinoma, Sun Yat-sen University Cancer Center, State Key Laboratory of Oncology in South China, Guangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and Therapy, Guangzhou, 510060, China
| | - Ying Ouyang
- Department of Experimental Research, Sun Yat-sen University Cancer Center, State Key Laboratory of Oncology in South China, Guangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and Therapy, Guangzhou, 510060, China
| | - Xiangfu Chen
- Department of Experimental Research, Sun Yat-sen University Cancer Center, State Key Laboratory of Oncology in South China, Guangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and Therapy, Guangzhou, 510060, China
| | - Qiuyan Chen
- Department of Nasopharyngeal Carcinoma, Sun Yat-sen University Cancer Center, State Key Laboratory of Oncology in South China, Guangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and Therapy, Guangzhou, 510060, China
| | - Yanqun Xiang
- Department of Nasopharyngeal Carcinoma, Sun Yat-sen University Cancer Center, State Key Laboratory of Oncology in South China, Guangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and Therapy, Guangzhou, 510060, China
| | - Xiang Guo
- Department of Nasopharyngeal Carcinoma, Sun Yat-sen University Cancer Center, State Key Laboratory of Oncology in South China, Guangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and Therapy, Guangzhou, 510060, China
| | - Xiaowu Deng
- Department of Radiation Oncology, Sun Yat-sen University Cancer Center, State Key Laboratory of Oncology in South China, Guangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and Therapy, Guangzhou, 510060, China
| | - Lin Wang
- Department of Nasopharyngeal Carcinoma, Sun Yat-sen University Cancer Center, State Key Laboratory of Oncology in South China, Guangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and Therapy, Guangzhou, 510060, China.
| | - Haiqiang Mai
- Department of Nasopharyngeal Carcinoma, Sun Yat-sen University Cancer Center, State Key Laboratory of Oncology in South China, Guangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and Therapy, Guangzhou, 510060, China.
| | - Chong Zhao
- Department of Nasopharyngeal Carcinoma, Sun Yat-sen University Cancer Center, State Key Laboratory of Oncology in South China, Guangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and Therapy, Guangzhou, 510060, China.
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8
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Roganowicz M, Bär D, Bersaglieri C, Aprigliano R, Santoro R. BAZ2A-RNA mediated association with TOP2A and KDM1A represses genes implicated in prostate cancer. Life Sci Alliance 2023; 6:e202301950. [PMID: 37184661 PMCID: PMC10130768 DOI: 10.26508/lsa.202301950] [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: 01/25/2023] [Revised: 04/13/2023] [Accepted: 04/17/2023] [Indexed: 05/16/2023] Open
Abstract
BAZ2A represses rRNA genes (rDNA) that are transcribed by RNA polymerase I. In prostate cancer (PCa), BAZ2A function goes beyond this role because it represses genes frequently silenced in metastatic disease. However, the mechanisms of this BAZ2A-mediated repression remain elusive. Here, we show that BAZ2A represses genes through its RNA-binding TAM domain using mechanisms differing from rDNA silencing. Although the TAM domain mediates BAZ2A recruitment to rDNA, in PCa, this is not required for BAZ2A association with target genes. Instead, the BAZ2A-TAM domain in association with RNA mediates the interaction with topoisomerase 2A (TOP2A) and histone demethylase KDM1A, whose expression positively correlates with BAZ2A levels in localized and metastatic PCa. TOP2A and KDM1A pharmacological inhibition up-regulate BAZ2A-repressed genes that are regulated by inactive enhancers bound by BAZ2A, whereas rRNA genes are not affected. Our findings showed a novel RNA-based mechanism of gene regulation in PCa. Furthermore, we determined that RNA-mediated interactions between BAZ2A and TOP2A and KDM1A repress genes critical to PCa and may prove to be useful to stratify prostate cancer risk and treatment in patients.
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Affiliation(s)
- Marcin Roganowicz
- Department of Molecular Mechanisms of Disease, DMMD, University of Zurich, Zurich, Switzerland
- RNA Biology Program, Life Science Zurich Graduate School, University of Zurich, Zurich, Switzerland
| | - Dominik Bär
- Department of Molecular Mechanisms of Disease, DMMD, University of Zurich, Zurich, Switzerland
| | - Cristiana Bersaglieri
- Department of Molecular Mechanisms of Disease, DMMD, University of Zurich, Zurich, Switzerland
| | - Rossana Aprigliano
- Department of Molecular Mechanisms of Disease, DMMD, University of Zurich, Zurich, Switzerland
| | - Raffaella Santoro
- Department of Molecular Mechanisms of Disease, DMMD, University of Zurich, Zurich, Switzerland
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9
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Tchurikov NA, Klushevskaya ES, Alembekov IR, Kretova AN, Chechetkin VR, Kravatskaya GI, Kravatsky YV. Induction of the Erythroid Differentiation of K562 Cells Is Coupled with Changes in the Inter-Chromosomal Contacts of rDNA Clusters. Int J Mol Sci 2023; 24:9842. [PMID: 37372991 DOI: 10.3390/ijms24129842] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2023] [Revised: 06/02/2023] [Accepted: 06/05/2023] [Indexed: 06/29/2023] Open
Abstract
The expression of clusters of rDNA genes influences pluripotency; however, the underlying mechanisms are not yet known. These clusters shape inter-chromosomal contacts with numerous genes controlling differentiation in human and Drosophila cells. This suggests a possible role of these contacts in the formation of 3D chromosomal structures and the regulation of gene expression in development. However, it has not yet been demonstrated whether inter-chromosomal rDNA contacts are changed during differentiation. In this study, we used human leukemia K562 cells and induced their erythroid differentiation in order to study both the changes in rDNA contacts and the expression of genes. We observed that approximately 200 sets of rDNA-contacting genes are co-expressed in different combinations in both untreated and differentiated K562 cells. rDNA contacts are changed during differentiation and coupled with the upregulation of genes whose products are mainly located in the nucleus and are highly associated with DNA- and RNA-binding, along with the downregulation of genes whose products mainly reside in the cytoplasm or intra- or extracellular vesicles. The most downregulated gene is ID3, which is known as an inhibitor of differentiation, and thus should be switched off to allow for differentiation. Our data suggest that the differentiation of K562 cells leads to alterations in the inter-chromosomal contacts of rDNA clusters and 3D structures in particular chromosomal regions as well as to changes in the expression of genes located in the corresponding chromosomal domains. We conclude that approximately half of the rDNA-contacting genes are co-expressed in human cells and that rDNA clusters are involved in the global regulation of gene expression.
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Affiliation(s)
- Nickolai A Tchurikov
- Department of Epigenetic Mechanisms of Gene Expression Regulation, Engelhardt Institute of Molecular Biology Russian Academy of Sciences, 119334 Moscow, Russia
| | - Elena S Klushevskaya
- Department of Epigenetic Mechanisms of Gene Expression Regulation, Engelhardt Institute of Molecular Biology Russian Academy of Sciences, 119334 Moscow, Russia
| | - Ildar R Alembekov
- Department of Epigenetic Mechanisms of Gene Expression Regulation, Engelhardt Institute of Molecular Biology Russian Academy of Sciences, 119334 Moscow, Russia
| | - Antonina N Kretova
- Department of Epigenetic Mechanisms of Gene Expression Regulation, Engelhardt Institute of Molecular Biology Russian Academy of Sciences, 119334 Moscow, Russia
| | - Vladimir R Chechetkin
- Department of Epigenetic Mechanisms of Gene Expression Regulation, Engelhardt Institute of Molecular Biology Russian Academy of Sciences, 119334 Moscow, Russia
| | - Galina I Kravatskaya
- Department of Epigenetic Mechanisms of Gene Expression Regulation, Engelhardt Institute of Molecular Biology Russian Academy of Sciences, 119334 Moscow, Russia
| | - Yuri V Kravatsky
- Department of Epigenetic Mechanisms of Gene Expression Regulation, Engelhardt Institute of Molecular Biology Russian Academy of Sciences, 119334 Moscow, Russia
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Engelhardt Institute of Molecular Biology Russian Academy of Sciences, 119334 Moscow, Russia
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10
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Pei H, Dai Y, Yu Y, Tang J, Cao Z, Zhang Y, Li B, Nie J, Hei TK, Zhou G. The Tumorigenic Effect of lncRNA AFAP1-AS1 is Mediated by Translated Peptide ATMLP Under the Control of m 6 A Methylation. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2023; 10:e2300314. [PMID: 36871154 PMCID: PMC10161021 DOI: 10.1002/advs.202300314] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/13/2023] [Indexed: 05/06/2023]
Abstract
Long noncoding RNAs (lncRNAs) in eukaryotic transcripts have long been believed to regulate various aspects of cellular processes, including carcinogenesis. Herein, it is found that lncRNA AFAP1-AS1 encodes a conserved 90-amino acid peptide located on mitochondria, named lncRNA AFAP1-AS1 translated mitochondrial-localized peptide (ATMLP), and it is not the lncRNA but the peptide that promotes the malignancy of nonsmall cell lung cancer (NSCLC). As the tumor progresses, the serum level of ATMLP increases. NSCLC patients with high levels of ATMLP display poorer prognosis. Translation of ATMLP is controlled by m6 A methylation at the 1313 adenine locus of AFAP1-AS1. Mechanistically, ATMLP binds to the 4-nitrophenylphosphatase domain and non-neuronal SNAP25-like protein homolog 1 (NIPSNAP1) and inhibits its transport from the inner to the outer mitochondrial membrane, which antagonizes the NIPSNAP1-mediated regulation of cell autolysosome formation. The findings uncover a complex regulatory mechanism of NSCLC malignancy orchestrated by a peptide encoded by a lncRNA. A comprehensive judgment of the application prospects of ATMLP as an early diagnostic biomarker for NSCLC is also made.
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Affiliation(s)
- Hailong Pei
- State Key Laboratory of Radiation Medicine and Protection, School of Radiation Medicine and Protection, Suzhou Medical College of Soochow University, Jiangsu, Suzhou, 215123, P. R. China
| | - Yingchu Dai
- State Key Laboratory of Radiation Medicine and Protection, School of Radiation Medicine and Protection, Suzhou Medical College of Soochow University, Jiangsu, Suzhou, 215123, P. R. China
| | - Yongduo Yu
- State Key Laboratory of Radiation Medicine and Protection, School of Radiation Medicine and Protection, Suzhou Medical College of Soochow University, Jiangsu, Suzhou, 215123, P. R. China
| | - Jiaxin Tang
- State Key Laboratory of Radiation Medicine and Protection, School of Radiation Medicine and Protection, Suzhou Medical College of Soochow University, Jiangsu, Suzhou, 215123, P. R. China
| | - Zhifei Cao
- Department of Pathology, The Second Affiliated Hospital of Soochow University, Jiangsu, Suzhou, 215004, P. R. China
| | - Yongsheng Zhang
- Department of Pathology, The Second Affiliated Hospital of Soochow University, Jiangsu, Suzhou, 215004, P. R. China
| | - Bingyan Li
- State Key Laboratory of Radiation Medicine and Protection, School of Radiation Medicine and Protection, Suzhou Medical College of Soochow University, Jiangsu, Suzhou, 215123, P. R. China
| | - Jing Nie
- State Key Laboratory of Radiation Medicine and Protection, School of Radiation Medicine and Protection, Suzhou Medical College of Soochow University, Jiangsu, Suzhou, 215123, P. R. China
| | - Tom K Hei
- Center for Radiological Research, College of Physician and Surgeons, Columbia University, New York, NY, 10032, USA
| | - Guangming Zhou
- State Key Laboratory of Radiation Medicine and Protection, School of Radiation Medicine and Protection, Suzhou Medical College of Soochow University, Jiangsu, Suzhou, 215123, P. R. China
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11
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Rodrigues A, MacQuarrie KL, Freeman E, Lin A, Willis AB, Xu Z, Alvarez AA, Ma Y, White BEP, Foltz DR, Huang S. Nucleoli and the nucleoli-centromere association are dynamic during normal development and in cancer. Mol Biol Cell 2023; 34:br5. [PMID: 36753381 PMCID: PMC10092642 DOI: 10.1091/mbc.e22-06-0237] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2022] [Revised: 01/19/2023] [Accepted: 01/30/2023] [Indexed: 02/09/2023] Open
Abstract
Centromeres are known to cluster around nucleoli in Drosophila and mammalian cells, but the significance of the nucleoli-centromere interaction remains underexplored. To determine whether the interaction is dynamic under different physiological and pathological conditions, we examined nucleolar structure and centromeres at various differentiation stages using cell culture models and the results showed dynamic changes in nucleolar characteristics and nucleoli-centromere interactions through differentiation and in cancer cells. Embryonic stem cells usually have a single large nucleolus, which is clustered with a high percentage of centromeres. As cells differentiate into intermediate states, the nucleolar number increases and the centromere association decreases. In terminally differentiated cells, including myotubes, neurons, and keratinocytes, the number of nucleoli and their association with centromeres are at the lowest. Cancer cells demonstrate the pattern of nucleoli number and nucleoli-centromere association that is akin to proliferative cell types, suggesting that nucleolar reorganization and changes in nucleoli-centromere interactions may play a role in facilitating malignant transformation. This idea is supported in a case of pediatric rhabdomyosarcoma, in which induced differentiation reduces the nucleolar number and centromere association. These findings suggest active roles of nucleolar structure in centromere function and genome organization critical for cellular function in both normal development and cancer.
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Affiliation(s)
- Aaron Rodrigues
- Department of Cell and Developmental Biology, Northwestern University Feinberg School of Medicine, Chicago, IL 60611
| | - Kyle L. MacQuarrie
- Division of Hematology, Oncology, and Stem Cell Transplantation, Department of Pediatrics, Northwestern University Feinberg School of Medicine, Chicago, IL 60611
| | - Emma Freeman
- Department of Cell and Developmental Biology, Northwestern University Feinberg School of Medicine, Chicago, IL 60611
| | - Alicia Lin
- Department of Cell and Developmental Biology, Northwestern University Feinberg School of Medicine, Chicago, IL 60611
| | - Alexander B. Willis
- Department of Biochemistry and Molecular Genetics, Northwestern University Feinberg School of Medicine, Chicago, IL 60611
| | - Zhaofa Xu
- Departments of Pediatrics, Neurology and Neuroscience, Northwestern University Feinberg School of Medicine, Chicago, IL 60611
- Ann & Robert H. Lurie Children’s Hospital of Chicago, Chicago, IL 60611
| | - Angel A. Alvarez
- Stem Cell Core and Ken & Ruth Davee Department of Neurology, Northwestern University Feinberg School of Medicine, Chicago, IL 60611
| | - Yongchao Ma
- Departments of Pediatrics, Neurology and Neuroscience, Northwestern University Feinberg School of Medicine, Chicago, IL 60611
- Ann & Robert H. Lurie Children’s Hospital of Chicago, Chicago, IL 60611
| | - Bethany E. Perez White
- Department of Dermatology and Skin Biology and Diseases Resource-based Center, Northwestern University Feinberg School of Medicine, Chicago, IL 60611
| | - Daniel R. Foltz
- Department of Biochemistry and Molecular Genetics, Northwestern University Feinberg School of Medicine, Chicago, IL 60611
| | - Sui Huang
- Department of Cell and Developmental Biology, Northwestern University Feinberg School of Medicine, Chicago, IL 60611
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12
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Sun Y, Hu X, Qiu D, Zhang Z, Lei L. rDNA Transcription in Developmental Diseases and Stem Cells. Stem Cell Rev Rep 2023; 19:839-852. [PMID: 36633782 DOI: 10.1007/s12015-023-10504-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/01/2023] [Indexed: 01/13/2023]
Abstract
As the first and rate-limiting step in ribosome biogenesis, rDNA transcription undergoes significant dynamic changes during cell pluripotency alteration. Over the past decades, rDNA activity has demonstrated dynamic changes, but most people view it as passive compliance with cellular needs. The evidence for rDNA transcriptional activity determining stem cell pluripotency is growing as research advances, resulting in the arrest of embryonic development and impairment of stem cell lines stemness by rDNA transcription inhibition. The exact mechanism by which rDNA activation influences pluripotency remains unknown. The first objective of this opinion article is to describe rDNA changes in the pathological and physiological course of life, including developmental diseases, tumor genesis, and stem cell differentiation. After that, we propose three hypotheses regarding rDNA regulation of pluripotency: 1) Specialized ribosomes synthesized from rDNA variant, 2) Nucleolar stress induced by the drop of rDNA transcription, 3) Interchromosomal interactions between rDNA and other genes. The pluripotency regulatory center is expected to focus strongly on rDNA. A small molecule inhibitor of rDNA is used to treat tumors caused by abnormal pluripotency activation. By understanding how rDNA regulates pluripotency, we hope to treat developmental diseases and safely apply somatic cell reprogramming in clinical settings.
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Affiliation(s)
- Yuchen Sun
- Department of Histology and Embryology, Basic Medical Science College, Harbin Medical University, 194 Xuefu Rd, Nangang District, Harbin, Heilongjiang Province, People's Republic of China, 150081
| | - Xinglin Hu
- Department of Histology and Embryology, Basic Medical Science College, Harbin Medical University, 194 Xuefu Rd, Nangang District, Harbin, Heilongjiang Province, People's Republic of China, 150081
| | - Dan Qiu
- Department of Histology and Embryology, Basic Medical Science College, Harbin Medical University, 194 Xuefu Rd, Nangang District, Harbin, Heilongjiang Province, People's Republic of China, 150081
| | - Zhijing Zhang
- Department of Histology and Embryology, Basic Medical Science College, Harbin Medical University, 194 Xuefu Rd, Nangang District, Harbin, Heilongjiang Province, People's Republic of China, 150081
| | - Lei Lei
- Department of Histology and Embryology, Basic Medical Science College, Harbin Medical University, 194 Xuefu Rd, Nangang District, Harbin, Heilongjiang Province, People's Republic of China, 150081.
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13
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Ballmer D, Tardat M, Ortiz R, Graff-Meyer A, Ozonov E, Genoud C, Peters A, Fanourgakis G. HP1 proteins regulate nucleolar structure and function by secluding pericentromeric constitutive heterochromatin. Nucleic Acids Res 2022; 51:117-143. [PMID: 36533441 PMCID: PMC9841413 DOI: 10.1093/nar/gkac1159] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2022] [Revised: 10/29/2022] [Accepted: 12/13/2022] [Indexed: 12/23/2022] Open
Abstract
Nucleoli are nuclear compartments regulating ribosome biogenesis and cell growth. In embryonic stem cells (ESCs), nucleoli containing transcriptionally active ribosomal genes are spatially separated from pericentromeric satellite repeat sequences packaged in largely repressed constitutive heterochromatin (PCH). To date, mechanisms underlying such nuclear partitioning and the physiological relevance thereof are unknown. Here we show that repressive chromatin at PCH ensures structural integrity and function of nucleoli during cell cycle progression. Loss of heterochromatin proteins HP1α and HP1β causes deformation of PCH, with reduced H3K9 trimethylation (H3K9me3) and HP1γ levels, absence of H4K20me3 and upregulated major satellites expression. Spatially, derepressed PCH aberrantly associates with nucleoli accumulating severe morphological defects during S/G2 cell cycle progression. Hp1α/β deficiency reduces cell proliferation, ribosomal RNA biosynthesis and mobility of Nucleophosmin, a major nucleolar component. Nucleolar integrity and function require HP1α/β proteins to be recruited to H3K9me3-marked PCH and their ability to dimerize. Correspondingly, ESCs deficient for both Suv39h1/2 H3K9 HMTs display similar nucleolar defects. In contrast, Suv4-20h1/2 mutant ESCs lacking H4K20me3 at PCH do not. Suv39h1/2 and Hp1α/β deficiency-induced nucleolar defects are reminiscent of those defining human ribosomopathy disorders. Our results reveal a novel role for SUV39H/HP1-marked repressive constitutive heterochromatin in regulating integrity, function and physiology of nucleoli.
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Affiliation(s)
- Daniel Ballmer
- Friedrich Miescher Institute for Biomedical Research, Maulbeerstrasse 66, 4058 Basel, Switzerland,Faculty of Sciences, University of Basel, 4056 Basel, Switzerland
| | - Mathieu Tardat
- Friedrich Miescher Institute for Biomedical Research, Maulbeerstrasse 66, 4058 Basel, Switzerland
| | - Raphael Ortiz
- Friedrich Miescher Institute for Biomedical Research, Maulbeerstrasse 66, 4058 Basel, Switzerland
| | - Alexandra Graff-Meyer
- Friedrich Miescher Institute for Biomedical Research, Maulbeerstrasse 66, 4058 Basel, Switzerland
| | - Evgeniy A Ozonov
- Friedrich Miescher Institute for Biomedical Research, Maulbeerstrasse 66, 4058 Basel, Switzerland
| | - Christel Genoud
- Friedrich Miescher Institute for Biomedical Research, Maulbeerstrasse 66, 4058 Basel, Switzerland
| | | | - Grigorios Fanourgakis
- Friedrich Miescher Institute for Biomedical Research, Maulbeerstrasse 66, 4058 Basel, Switzerland
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14
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Yan D, Hua L. Nucleolar stress: Friend or foe in cardiac function? Front Cardiovasc Med 2022; 9:1045455. [PMID: 36386352 PMCID: PMC9659567 DOI: 10.3389/fcvm.2022.1045455] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2022] [Accepted: 10/17/2022] [Indexed: 03/14/2024] Open
Abstract
Studies in the past decades have uncovered an emerging role of the nucleolus in stress response and human disease progression. The disruption of ribosome biogenesis in the nucleolus causes aberrant nucleolar architecture and function, termed nucleolar stress, to initiate stress-responsive pathways via nucleolar release sequestration of various proteins. While data obtained from both clinical and basic investigations have faithfully demonstrated an involvement of nucleolar stress in the pathogenesis of cardiomyopathy, much remains unclear regarding its precise role in the progression of cardiac diseases. On the one hand, the initiation of nucleolar stress following acute myocardial damage leads to the upregulation of various cardioprotective nucleolar proteins, including nucleostemin (NS), nucleophosmin (NPM) and nucleolin (NCL). As a result, nucleolar stress plays an important role in facilitating the survival and repair of cardiomyocytes. On the other hand, abnormalities in nucleolar architecture and function are correlated with the deterioration of cardiac diseases. Notably, the cardiomyocytes of advanced ischemic and dilated cardiomyopathy display impaired silver-stained nucleolar organiser regions (AgNORs) and enlarged nucleoli, resembling the characteristics of tissue aging. Collectively, nucleolar abnormalities are critically involved in the development of cardiac diseases.
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Affiliation(s)
- Daliang Yan
- Department of Cardiovascular Surgery, Taizhou People’s Hospital, Taizhou, China
| | - Lu Hua
- Department of Oncology, Taizhou People’s Hospital, Taizhou, China
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15
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Fu Y, Liu Y, Wen T, Fang J, Chen Y, Zhou Z, Gu X, Wu H, Sheng J, Xu Z, Zou W, Chen B. Real-time imaging of RNA polymerase I activity in living human cells. J Biophys Biochem Cytol 2022; 222:213608. [PMID: 36282216 PMCID: PMC9606689 DOI: 10.1083/jcb.202202110] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2022] [Revised: 08/19/2022] [Accepted: 09/27/2022] [Indexed: 11/22/2022] Open
Abstract
RNA polymerase I (Pol I) synthesizes about 60% of cellular RNA by transcribing multiple copies of the ribosomal RNA gene (rDNA). The transcriptional activity of Pol I controls the level of ribosome biogenesis and cell growth. However, there is currently a lack of methods for monitoring Pol I activity in real time. Here, we develop LiveArt (live imaging-based analysis of rDNA transcription) to visualize and quantify the spatiotemporal dynamics of endogenous ribosomal RNA (rRNA) synthesis. LiveArt reveals mitotic silencing and reactivation of rDNA transcription, as well as the transcriptional kinetics of interphase rDNA. Using LiveArt, we identify SRFBP1 as a potential regulator of rRNA synthesis. We show that rDNA transcription occurs in bursts and can be altered by modulating burst duration and amplitude. Importantly, LiveArt is highly effective in the screening application for anticancer drugs targeting Pol I transcription. These approaches pave the way for a deeper understanding of the mechanisms underlying nucleolar functions.
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Affiliation(s)
- Yujuan Fu
- Department of Cell Biology and Bone Marrow Transplantation Center of the First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China,Liangzhu Laboratory, Zhejiang University Medical Center, Hangzhou, China
| | - Yaxin Liu
- Institute of Environmental Medicine, and Department of General Surgery, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Tanye Wen
- Department of Cell Biology and Bone Marrow Transplantation Center of the First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Jie Fang
- Department of Cell Biology and Bone Marrow Transplantation Center of the First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China,Liangzhu Laboratory, Zhejiang University Medical Center, Hangzhou, China
| | - Yalong Chen
- Department of Cell Biology and Bone Marrow Transplantation Center of the First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Ziying Zhou
- Department of Cell Biology and Bone Marrow Transplantation Center of the First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Xinyi Gu
- Department of Cell Biology and Bone Marrow Transplantation Center of the First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Hao Wu
- Department of Cell Biology and Bone Marrow Transplantation Center of the First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Jinghao Sheng
- Institute of Environmental Medicine, and Department of General Surgery, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Zhengping Xu
- Liangzhu Laboratory, Zhejiang University Medical Center, Hangzhou, China,Institute of Environmental Medicine, and Department of General Surgery, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Wei Zou
- The Fourth Affiliated Hospital, Zhejiang University School of Medicine, Yiwu, China,Insititute of Translational Medicine, Zhejiang University, Hangzhou, China,Wei Zou:
| | - Baohui Chen
- Department of Cell Biology and Bone Marrow Transplantation Center of the First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China,Liangzhu Laboratory, Zhejiang University Medical Center, Hangzhou, China,Institute of Hematology, Zhejiang University and Zhejiang Engineering Laboratory for Stem Cell and Immunotherapy, Hangzhou, China,Zhejiang Provincial Key Laboratory of Genetic & Developmental Disorders, Hangzhou, China,Correspondence to Baohui Chen:
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16
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Nucleolus and Nucleolar Stress: From Cell Fate Decision to Disease Development. Cells 2022; 11:cells11193017. [PMID: 36230979 PMCID: PMC9563748 DOI: 10.3390/cells11193017] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2022] [Revised: 09/19/2022] [Accepted: 09/22/2022] [Indexed: 11/30/2022] Open
Abstract
Besides the canonical function in ribosome biogenesis, there have been significant recent advances towards the fascinating roles of the nucleolus in stress response, cell destiny decision and disease progression. Nucleolar stress, an emerging concept describing aberrant nucleolar structure and function as a result of impaired rRNA synthesis and ribosome biogenesis under stress conditions, has been linked to a variety of signaling transductions, including but not limited to Mdm2-p53, NF-κB and HIF-1α pathways. Studies have uncovered that nucleolus is a stress sensor and signaling hub when cells encounter various stress conditions, such as nutrient deprivation, DNA damage and oxidative and thermal stress. Consequently, nucleolar stress plays a pivotal role in the determination of cell fate, such as apoptosis, senescence, autophagy and differentiation, in response to stress-induced damage. Nucleolar homeostasis has been involved in the pathogenesis of various chronic diseases, particularly tumorigenesis, neurodegenerative diseases and metabolic disorders. Mechanistic insights have revealed the indispensable role of nucleolus-initiated signaling in the progression of these diseases. Accordingly, the intervention of nucleolar stress may pave the path for developing novel therapies against these diseases. In this review, we systemically summarize recent findings linking the nucleolus to stress responses, signaling transduction and cell-fate decision, set the spotlight on the mechanisms by which nucleolar stress drives disease progression, and highlight the merit of the intervening nucleolus in disease treatment.
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17
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Feng S, Manley JL. Beyond rRNA: nucleolar transcription generates a complex network of RNAs with multiple roles in maintaining cellular homeostasis. Genes Dev 2022; 36:876-886. [PMID: 36207140 PMCID: PMC9575697 DOI: 10.1101/gad.349969.122] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022]
Abstract
Nucleoli are the major cellular compartments for the synthesis of rRNA and assembly of ribosomes, the macromolecular complexes responsible for protein synthesis. Given the abundance of ribosomes, there is a huge demand for rRNA, which indeed constitutes ∼80% of the mass of RNA in the cell. Thus, nucleoli are characterized by extensive transcription of multiple rDNA loci by the dedicated polymerase, RNA polymerase (Pol) I. However, in addition to producing rRNAs, there is considerable additional transcription in nucleoli by RNA Pol II as well as Pol I, producing multiple noncoding (nc) and, in one instance, coding RNAs. In this review, we discuss important features of these transcripts, which often appear species-specific and reflect transcription antisense to pre-rRNA by Pol II and within the intergenic spacer regions on both strands by both Pol I and Pol II. We discuss how expression of these RNAs is regulated, their propensity to form cotranscriptional R loops, and how they modulate rRNA transcription, nucleolar structure, and cellular homeostasis more generally.
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18
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Genome-wide maps of nucleolus interactions reveal distinct layers of repressive chromatin domains. Nat Commun 2022; 13:1483. [PMID: 35304483 PMCID: PMC8933459 DOI: 10.1038/s41467-022-29146-2] [Citation(s) in RCA: 25] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2021] [Accepted: 02/28/2022] [Indexed: 12/22/2022] Open
Abstract
Eukaryotic chromosomes are folded into hierarchical domains, forming functional compartments. Nuclear periphery and nucleolus are two nuclear landmarks contributing to repressive chromosome architecture. However, while the role of nuclear lamina (NL) in genome organization has been well documented, the function of the nucleolus remains under-investigated due to the lack of methods for the identification of nucleolar associated domains (NADs). Here we have established DamID- and HiC-based methodologies to generate accurate genome-wide maps of NADs in embryonic stem cells (ESCs) and neural progenitor cells (NPCs), revealing layers of genome compartmentalization with distinct, repressive chromatin states based on the interaction with the nucleolus, NL, or both. NADs show higher H3K9me2 and lower H3K27me3 content than regions exclusively interacting with NL. Upon ESC differentiation into NPCs, chromosomes around the nucleolus acquire a more compact, rigid architecture with neural genes moving away from nucleoli and becoming unlocked for later activation. Further, histone modifications and the interaction strength within A and B compartments of NADs and LADs in ESCs set the choice to associate with NL or nucleoli upon dissociation from their respective compartments during differentiation. The methodologies here developed will make possible to include the nucleolar contribution in nuclear space and genome function in diverse biological systems.
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19
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Epigenetic regulation of human non-coding RNA gene transcription. Biochem Soc Trans 2022; 50:723-736. [PMID: 35285478 DOI: 10.1042/bst20210860] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2022] [Revised: 02/18/2022] [Accepted: 02/21/2022] [Indexed: 12/12/2022]
Abstract
Recent investigations on the non-protein-coding transcriptome of human cells have revealed previously hidden layers of gene regulation relying on regulatory non-protein-coding (nc) RNAs, including the widespread ncRNA-dependent regulation of epigenetic chromatin states and of mRNA translation and stability. However, despite its centrality, the epigenetic regulation of ncRNA genes has received relatively little attention. In this mini-review, we attempt to provide a synthetic account of recent literature suggesting an unexpected complexity in chromatin-dependent regulation of ncRNA gene transcription by the three human nuclear RNA polymerases. Emerging common features, like the heterogeneity of chromatin states within ncRNA multigene families and their influence on 3D genome organization, point to unexplored issues whose investigation could lead to a better understanding of the whole human epigenomic network.
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20
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Tchurikov NA, Klushevskaya ES, Alembekov IR, Bukreeva AS, Kretova AN, Chechetkin VR, Kravatskaya GI, Kravatsky YV. Fragments of rDNA Genes Scattered over the Human Genome Are Targets of Small RNAs. Int J Mol Sci 2022; 23:ijms23063014. [PMID: 35328433 PMCID: PMC8954558 DOI: 10.3390/ijms23063014] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2022] [Revised: 03/08/2022] [Accepted: 03/09/2022] [Indexed: 02/06/2023] Open
Abstract
Small noncoding RNAs of different origins and classes play several roles in the regulation of gene expression. Here, we show that diverged and rearranged fragments of rDNA units are scattered throughout the human genome and that endogenous small noncoding RNAs are processed by the Microprocessor complex from specific regions of ribosomal RNAs shaping hairpins. These small RNAs correspond to particular sites inside the fragments of rDNA that mostly reside in intergenic regions or the introns of about 1500 genes. The targets of these small ribosomal RNAs (srRNAs) are characterized by a set of epigenetic marks, binding sites of Pol II, RAD21, CBP, and P300, DNase I hypersensitive sites, and by enrichment or depletion of active histone marks. In HEK293T cells, genes that are targeted by srRNAs (srRNA target genes) are involved in differentiation and development. srRNA target genes are enriched with more actively transcribed genes. Our data suggest that remnants of rDNA sequences and srRNAs may be involved in the upregulation or downregulation of a specific set of genes in human cells. These results have implications for diverse fields, including epigenetics and gene therapy.
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Affiliation(s)
- Nickolai A. Tchurikov
- Department of Epigenetic Mechanisms of Gene Expression Regulation, Engelhardt Institute of Molecular Biology Russian Academy of Sciences, 119334 Moscow, Russia; (E.S.K.); (I.R.A.); (A.S.B.); (A.N.K.); (V.R.C.); (G.I.K.); (Y.V.K.)
- Correspondence:
| | - Elena S. Klushevskaya
- Department of Epigenetic Mechanisms of Gene Expression Regulation, Engelhardt Institute of Molecular Biology Russian Academy of Sciences, 119334 Moscow, Russia; (E.S.K.); (I.R.A.); (A.S.B.); (A.N.K.); (V.R.C.); (G.I.K.); (Y.V.K.)
| | - Ildar R. Alembekov
- Department of Epigenetic Mechanisms of Gene Expression Regulation, Engelhardt Institute of Molecular Biology Russian Academy of Sciences, 119334 Moscow, Russia; (E.S.K.); (I.R.A.); (A.S.B.); (A.N.K.); (V.R.C.); (G.I.K.); (Y.V.K.)
| | - Anastasiia S. Bukreeva
- Department of Epigenetic Mechanisms of Gene Expression Regulation, Engelhardt Institute of Molecular Biology Russian Academy of Sciences, 119334 Moscow, Russia; (E.S.K.); (I.R.A.); (A.S.B.); (A.N.K.); (V.R.C.); (G.I.K.); (Y.V.K.)
| | - Antonina N. Kretova
- Department of Epigenetic Mechanisms of Gene Expression Regulation, Engelhardt Institute of Molecular Biology Russian Academy of Sciences, 119334 Moscow, Russia; (E.S.K.); (I.R.A.); (A.S.B.); (A.N.K.); (V.R.C.); (G.I.K.); (Y.V.K.)
| | - Vladimir R. Chechetkin
- Department of Epigenetic Mechanisms of Gene Expression Regulation, Engelhardt Institute of Molecular Biology Russian Academy of Sciences, 119334 Moscow, Russia; (E.S.K.); (I.R.A.); (A.S.B.); (A.N.K.); (V.R.C.); (G.I.K.); (Y.V.K.)
| | - Galina I. Kravatskaya
- Department of Epigenetic Mechanisms of Gene Expression Regulation, Engelhardt Institute of Molecular Biology Russian Academy of Sciences, 119334 Moscow, Russia; (E.S.K.); (I.R.A.); (A.S.B.); (A.N.K.); (V.R.C.); (G.I.K.); (Y.V.K.)
| | - Yuri V. Kravatsky
- Department of Epigenetic Mechanisms of Gene Expression Regulation, Engelhardt Institute of Molecular Biology Russian Academy of Sciences, 119334 Moscow, Russia; (E.S.K.); (I.R.A.); (A.S.B.); (A.N.K.); (V.R.C.); (G.I.K.); (Y.V.K.)
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Engelhardt Institute of Molecular Biology Russian Academy of Sciences, 119334 Moscow, Russia
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21
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In vivo CRISPR screening identifies BAZ2 chromatin remodelers as druggable regulators of mammalian liver regeneration. Cell Stem Cell 2022; 29:372-385.e8. [PMID: 35090595 PMCID: PMC8897233 DOI: 10.1016/j.stem.2022.01.001] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2020] [Revised: 09/17/2021] [Accepted: 12/30/2021] [Indexed: 12/17/2022]
Abstract
Identifying new pathways that regulate mammalian regeneration is challenging due to the paucity of in vivo screening approaches. We employed pooled CRISPR knockout and activation screening in the regenerating liver to evaluate 165 chromatin regulatory proteins. Both screens identified the imitation-SWI chromatin remodeling components Baz2a and Baz2b, not previously implicated in regeneration. In vivo sgRNA, siRNA, and knockout strategies against either paralog confirmed increased regeneration. Distinct BAZ2-specific bromodomain inhibitors, GSK2801 and BAZ2-ICR, resulted in accelerated liver healing after diverse injuries. Inhibitor-treated mice also exhibited improved healing in an inflammatory bowel disease model, suggesting multi-tissue applicability. Transcriptomics on regenerating livers showed increases in ribosomal and cell cycle mRNAs. Surprisingly, CRISPRa screening to define mechanisms showed that overproducing Rpl10a or Rpl24 was sufficient to drive regeneration, whereas Rpl24 haploinsufficiency was rate limiting for BAZ2 inhibition-mediated regeneration. The discovery of regenerative roles for imitation-SWI components provides immediate strategies to enhance tissue repair.
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22
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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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23
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Denisenko O. Epigenetics of Ribosomal RNA Genes. BIOCHEMISTRY. BIOKHIMIIA 2022; 87:S103-S131. [PMID: 35501990 DOI: 10.1134/s0006297922140097] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/27/2021] [Revised: 10/11/2021] [Accepted: 10/12/2021] [Indexed: 06/14/2023]
Abstract
This review is focused on biology of genes encoding ribosomal RNA (rRNA) in mammals. rRNA is a structural component of the most abundant cellular molecule, the ribosome. There are many copies of rRNA genes per genome that are under tight transcriptional control by epigenetic mechanisms serving to meet cellular needs in protein synthesis. Curiously, only a fraction of rRNA genes is used even in the fast-growing cells, raising a question why unused copies of these genes have not been lost during evolution. Two plausible explanations are discussed. First, there is evidence that besides their direct function in production of rRNA, ribosomal RNA genes are involved in regulation of many other genes in the nucleus by forming either temporary or persistent complexes with these genes. Second, it seems that rRNA genes also play a role in the maintenance of genome stability, where lower copy number of rRNA genes destabilizes the genome. These "additional" functions of rRNA genes make them recurrent candidate drivers of chronic human diseases and aging. Experimental support for the involvement of these genes in human diseases and potential mechanisms are also discussed.
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Affiliation(s)
- Oleg Denisenko
- Department of Medicine, University of Washington, Seattle, WA, USA.
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24
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Cockrell AJ, Gerton JL. Nucleolar Organizer Regions as Transcription-Based Scaffolds of Nucleolar Structure and Function. Results Probl Cell Differ 2022; 70:551-580. [PMID: 36348121 DOI: 10.1007/978-3-031-06573-6_19] [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] [Indexed: 06/16/2023]
Abstract
Eukaryotic genomes maintain multiple copies of ribosomal DNA gene repeats in tandem arrays to provide sufficient ribosomal RNAs to make ribosomes. These DNA repeats are the most highly transcribed regions of the genome, with dedicated transcriptional machinery to manage the enormous task of producing more than 50% of the total RNA in a proliferating cell. The arrays are called nucleolar organizer regions (NORs) and constitute the scaffold of the nucleolar compartment, where ribosome biogenesis occurs. Advances in molecular and cellular biology have brought great insights into how these arrays are transcribed and organized within genomes. Much of their biology is driven by their high transcription level, which has also driven the development of unique methods to understand rDNA gene activity, beginning with classic techniques such as silver staining and Miller spreads. However, the application of modern methodologies such as CRISPR gene editing, super-resolution microscopy, and long-read sequencing has enabled recent advances described herein, with many more discoveries possible soon. This chapter highlights what is known about NOR transcription and organization and the techniques applied historically and currently. Given the potential for NORs to impact organismal health and disease, as highlighted at the end of the chapter, the field must continue to develop and apply innovative analysis to understand genetic, epigenetic, and organizer properties of the ribosomal DNA repeats.
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Affiliation(s)
- Alexandria J Cockrell
- Stowers Institute for Medical Research, Kansas City, MO, USA
- Department of Biochemistry and Molecular Biology, University of Kansas Medical Center, Kansas City, KS, USA
| | - Jennifer L Gerton
- Stowers Institute for Medical Research, Kansas City, MO, USA.
- Department of Biochemistry and Molecular Biology, University of Kansas Medical Center, Kansas City, KS, USA.
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25
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Feng S, Manley JL. Replication protein A associates with nucleolar R loops and regulates rRNA transcription and nucleolar morphology. Genes Dev 2021; 35:1579-1594. [PMID: 34819354 PMCID: PMC8653787 DOI: 10.1101/gad.348858.121] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2021] [Accepted: 10/22/2021] [Indexed: 11/24/2022]
Abstract
Here, Feng and Manley report novel functions of the DNA replication and repair factor replication protein A (RPA) in control of nucleolar homeostasis. Their findings both indicate new roles for RPA in nucleoli through pre-rRNA transcriptional control and also emphasize that RPA function in nucleolar homeostasis is linked to R-loop resolution under both physiological and pathological conditions. The nucleolus is an important cellular compartment in which ribosomal RNAs (rRNAs) are transcribed and where certain stress pathways that are crucial for cell growth are coordinated. Here we report novel functions of the DNA replication and repair factor replication protein A (RPA) in control of nucleolar homeostasis. We show that loss of the DNA:RNA helicase senataxin (SETX) promotes RPA nucleolar localization, and that this relocalization is dependent on the presence of R loops. Notably, this nucleolar RPA phenotype was also observed in the presence of camptothecin (CPT)-induced genotoxic stress, as well as in SETX-deficient AOA2 patient fibroblasts. Extending these results, we found that RPA is recruited to rDNA following CPT treatment, where RPA prevents R-loop-induced DNA double-strand breaks. Furthermore, we show that loss of RPA significantly decreased 47S pre-rRNA levels, which was accompanied by increased expression of both RNAP II-mediated “promoter and pre-rRNA antisense” RNA as well as RNAP I-transcribed intragenic spacer RNAs. Finally, and likely reflecting the above, we found that loss of RPA promoted nucleolar structural disorganization, characterized by the appearance of reduced size nucleoli. Our findings both indicate new roles for RPA in nucleoli through pre-rRNA transcriptional control and also emphasize that RPA function in nucleolar homeostasis is linked to R-loop resolution under both physiological and pathological conditions.
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Affiliation(s)
- Shuang Feng
- Department of Biological Sciences, Columbia University, New York, New York 10027, USA
| | - James L Manley
- Department of Biological Sciences, Columbia University, New York, New York 10027, USA
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26
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Yu H, Sun Z, Tan T, Pan H, Zhao J, Zhang L, Chen J, Lei A, Zhu Y, Chen L, Xu Y, Liu Y, Chen M, Sheng J, Xu Z, Qian P, Li C, Gao S, Daley GQ, Zhang J. rRNA biogenesis regulates mouse 2C-like state by 3D structure reorganization of peri-nucleolar heterochromatin. Nat Commun 2021; 12:6365. [PMID: 34753899 PMCID: PMC8578659 DOI: 10.1038/s41467-021-26576-2] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2021] [Accepted: 10/06/2021] [Indexed: 11/09/2022] Open
Abstract
The nucleolus is the organelle for ribosome biogenesis and sensing various types of stress. However, its role in regulating stem cell fate remains unclear. Here, we present evidence that nucleolar stress induced by interfering rRNA biogenesis can drive the 2-cell stage embryo-like (2C-like) program and induce an expanded 2C-like cell population in mouse embryonic stem (mES) cells. Mechanistically, nucleolar integrity maintains normal liquid-liquid phase separation (LLPS) of the nucleolus and the formation of peri-nucleolar heterochromatin (PNH). Upon defects in rRNA biogenesis, the natural state of nucleolus LLPS is disrupted, causing dissociation of the NCL/TRIM28 complex from PNH and changes in epigenetic state and reorganization of the 3D structure of PNH, which leads to release of Dux, a 2C program transcription factor, from PNH to activate a 2C-like program. Correspondingly, embryos with rRNA biogenesis defect are unable to develop from 2-cell (2C) to 4-cell embryos, with delayed repression of 2C/ERV genes and a transcriptome skewed toward earlier cleavage embryo signatures. Our results highlight that rRNA-mediated nucleolar integrity and 3D structure reshaping of the PNH compartment regulates the fate transition of mES cells to 2C-like cells, and that rRNA biogenesis is a critical regulator during the 2-cell to 4-cell transition of murine pre-implantation embryo development.
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Affiliation(s)
- Hua Yu
- Center of Stem Cell and Regenerative Medicine, Department of Basic Medical Sciences, and Bone Marrow Transplantation Center of the First Affiliated Hospital, Zhejiang University School of Medicine, 310003, Hangzhou, China
- Zhejiang Laboratory for Systems & Precision Medicine, Zhejiang University Medical Center, 1369 West Wenyi Road, 311121, Hangzhou, China
- Institute of Hematology, Zhejiang University, 310058, Hangzhou, China
- Center of Gene/Cell Engineering and Genome Medicine, 310058, Hangzhou, Zhejiang, China
| | - Zhen Sun
- Center of Stem Cell and Regenerative Medicine, Department of Basic Medical Sciences, and Bone Marrow Transplantation Center of the First Affiliated Hospital, Zhejiang University School of Medicine, 310003, Hangzhou, China
- Zhejiang Laboratory for Systems & Precision Medicine, Zhejiang University Medical Center, 1369 West Wenyi Road, 311121, Hangzhou, China
- Institute of Hematology, Zhejiang University, 310058, Hangzhou, China
- Center of Gene/Cell Engineering and Genome Medicine, 310058, Hangzhou, Zhejiang, China
| | - Tianyu Tan
- Center of Stem Cell and Regenerative Medicine, Department of Basic Medical Sciences, and Bone Marrow Transplantation Center of the First Affiliated Hospital, Zhejiang University School of Medicine, 310003, Hangzhou, China
- Zhejiang Laboratory for Systems & Precision Medicine, Zhejiang University Medical Center, 1369 West Wenyi Road, 311121, Hangzhou, China
- Institute of Hematology, Zhejiang University, 310058, Hangzhou, China
- Center of Gene/Cell Engineering and Genome Medicine, 310058, Hangzhou, Zhejiang, China
| | - Hongru Pan
- Center of Stem Cell and Regenerative Medicine, Department of Basic Medical Sciences, and Bone Marrow Transplantation Center of the First Affiliated Hospital, Zhejiang University School of Medicine, 310003, Hangzhou, China
- Zhejiang Laboratory for Systems & Precision Medicine, Zhejiang University Medical Center, 1369 West Wenyi Road, 311121, Hangzhou, China
- Institute of Hematology, Zhejiang University, 310058, Hangzhou, China
- Center of Gene/Cell Engineering and Genome Medicine, 310058, Hangzhou, Zhejiang, China
| | - Jing Zhao
- Center of Stem Cell and Regenerative Medicine, Department of Basic Medical Sciences, and Bone Marrow Transplantation Center of the First Affiliated Hospital, Zhejiang University School of Medicine, 310003, Hangzhou, China
- Zhejiang Laboratory for Systems & Precision Medicine, Zhejiang University Medical Center, 1369 West Wenyi Road, 311121, Hangzhou, China
- Institute of Hematology, Zhejiang University, 310058, Hangzhou, China
- Center of Gene/Cell Engineering and Genome Medicine, 310058, Hangzhou, Zhejiang, China
| | - Ling Zhang
- Center of Stem Cell and Regenerative Medicine, Department of Basic Medical Sciences, and Bone Marrow Transplantation Center of the First Affiliated Hospital, Zhejiang University School of Medicine, 310003, Hangzhou, China
- Zhejiang Laboratory for Systems & Precision Medicine, Zhejiang University Medical Center, 1369 West Wenyi Road, 311121, Hangzhou, China
- Institute of Hematology, Zhejiang University, 310058, Hangzhou, China
- Center of Gene/Cell Engineering and Genome Medicine, 310058, Hangzhou, Zhejiang, China
| | - Jiayu Chen
- Clinical and Translational Research Center of Shanghai First Maternity and Infant Hospital, Shanghai Key Laboratory of Signaling and Disease Research, School of Life Sciences and Technology, Tongji University, Shanghai, China
| | - Anhua Lei
- Center of Stem Cell and Regenerative Medicine, Department of Basic Medical Sciences, and Bone Marrow Transplantation Center of the First Affiliated Hospital, Zhejiang University School of Medicine, 310003, Hangzhou, China
- Zhejiang Laboratory for Systems & Precision Medicine, Zhejiang University Medical Center, 1369 West Wenyi Road, 311121, Hangzhou, China
- Institute of Hematology, Zhejiang University, 310058, Hangzhou, China
- Center of Gene/Cell Engineering and Genome Medicine, 310058, Hangzhou, Zhejiang, China
| | - Yuqing Zhu
- Center of Stem Cell and Regenerative Medicine, Department of Basic Medical Sciences, and Bone Marrow Transplantation Center of the First Affiliated Hospital, Zhejiang University School of Medicine, 310003, Hangzhou, China
- Zhejiang Laboratory for Systems & Precision Medicine, Zhejiang University Medical Center, 1369 West Wenyi Road, 311121, Hangzhou, China
- Institute of Hematology, Zhejiang University, 310058, Hangzhou, China
- Center of Gene/Cell Engineering and Genome Medicine, 310058, Hangzhou, Zhejiang, China
| | - Lang Chen
- Center of Stem Cell and Regenerative Medicine, Department of Basic Medical Sciences, and Bone Marrow Transplantation Center of the First Affiliated Hospital, Zhejiang University School of Medicine, 310003, Hangzhou, China
- Zhejiang Laboratory for Systems & Precision Medicine, Zhejiang University Medical Center, 1369 West Wenyi Road, 311121, Hangzhou, China
- Institute of Hematology, Zhejiang University, 310058, Hangzhou, China
- Center of Gene/Cell Engineering and Genome Medicine, 310058, Hangzhou, Zhejiang, China
| | - Yuyan Xu
- Center of Stem Cell and Regenerative Medicine, Department of Basic Medical Sciences, and Bone Marrow Transplantation Center of the First Affiliated Hospital, Zhejiang University School of Medicine, 310003, Hangzhou, China
- Zhejiang Laboratory for Systems & Precision Medicine, Zhejiang University Medical Center, 1369 West Wenyi Road, 311121, Hangzhou, China
- Institute of Hematology, Zhejiang University, 310058, Hangzhou, China
- Center of Gene/Cell Engineering and Genome Medicine, 310058, Hangzhou, Zhejiang, China
| | - Yaxin Liu
- Center of Stem Cell and Regenerative Medicine, Department of Basic Medical Sciences, and Bone Marrow Transplantation Center of the First Affiliated Hospital, Zhejiang University School of Medicine, 310003, Hangzhou, China
| | - Ming Chen
- College of Life Sciences, Zhejiang University, 310058, Hangzhou, China
| | - Jinghao Sheng
- Institute of Environmental Medicine, and Cancer Center of the First Affiliated Hospital, Zhejiang University School of Medicine, 310058, Hangzhou, China
| | - Zhengping Xu
- Institute of Environmental Medicine, and Cancer Center of the First Affiliated Hospital, Zhejiang University School of Medicine, 310058, Hangzhou, China
| | - Pengxu Qian
- Center of Stem Cell and Regenerative Medicine, Department of Basic Medical Sciences, and Bone Marrow Transplantation Center of the First Affiliated Hospital, Zhejiang University School of Medicine, 310003, Hangzhou, China
- Zhejiang Laboratory for Systems & Precision Medicine, Zhejiang University Medical Center, 1369 West Wenyi Road, 311121, Hangzhou, China
- Institute of Hematology, Zhejiang University, 310058, Hangzhou, China
| | - Cheng Li
- Center for Bioinformatics, School of Life Sciences, Center for Statistical Science, Peking University, 100871, Beijing, China
| | - Shaorong Gao
- Clinical and Translational Research Center of Shanghai First Maternity and Infant Hospital, Shanghai Key Laboratory of Signaling and Disease Research, School of Life Sciences and Technology, Tongji University, Shanghai, China
| | - George Q Daley
- Stem Cell Transplantation Program, Division of Pediatric Hematology Oncology, Boston Children's Hospital, Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, USA
| | - Jin Zhang
- Center of Stem Cell and Regenerative Medicine, Department of Basic Medical Sciences, and Bone Marrow Transplantation Center of the First Affiliated Hospital, Zhejiang University School of Medicine, 310003, Hangzhou, China.
- Zhejiang Laboratory for Systems & Precision Medicine, Zhejiang University Medical Center, 1369 West Wenyi Road, 311121, Hangzhou, China.
- Institute of Hematology, Zhejiang University, 310058, Hangzhou, China.
- Center of Gene/Cell Engineering and Genome Medicine, 310058, Hangzhou, Zhejiang, China.
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27
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Tchurikov NA, Kravatsky YV. The Role of rDNA Clusters in Global Epigenetic Gene Regulation. Front Genet 2021; 12:730633. [PMID: 34531902 PMCID: PMC8438155 DOI: 10.3389/fgene.2021.730633] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2021] [Accepted: 08/02/2021] [Indexed: 12/26/2022] Open
Abstract
The regulation of gene expression has been studied for decades, but the underlying mechanisms are still not fully understood. As well as local and distant regulation, there are specific mechanisms of regulation during development and physiological modulation of gene activity in differentiated cells. Current research strongly supports a role for the 3D chromosomal structure in the regulation of gene expression. However, it is not known whether the genome structure reflects the formation of active or repressed chromosomal domains or if these structures play a primary role in the regulation of gene expression. During early development, heterochromatinization of ribosomal DNA (rDNA) is coupled with silencing or activation of the expression of different sets of genes. Although the mechanisms behind this type of regulation are not known, rDNA clusters shape frequent inter-chromosomal contacts with a large group of genes controlling development. This review aims to shed light on the involvement of clusters of ribosomal genes in the global regulation of gene expression. We also discuss the possible role of RNA-mediated and phase-separation mechanisms in the global regulation of gene expression by nucleoli.
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Affiliation(s)
- Nickolai A Tchurikov
- Engelhardt Institute of Molecular Biology Russian Academy of Sciences, Moscow, Russia
| | - Yuri V Kravatsky
- Engelhardt Institute of Molecular Biology Russian Academy of Sciences, Moscow, Russia
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28
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Regulatory roles of nucleolus organizer region-derived long non-coding RNAs. Mamm Genome 2021; 33:402-411. [PMID: 34436664 DOI: 10.1007/s00335-021-09906-z] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2021] [Accepted: 08/20/2021] [Indexed: 12/13/2022]
Abstract
The nucleolus is the largest sub-nuclear domain, serving primarily as the place for ribosome biogenesis. A delicately regulated function of the nucleolus is vital to the cell not only for maintaining proper protein synthesis but is also tightly associated with responses to different types of cellular stresses. Recently, several long non-coding RNAs (lncRNAs) were found to be part of the regulatory network that modulate nucleolar functions. Several of these lncRNAs are encoded in the ribosomal DNA (rDNA) repeats or are transcribed from the genomic regions that are located near the nucleolus organizer regions (NORs). In this review, we first discuss the current understanding of the sequence of the NORs and variations between different NORs. We then focus on the NOR-derived lncRNAs in mammalian cells and their functions in rRNA transcription and the organization of nucleolar structure under different cellular conditions. The identification of these lncRNAs reveals great potential of the NORs in harboring novel genes involved in the regulation of nucleolar functions.
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29
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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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30
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Erenpreisa J, Krigerts J, Salmina K, Gerashchenko BI, Freivalds T, Kurg R, Winter R, Krufczik M, Zayakin P, Hausmann M, Giuliani A. Heterochromatin Networks: Topology, Dynamics, and Function (a Working Hypothesis). Cells 2021; 10:1582. [PMID: 34201566 PMCID: PMC8304199 DOI: 10.3390/cells10071582] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2021] [Revised: 06/17/2021] [Accepted: 06/21/2021] [Indexed: 12/21/2022] Open
Abstract
Open systems can only exist by self-organization as pulsing structures exchanging matter and energy with the outer world. This review is an attempt to reveal the organizational principles of the heterochromatin supra-intra-chromosomal network in terms of nonlinear thermodynamics. The accessibility of the linear information of the genetic code is regulated by constitutive heterochromatin (CHR) creating the positional information in a system of coordinates. These features include scale-free splitting-fusing of CHR with the boundary constraints of the nucleolus and nuclear envelope. The analysis of both the literature and our own data suggests a radial-concentric network as the main structural organization principle of CHR regulating transcriptional pulsing. The dynamic CHR network is likely created together with nucleolus-associated chromatin domains, while the alveoli of this network, including springy splicing speckles, are the pulsing transcription hubs. CHR contributes to this regulation due to the silencing position variegation effect, stickiness, and flexible rigidity determined by the positioning of nucleosomes. The whole system acts in concert with the elastic nuclear actomyosin network which also emerges by self-organization during the transcriptional pulsing process. We hypothesize that the the transcriptional pulsing, in turn, adjusts its frequency/amplitudes specified by topologically associating domains to the replication timing code that determines epigenetic differentiation memory.
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Affiliation(s)
- Jekaterina Erenpreisa
- Latvian Biomedicine Research and Study Centre, LV-1067 Riga, Latvia; (J.K.); (K.S.); (P.Z.)
| | - Jekabs Krigerts
- Latvian Biomedicine Research and Study Centre, LV-1067 Riga, Latvia; (J.K.); (K.S.); (P.Z.)
| | - Kristine Salmina
- Latvian Biomedicine Research and Study Centre, LV-1067 Riga, Latvia; (J.K.); (K.S.); (P.Z.)
| | - Bogdan I. Gerashchenko
- R.E. Kavetsky Institute of Experimental Pathology, Oncology and Radiobiology, National Academy of Sciences of Ukraine, 03022 Kyiv, Ukraine;
| | - Talivaldis Freivalds
- Institute of Cardiology and Regenerative Medicine, University of Latvia, LV-1004 Riga, Latvia;
| | - Reet Kurg
- Institute of Technology, University of Tartu, 50411 Tartu, Estonia;
| | - Ruth Winter
- Kirchhoff Institute for Physics, Heidelberg University, 69120 Heidelberg, Germany; (R.W.); (M.K.); (M.H.)
| | - Matthias Krufczik
- Kirchhoff Institute for Physics, Heidelberg University, 69120 Heidelberg, Germany; (R.W.); (M.K.); (M.H.)
| | - Pawel Zayakin
- Latvian Biomedicine Research and Study Centre, LV-1067 Riga, Latvia; (J.K.); (K.S.); (P.Z.)
| | - Michael Hausmann
- Kirchhoff Institute for Physics, Heidelberg University, 69120 Heidelberg, Germany; (R.W.); (M.K.); (M.H.)
| | - Alessandro Giuliani
- Istituto Superiore di Sanita Environment and Health Department, 00161 Roma, Italy
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31
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The Ribosomal Gene Loci-The Power behind the Throne. Genes (Basel) 2021; 12:genes12050763. [PMID: 34069807 PMCID: PMC8157237 DOI: 10.3390/genes12050763] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2021] [Revised: 05/12/2021] [Accepted: 05/14/2021] [Indexed: 12/20/2022] Open
Abstract
Nucleoli form around actively transcribed ribosomal RNA (rRNA) genes (rDNA), and the morphology and location of nucleolus-associated genomic domains (NADs) are linked to the RNA Polymerase I (Pol I) transcription status. The number of rDNA repeats (and the proportion of actively transcribed rRNA genes) is variable between cell types, individuals and disease state. Substantial changes in nucleolar morphology and size accompanied by concomitant changes in the Pol I transcription rate have long been documented during normal cell cycle progression, development and malignant transformation. This demonstrates how dynamic the nucleolar structure can be. Here, we will discuss how the structure of the rDNA loci, the nucleolus and the rate of Pol I transcription are important for dynamic regulation of global gene expression and genome stability, e.g., through the modulation of long-range genomic interactions with the suppressive NAD environment. These observations support an emerging paradigm whereby the rDNA repeats and the nucleolus play a key regulatory role in cellular homeostasis during normal development as well as disease, independent of their role in determining ribosome capacity and cellular growth rates.
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32
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Bertels S, Jaggy M, Richter B, Keppler S, Weber K, Genthner E, Fischer AC, Thiel M, Wegener M, Greiner AM, Autenrieth TJ, Bastmeyer M. Geometrically defined environments direct cell division rate and subcellular YAP localization in single mouse embryonic stem cells. Sci Rep 2021; 11:9269. [PMID: 33927254 PMCID: PMC8084931 DOI: 10.1038/s41598-021-88336-y] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2019] [Accepted: 04/01/2021] [Indexed: 01/09/2023] Open
Abstract
Mechanotransduction via yes-associated protein (YAP) is a central mechanism for decision-making in mouse embryonic stem cells (mESCs). Nuclear localization of YAP is tightly connected to pluripotency and increases the cell division rate (CDR). How the geometry of the extracellular environment influences mechanotransduction, thereby YAP localization, and decision-making of single isolated mESCs is largely unknown. To investigate this relation, we produced well-defined 2D and 2.5D microenvironments and monitored CDR and subcellular YAP localization in single mESCs hence excluding cell–cell interactions. By systematically varying size and shape of the 2D and 2.5D substrates we observed that the geometry of the growth environment affects the CDR. Whereas CDR increases with increasing adhesive area in 2D, CDR is highest in small 2.5D micro-wells. Here, mESCs attach to all four walls and exhibit a cross-shaped cell and nuclear morphology. This observation indicates that changes in cell shape are linked to a high CDR. Inhibition of actomyosin activity abrogate these effects. Correspondingly, nuclear YAP localization decreases in inhibitor treated cells, suggesting a relation between cell shape, intracellular forces, and cell division rate. The simplicity of our system guarantees high standardization and reproducibility for monitoring stem cell reactions and allows addressing a variety of fundamental biological questions on a single cell level.
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Affiliation(s)
- Sarah Bertels
- Zoological Institute, Cell- and Neurobiology, Karlsruhe Institute of Technology, Fritz-Haber-Weg 4, 76131, Karlsruhe, Germany.,Institute of Functional Interfaces, Karlsruhe Institute of Technology, Hermann-von-Helmholtz-Platz 1, 76344, Eggenstein-Leopoldshafen, Germany.,3DMM2O - Cluster of Excellence (EXC-2082/1 - 390761711), Karlsruhe, Germany
| | - Mona Jaggy
- Zoological Institute, Cell- and Neurobiology, Karlsruhe Institute of Technology, Fritz-Haber-Weg 4, 76131, Karlsruhe, Germany.,Institute of Functional Interfaces, Karlsruhe Institute of Technology, Hermann-von-Helmholtz-Platz 1, 76344, Eggenstein-Leopoldshafen, Germany
| | - Benjamin Richter
- Zoological Institute, Cell- and Neurobiology, Karlsruhe Institute of Technology, Fritz-Haber-Weg 4, 76131, Karlsruhe, Germany
| | - Stephan Keppler
- Zoological Institute, Cell- and Neurobiology, Karlsruhe Institute of Technology, Fritz-Haber-Weg 4, 76131, Karlsruhe, Germany.,3DMM2O - Cluster of Excellence (EXC-2082/1 - 390761711), Karlsruhe, Germany
| | - Kerstin Weber
- Zoological Institute, Cell- and Neurobiology, Karlsruhe Institute of Technology, Fritz-Haber-Weg 4, 76131, Karlsruhe, Germany
| | - Elisa Genthner
- Zoological Institute, Cell- and Neurobiology, Karlsruhe Institute of Technology, Fritz-Haber-Weg 4, 76131, Karlsruhe, Germany.,3DMM2O - Cluster of Excellence (EXC-2082/1 - 390761711), Karlsruhe, Germany
| | - Andrea C Fischer
- Zoological Institute, Cell- and Neurobiology, Karlsruhe Institute of Technology, Fritz-Haber-Weg 4, 76131, Karlsruhe, Germany.,Institute of Applied Physics, Karlsruhe Institute of Technology, Wolfgang-Gaede-Straße 1, 76131, Karlsruhe, Germany
| | - Michael Thiel
- Nanoscribe GmbH, Hermann-von-Helmholtz-Platz 1, 76344, Eggenstein-Leopoldshafen, Germany
| | - Martin Wegener
- Institute of Applied Physics, Karlsruhe Institute of Technology, Wolfgang-Gaede-Straße 1, 76131, Karlsruhe, Germany.,Institute of Nanotechnology, Karlsruhe Institute of Technology, Hermann-von-Helmholtz-Platz 1, 76344, Eggenstein-Leopoldshafen, Germany.,3DMM2O - Cluster of Excellence (EXC-2082/1 - 390761711), Karlsruhe, Germany
| | - Alexandra M Greiner
- Zoological Institute, Cell- and Neurobiology, Karlsruhe Institute of Technology, Fritz-Haber-Weg 4, 76131, Karlsruhe, Germany
| | - Tatjana J Autenrieth
- Zoological Institute, Cell- and Neurobiology, Karlsruhe Institute of Technology, Fritz-Haber-Weg 4, 76131, Karlsruhe, Germany.,Institute of Functional Interfaces, Karlsruhe Institute of Technology, Hermann-von-Helmholtz-Platz 1, 76344, Eggenstein-Leopoldshafen, Germany
| | - Martin Bastmeyer
- Zoological Institute, Cell- and Neurobiology, Karlsruhe Institute of Technology, Fritz-Haber-Weg 4, 76131, Karlsruhe, Germany. .,Institute of Functional Interfaces, Karlsruhe Institute of Technology, Hermann-von-Helmholtz-Platz 1, 76344, Eggenstein-Leopoldshafen, Germany. .,3DMM2O - Cluster of Excellence (EXC-2082/1 - 390761711), Karlsruhe, Germany. .,Karlsruhe Institute of Technology, Hermann-von-Helmholtz-Platz 1, 76344, Eggenstein-Leopoldshafen, Germany.
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33
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Tchurikov NA, Klushevskaya ES, Kravatsky YV, Kravatskaya GI, Fedoseeva DM. Interchromosomal Contacts of rDNA Clusters in Three Human Cell Lines Are Associated with Silencing of Genes Controlling Morphogenesis. DOKL BIOCHEM BIOPHYS 2021; 496:22-26. [PMID: 33689069 DOI: 10.1134/s1607672921010038] [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: 10/05/2020] [Revised: 10/09/2020] [Accepted: 10/10/2020] [Indexed: 01/27/2023]
Abstract
To study the rDNA contacts with genes in three human cell lines of different origin, we used 4C approach. Our data indicate that the same set of about five hundred genes frequently shape contacts with rDNA clusters in HEK293T, K652, and hESM01 cells. Gene ontology search suggests that the genes are involved in development and morphogenesis. Approximately one hundred of these genes are highly associated with silencing by H3K27me3 mark in different normal cells, including bronchial epithelial cells, keratinocytes, myoblasts, monocytes, endothelial cells, kidney epithelial cells, and some others. We conclude that the concerted silencing of specific group of rDNA-contacting genes controlling development occurs during differentiation. We assume that the phase separation mechanisms may be involved in the rDNA-mediated silencing of a set of genes via the contacts with inactive rDNA clusters.
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Affiliation(s)
- N A Tchurikov
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia.
| | - E S Klushevskaya
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia
| | - Y V Kravatsky
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia
| | - G I Kravatskaya
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia
| | - D M Fedoseeva
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia
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34
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MicroRNAs and long non-coding RNAs as novel regulators of ribosome biogenesis. Biochem Soc Trans 2021; 48:595-612. [PMID: 32267487 PMCID: PMC7200637 DOI: 10.1042/bst20190854] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2020] [Revised: 03/12/2020] [Accepted: 03/16/2020] [Indexed: 12/14/2022]
Abstract
Ribosome biogenesis is the fine-tuned, essential process that generates mature ribosomal subunits and ultimately enables all protein synthesis within a cell. Novel regulators of ribosome biogenesis continue to be discovered in higher eukaryotes. While many known regulatory factors are proteins or small nucleolar ribonucleoproteins, microRNAs (miRNAs), and long non-coding RNAs (lncRNAs) are emerging as a novel modulatory layer controlling ribosome production. Here, we summarize work uncovering non-coding RNAs (ncRNAs) as novel regulators of ribosome biogenesis and highlight their links to diseases of defective ribosome biogenesis. It is still unclear how many miRNAs or lncRNAs are involved in phenotypic or pathological disease outcomes caused by impaired ribosome production, as in the ribosomopathies, or by increased ribosome production, as in cancer. In time, we hypothesize that many more ncRNA regulators of ribosome biogenesis will be discovered, which will be followed by an effort to establish connections between disease pathologies and the molecular mechanisms of this additional layer of ribosome biogenesis control.
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35
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Zhang H, Wu Z, Lu JY, Huang B, Zhou H, Xie W, Wang J, Shen X. DEAD-Box Helicase 18 Counteracts PRC2 to Safeguard Ribosomal DNA in Pluripotency Regulation. Cell Rep 2021; 30:81-97.e7. [PMID: 31914400 DOI: 10.1016/j.celrep.2019.12.021] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2019] [Revised: 10/24/2019] [Accepted: 12/06/2019] [Indexed: 12/22/2022] Open
Abstract
Embryonic stem cells (ESCs) exhibit high levels of ribosomal RNA (rRNA) transcription and ribosome biogenesis. Here, we reveal an unexpected role for an essential DEAD-box helicase, DDX18, in antagonizing the polycomb repressive complex 2 (PRC2) to prevent deposition of the repressive H3K27me3 mark onto rDNA in pluripotent cells. DDX18 binds and sequesters PRC2 in the outer layer of the nucleolus and counteracts PRC2 complex formation in vivo and in vitro. DDX18 knockdown leads to increased occupancy of PRC2 and H3K27me3 at rDNA loci, accompanied by drastically decreased rRNA transcription and reduced ribosomal protein expression and translation. Auxin-induced rapid degradation of DDX18 enhances PRC2 binding at rDNA. The inhibition of PRC2 partially rescues the effects of DDX18 depletion on rRNA transcription and ESC self-renewal. These results demonstrate a critical role for DDX18 in safeguarding the chromatin and transcriptional integrity of rDNA by counteracting the epigenetic silencing machinery to promote pluripotency.
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Affiliation(s)
- Hui Zhang
- Tsinghua Center for Life Sciences, Department of Basic Medical Sciences in School of Medicine, and School of Life Sciences, Tsinghua University, Beijing 100084, China.
| | - Zhongyang Wu
- Tsinghua Center for Life Sciences, Department of Basic Medical Sciences in School of Medicine, and School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - J Yuyang Lu
- Tsinghua Center for Life Sciences, Department of Basic Medical Sciences in School of Medicine, and School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Bo Huang
- Tsinghua Center for Life Sciences, Department of Basic Medical Sciences in School of Medicine, and School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Hongwei Zhou
- The Black Family Stem Cell Institute and Department of Cell, Developmental, and Regenerative Biology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Wei Xie
- Tsinghua Center for Life Sciences, Department of Basic Medical Sciences in School of Medicine, and School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Jianlong Wang
- The Black Family Stem Cell Institute and Department of Cell, Developmental, and Regenerative Biology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Xiaohua Shen
- Tsinghua Center for Life Sciences, Department of Basic Medical Sciences in School of Medicine, and School of Life Sciences, Tsinghua University, Beijing 100084, China.
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36
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Bizhanova A, Kaufman PD. Close to the edge: Heterochromatin at the nucleolar and nuclear peripheries. BIOCHIMICA ET BIOPHYSICA ACTA. GENE REGULATORY MECHANISMS 2021; 1864:194666. [PMID: 33307247 PMCID: PMC7855492 DOI: 10.1016/j.bbagrm.2020.194666] [Citation(s) in RCA: 46] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/09/2020] [Revised: 11/11/2020] [Accepted: 11/29/2020] [Indexed: 02/06/2023]
Abstract
Chromatin is a dynamic structure composed of DNA, RNA, and proteins, regulating storage and expression of the genetic material in the nucleus. Heterochromatin plays a crucial role in driving the three-dimensional arrangement of the interphase genome, and in preserving genome stability by maintaining a subset of the genome in a silent state. Spatial genome organization contributes to normal patterns of gene function and expression, and is therefore of broad interest. Mammalian heterochromatin, the focus of this review, mainly localizes at the nuclear periphery, forming Lamina-associated domains (LADs), and at the nucleolar periphery, forming Nucleolus-associated domains (NADs). Together, these regions comprise approximately one-half of mammalian genomes, and most but not all loci within these domains are stochastically placed at either of these two locations after exit from mitosis at each cell cycle. Excitement about the role of these heterochromatic domains in early development has recently been heightened by the discovery that LADs appear at some loci in the preimplantation mouse embryo prior to other chromosomal features like compartmental identity and topologically-associated domains (TADs). While LADs have been extensively studied and mapped during cellular differentiation and early embryonic development, NADs have been less thoroughly studied. Here, we summarize pioneering studies of NADs and LADs, more recent advances in our understanding of cis/trans-acting factors that mediate these localizations, and discuss the functional significance of these associations.
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Affiliation(s)
- Aizhan Bizhanova
- Department of Molecular, Cell and Cancer Biology, University of Massachusetts Medical School, Worcester, MA 01605, USA
| | - Paul D Kaufman
- Department of Molecular, Cell and Cancer Biology, University of Massachusetts Medical School, Worcester, MA 01605, USA.
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37
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Kaliatsi EG, Giarimoglou N, Stathopoulos C, Stamatopoulou V. Non-Coding RNA-Driven Regulation of rRNA Biogenesis. Int J Mol Sci 2020; 21:E9738. [PMID: 33419375 PMCID: PMC7766524 DOI: 10.3390/ijms21249738] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2020] [Revised: 12/15/2020] [Accepted: 12/17/2020] [Indexed: 12/30/2022] Open
Abstract
Ribosomal RNA (rRNA) biogenesis takes place in the nucleolus, the most prominent condensate of the eukaryotic nucleus. The proper assembly and integrity of the nucleolus reflects the accurate synthesis and processing of rRNAs which in turn, as major components of ribosomes, ensure the uninterrupted flow of the genetic information during translation. Therefore, the abundant production of rRNAs in a precisely functional nucleolus is of outmost importance for the cell viability and requires the concerted action of essential enzymes, associated factors and epigenetic marks. The coordination and regulation of such an elaborate process depends on not only protein factors, but also on numerous regulatory non-coding RNAs (ncRNAs). Herein, we focus on RNA-mediated mechanisms that control the synthesis, processing and modification of rRNAs in mammals. We highlight the significance of regulatory ncRNAs in rRNA biogenesis and the maintenance of the nucleolar morphology, as well as their role in human diseases and as novel druggable molecular targets.
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Affiliation(s)
| | | | - Constantinos Stathopoulos
- Department of Biochemistry, School of Medicine, University of Patras, 26504 Patras, Greece; (E.G.K.); (N.G.)
| | - Vassiliki Stamatopoulou
- Department of Biochemistry, School of Medicine, University of Patras, 26504 Patras, Greece; (E.G.K.); (N.G.)
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38
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Ramírez-Colmenero A, Oktaba K, Fernandez-Valverde SL. Evolution of Genome-Organizing Long Non-coding RNAs in Metazoans. Front Genet 2020; 11:589697. [PMID: 33329735 PMCID: PMC7734150 DOI: 10.3389/fgene.2020.589697] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2020] [Accepted: 11/09/2020] [Indexed: 12/28/2022] Open
Abstract
Long non-coding RNAs (lncRNAs) have important regulatory functions across eukarya. It is now clear that many of these functions are related to gene expression regulation through their capacity to recruit epigenetic modifiers and establish chromatin interactions. Several lncRNAs have been recently shown to participate in modulating chromatin within the spatial organization of the genome in the three-dimensional space of the nucleus. The identification of lncRNA candidates is challenging, as it is their functional characterization. Conservation signatures of lncRNAs are different from those of protein-coding genes, making identifying lncRNAs under selection a difficult task, and the homology between lncRNAs may not be readily apparent. Here, we review the evidence for these higher-order genome organization functions of lncRNAs in animals and the evolutionary signatures they display.
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Affiliation(s)
- América Ramírez-Colmenero
- Unidad de Genómica Avanzada (Langebio), Centro de Investigación y de Estudios Avanzados del IPN, Irapuato, México
| | - Katarzyna Oktaba
- Unidad Irapuato, Centro de Investigación y de Estudios Avanzados del IPN, Irapuato, México
| | - Selene L Fernandez-Valverde
- Unidad de Genómica Avanzada (Langebio), Centro de Investigación y de Estudios Avanzados del IPN, Irapuato, México
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39
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Gupta S, Santoro R. Regulation and Roles of the Nucleolus in Embryonic Stem Cells: From Ribosome Biogenesis to Genome Organization. Stem Cell Reports 2020; 15:1206-1219. [PMID: 32976768 PMCID: PMC7724472 DOI: 10.1016/j.stemcr.2020.08.012] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2020] [Revised: 08/25/2020] [Accepted: 08/25/2020] [Indexed: 12/13/2022] Open
Abstract
The nucleolus is the largest compartment of the eukaryotic cell's nucleus. It acts as a ribosome factory, thereby sustaining the translation machinery. The nucleolus is also the subnuclear compartment with the highest transcriptional activity in the cell, where hundreds of ribosomal RNA (rRNA) genes transcribe the overwhelming majority of RNAs. The structure and composition of the nucleolus change according to the developmental state. For instance, in embryonic stem cells (ESCs), rRNA genes display a hyperactive transcriptional state and open chromatin structure compared with differentiated cells. Increasing evidence indicates that the role of the nucleolus and rRNA genes might go beyond the control of ribosome biogenesis. One such role is linked to the genome architecture, since repressive domains are often located close to the nucleolus. This review highlights recent findings describing how the nucleolus is regulated in ESCs and its role in regulating ribosome biogenesis and genome organization for the maintenance of stem cell identity.
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Affiliation(s)
- Shivani Gupta
- Department of Molecular Mechanisms of Disease, DMMD, University of Zurich, 8057 Zurich, Switzerland
| | - Raffaella Santoro
- Department of Molecular Mechanisms of Disease, DMMD, University of Zurich, 8057 Zurich, Switzerland.
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40
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Tchurikov NA, Klushevskaya ES, Fedoseeva DM, Alembekov IR, Kravatskaya GI, Chechetkin VR, Kravatsky YV, Kretova OV. Dynamics of Whole-Genome Contacts of Nucleoli in Drosophila Cells Suggests a Role for rDNA Genes in Global Epigenetic Regulation. Cells 2020; 9:cells9122587. [PMID: 33287227 PMCID: PMC7761670 DOI: 10.3390/cells9122587] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2020] [Revised: 11/27/2020] [Accepted: 11/30/2020] [Indexed: 01/06/2023] Open
Abstract
Chromosomes are organized into 3D structures that are important for the regulation of gene expression and differentiation. Important role in formation of inter-chromosome contacts play rDNA clusters that make up nucleoli. In the course of differentiation, heterochromatization of rDNA units in mouse cells is coupled with the repression or activation of different genes. Furthermore, the nucleoli of human cells shape the direct contacts with genes that are involved in differentiation and cancer. Here, we identified and categorized the genes located in the regions where rDNA clusters make frequent contacts. Using a 4C approach, we demonstrate that in Drosophila S2 cells, rDNA clusters form contacts with genes that are involved in chromosome organization and differentiation. Heat shock treatment induces changes in the contacts between nucleoli and hundreds of genes controlling morphogenesis. We show that nucleoli form contacts with regions that are enriched with active or repressive histone marks and where small non-coding RNAs are mapped. These data indicate that rDNA contacts are involved in the repression and activation of gene expression and that rDNA clusters orchestrate large groups of Drosophila genes involved in differentiation.
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41
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Dalcher D, Tan JY, Bersaglieri C, Peña‐Hernández R, Vollenweider E, Zeyen S, Schmid MW, Bianchi V, Butz S, Roganowicz M, Kuzyakiv R, Baubec T, Marques AC, Santoro R. BAZ2A safeguards genome architecture of ground-state pluripotent stem cells. EMBO J 2020; 39:e105606. [PMID: 33433018 PMCID: PMC7705451 DOI: 10.15252/embj.2020105606] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2020] [Revised: 08/31/2020] [Accepted: 09/02/2020] [Indexed: 12/30/2022] Open
Abstract
Chromosomes have an intrinsic tendency to segregate into compartments, forming long-distance contacts between loci of similar chromatin states. How genome compartmentalization is regulated remains elusive. Here, comparison of mouse ground-state embryonic stem cells (ESCs) characterized by open and active chromatin, and advanced serum ESCs with a more closed and repressed genome, reveals distinct regulation of their genome organization due to differential dependency on BAZ2A/TIP5, a component of the chromatin remodeling complex NoRC. On ESC chromatin, BAZ2A interacts with SNF2H, DNA topoisomerase 2A (TOP2A) and cohesin. BAZ2A associates with chromatin sub-domains within the active A compartment, which intersect through long-range contacts. We found that ground-state chromatin selectively requires BAZ2A to limit the invasion of active domains into repressive compartments. BAZ2A depletion increases chromatin accessibility at B compartments. Furthermore, BAZ2A regulates H3K27me3 genome occupancy in a TOP2A-dependent manner. Finally, ground-state ESCs require BAZ2A for growth, differentiation, and correct expression of developmental genes. Our results uncover the propensity of open chromatin domains to invade repressive domains, which is counteracted by chromatin remodeling to establish genome partitioning and preserve cell identity.
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Affiliation(s)
- Damian Dalcher
- Department of Molecular Mechanisms of Disease, DMMDUniversity of ZurichZurichSwitzerland
- Molecular Life Science ProgramLife Science Zurich Graduate SchoolUniversity of ZurichZurichSwitzerland
| | - Jennifer Yihong Tan
- Department of Computational BiologyUniversity of LausanneLausanneSwitzerland
| | - Cristiana Bersaglieri
- Department of Molecular Mechanisms of Disease, DMMDUniversity of ZurichZurichSwitzerland
- Molecular Life Science ProgramLife Science Zurich Graduate SchoolUniversity of ZurichZurichSwitzerland
| | - Rodrigo Peña‐Hernández
- Department of Molecular Mechanisms of Disease, DMMDUniversity of ZurichZurichSwitzerland
- Molecular Life Science ProgramLife Science Zurich Graduate SchoolUniversity of ZurichZurichSwitzerland
| | - Eva Vollenweider
- Department of Molecular Mechanisms of Disease, DMMDUniversity of ZurichZurichSwitzerland
- Molecular Life Science ProgramLife Science Zurich Graduate SchoolUniversity of ZurichZurichSwitzerland
| | - Stefan Zeyen
- Department of Molecular Mechanisms of Disease, DMMDUniversity of ZurichZurichSwitzerland
- Molecular Life Science ProgramLife Science Zurich Graduate SchoolUniversity of ZurichZurichSwitzerland
| | - Marc W Schmid
- Service and Support for Science ITUniversity of ZurichZurichSwitzerland
| | - Valerio Bianchi
- Oncode InstituteHubrecht Institute‐KNAWUniversity Medical Center UtrechtUtrechtThe Netherlands
| | - Stefan Butz
- Department of Molecular Mechanisms of Disease, DMMDUniversity of ZurichZurichSwitzerland
- Molecular Life Science ProgramLife Science Zurich Graduate SchoolUniversity of ZurichZurichSwitzerland
| | - Marcin Roganowicz
- Department of Molecular Mechanisms of Disease, DMMDUniversity of ZurichZurichSwitzerland
- Molecular Life Science ProgramLife Science Zurich Graduate SchoolUniversity of ZurichZurichSwitzerland
| | - Rostyslav Kuzyakiv
- Department of Molecular Mechanisms of Disease, DMMDUniversity of ZurichZurichSwitzerland
- Service and Support for Science ITUniversity of ZurichZurichSwitzerland
| | - Tuncay Baubec
- Department of Molecular Mechanisms of Disease, DMMDUniversity of ZurichZurichSwitzerland
| | - Ana Claudia Marques
- Department of Computational BiologyUniversity of LausanneLausanneSwitzerland
| | - Raffaella Santoro
- Department of Molecular Mechanisms of Disease, DMMDUniversity of ZurichZurichSwitzerland
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42
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Abraham KJ, Khosraviani N, Chan JNY, Gorthi A, Samman A, Zhao DY, Wang M, Bokros M, Vidya E, Ostrowski LA, Oshidari R, Pietrobon V, Patel PS, Algouneh A, Singhania R, Liu Y, Yerlici VT, De Carvalho DD, Ohh M, Dickson BC, Hakem R, Greenblatt JF, Lee S, Bishop AJR, Mekhail K. Nucleolar RNA polymerase II drives ribosome biogenesis. Nature 2020; 585:298-302. [PMID: 32669707 PMCID: PMC7486236 DOI: 10.1038/s41586-020-2497-0] [Citation(s) in RCA: 111] [Impact Index Per Article: 27.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2018] [Accepted: 04/21/2020] [Indexed: 12/16/2022]
Abstract
Proteins are manufactured by ribosomes-macromolecular complexes of protein and RNA molecules that are assembled within major nuclear compartments called nucleoli1,2. Existing models suggest that RNA polymerases I and III (Pol I and Pol III) are the only enzymes that directly mediate the expression of the ribosomal RNA (rRNA) components of ribosomes. Here we show, however, that RNA polymerase II (Pol II) inside human nucleoli operates near genes encoding rRNAs to drive their expression. Pol II, assisted by the neurodegeneration-associated enzyme senataxin, generates a shield comprising triplex nucleic acid structures known as R-loops at intergenic spacers flanking nucleolar rRNA genes. The shield prevents Pol I from producing sense intergenic noncoding RNAs (sincRNAs) that can disrupt nucleolar organization and rRNA expression. These disruptive sincRNAs can be unleashed by Pol II inhibition, senataxin loss, Ewing sarcoma or locus-associated R-loop repression through an experimental system involving the proteins RNaseH1, eGFP and dCas9 (which we refer to as 'red laser'). We reveal a nucleolar Pol-II-dependent mechanism that drives ribosome biogenesis, identify disease-associated disruption of nucleoli by noncoding RNAs, and establish locus-targeted R-loop modulation. Our findings revise theories of labour division between the major RNA polymerases, and identify nucleolar Pol II as a major factor in protein synthesis and nuclear organization, with potential implications for health and disease.
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Affiliation(s)
- Karan J Abraham
- Department of Laboratory Medicine and Pathobiology, Faculty of Medicine, University of Toronto, Toronto, Ontario, Canada
| | - Negin Khosraviani
- Department of Laboratory Medicine and Pathobiology, Faculty of Medicine, University of Toronto, Toronto, Ontario, Canada
| | - Janet N Y Chan
- Department of Laboratory Medicine and Pathobiology, Faculty of Medicine, University of Toronto, Toronto, Ontario, Canada
| | - Aparna Gorthi
- Greehey Children's Cancer Research Institute, Department of Cell Systems and Anatomy, University of Texas Health at San Antonio, San Antonio, TX, USA
| | - Anas Samman
- Department of Laboratory Medicine and Pathobiology, Faculty of Medicine, University of Toronto, Toronto, Ontario, Canada
| | - Dorothy Y Zhao
- Department of Molecular Genetics, Faculty of Medicine, University of Toronto, Toronto, Ontario, Canada
- Donnelly Centre, University of Toronto, Toronto, Ontario, Canada
| | - Miling Wang
- Sylvester Comprehensive Cancer Center, Department of Biochemistry and Molecular Biology, Miller School of Medicine, University of Miami, Miami, FL, USA
| | - Michael Bokros
- Sylvester Comprehensive Cancer Center, Department of Biochemistry and Molecular Biology, Miller School of Medicine, University of Miami, Miami, FL, USA
| | - Elva Vidya
- Department of Laboratory Medicine and Pathobiology, Faculty of Medicine, University of Toronto, Toronto, Ontario, Canada
| | - Lauren A Ostrowski
- Department of Laboratory Medicine and Pathobiology, Faculty of Medicine, University of Toronto, Toronto, Ontario, Canada
| | - Roxanne Oshidari
- Department of Laboratory Medicine and Pathobiology, Faculty of Medicine, University of Toronto, Toronto, Ontario, Canada
| | - Violena Pietrobon
- Department of Laboratory Medicine and Pathobiology, Faculty of Medicine, University of Toronto, Toronto, Ontario, Canada
| | - Parasvi S Patel
- Princess Margaret Cancer Research Centre, University Health Network, and Department of Medical Biophysics, Faculty of Medicine, University of Toronto, Toronto, Ontario, Canada
| | - Arash Algouneh
- Department of Laboratory Medicine and Pathobiology, Faculty of Medicine, University of Toronto, Toronto, Ontario, Canada
- Princess Margaret Cancer Research Centre, University Health Network, and Department of Medical Biophysics, Faculty of Medicine, University of Toronto, Toronto, Ontario, Canada
| | - Rajat Singhania
- Princess Margaret Cancer Research Centre, University Health Network, and Department of Medical Biophysics, Faculty of Medicine, University of Toronto, Toronto, Ontario, Canada
| | - Yupeng Liu
- Department of Laboratory Medicine and Pathobiology, Faculty of Medicine, University of Toronto, Toronto, Ontario, Canada
| | - V Talya Yerlici
- Department of Laboratory Medicine and Pathobiology, Faculty of Medicine, University of Toronto, Toronto, Ontario, Canada
| | - Daniel D De Carvalho
- Princess Margaret Cancer Research Centre, University Health Network, and Department of Medical Biophysics, Faculty of Medicine, University of Toronto, Toronto, Ontario, Canada
| | - Michael Ohh
- Department of Laboratory Medicine and Pathobiology, Faculty of Medicine, University of Toronto, Toronto, Ontario, Canada
- Department of Biochemistry, Faculty of Medicine, University of Toronto, Toronto, Ontario, Canada
| | - Brendan C Dickson
- Department of Laboratory Medicine and Pathobiology, Faculty of Medicine, University of Toronto, Toronto, Ontario, Canada
- Lunenfeld Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, Ontario, Canada
| | - Razq Hakem
- Princess Margaret Cancer Research Centre, University Health Network, and Department of Medical Biophysics, Faculty of Medicine, University of Toronto, Toronto, Ontario, Canada
| | - Jack F Greenblatt
- Department of Molecular Genetics, Faculty of Medicine, University of Toronto, Toronto, Ontario, Canada
- Donnelly Centre, University of Toronto, Toronto, Ontario, Canada
| | - Stephen Lee
- Sylvester Comprehensive Cancer Center, Department of Biochemistry and Molecular Biology, Miller School of Medicine, University of Miami, Miami, FL, USA
| | - Alexander J R Bishop
- Greehey Children's Cancer Research Institute, Department of Cell Systems and Anatomy, University of Texas Health at San Antonio, San Antonio, TX, USA
- Mays Cancer Center, University of Texas Health at San Antonio, San Antonio, TX, USA
| | - Karim Mekhail
- Department of Laboratory Medicine and Pathobiology, Faculty of Medicine, University of Toronto, Toronto, Ontario, Canada.
- Canada Research Chairs Program, Faculty of Medicine, University of Toronto, Toronto, Ontario, Canada.
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Mapping and Quantification of Non-Coding RNA Originating from the rDNA in Human Glioma Cells. Cancers (Basel) 2020; 12:cancers12082090. [PMID: 32731436 PMCID: PMC7464196 DOI: 10.3390/cancers12082090] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2020] [Revised: 07/24/2020] [Accepted: 07/25/2020] [Indexed: 12/14/2022] Open
Abstract
Ribosomal DNA is one of the most conserved parts of the genome, especially in its rRNA coding regions, but some puzzling pieces of its noncoding repetitive sequences harbor secrets of cell growth and development machinery. Disruptions in the neat mechanisms of rDNA orchestrating the cell functioning result in malignant conversion. In cancer cells, the organization of rRNA coding genes and their transcription somehow differ from that of normal cells, but little is known about the particular mechanism for this switch. In this study, we demonstrate that the region ~2 kb upstream of the rDNA promoter is transcriptionally active in one type of the most malignant human brain tumors, and we compare its expression rate to that of healthy human tissues and cell cultures. Sense and antisense non-coding RNA transcripts were detected and mapped, but their secondary structure and functions remain to be elucidated. We propose that the transcripts may relate to a new class of so-called promoter-associated RNAs (pRNAs), or have some other regulatory functions. We also hope that the expression of these non-coding RNAs can be used as a marker in glioma diagnostics and prognosis.
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Son J, Hannan KM, Poortinga G, Hein N, Cameron DP, Ganley ARD, Sheppard KE, Pearson RB, Hannan RD, Sanij E. rDNA Chromatin Activity Status as a Biomarker of Sensitivity to the RNA Polymerase I Transcription Inhibitor CX-5461. Front Cell Dev Biol 2020; 8:568. [PMID: 32719798 PMCID: PMC7349920 DOI: 10.3389/fcell.2020.00568] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2019] [Accepted: 06/15/2020] [Indexed: 12/13/2022] Open
Abstract
Hyperactivation of RNA polymerase I (Pol I) transcription of ribosomal RNA (rRNA) genes (rDNA) is a key determinant of growth and proliferation and a consistent feature of cancer cells. We have demonstrated that inhibition of rDNA transcription by the Pol I transcription inhibitor CX-5461 selectively kills tumor cells in vivo. Moreover, the first-in human trial of CX-5461 has demonstrated CX-5461 is well-tolerated in patients and has single-agent anti-tumor activity in hematologic malignancies. However, the mechanisms underlying tumor cell sensitivity to CX-5461 remain unclear. Understanding these mechanisms is crucial for the development of predictive biomarkers of response that can be utilized for stratifying patients who may benefit from CX-5461. The rDNA repeats exist in four different and dynamic chromatin states: inactive rDNA can be either methylated silent or unmethylated pseudo-silent; while active rDNA repeats are described as either transcriptionally competent but non-transcribed or actively transcribed, depending on the level of rDNA promoter methylation, loading of the essential rDNA chromatin remodeler UBF and histone marks status. In addition, the number of rDNA repeats per human cell can reach hundreds of copies. Here, we tested the hypothesis that the number and/or chromatin status of the rDNA repeats, is a critical determinant of tumor cell sensitivity to Pol I therapy. We systematically examined a panel of ovarian cancer (OVCA) cell lines to identify rDNA chromatin associated biomarkers that might predict sensitivity to CX-5461. We demonstrated that an increased proportion of active to inactive rDNA repeats, independent of rDNA copy number, determines OVCA cell line sensitivity to CX-5461. Further, using zinc finger nuclease genome editing we identified that reducing rDNA copy number leads to an increase in the proportion of active rDNA repeats and confers sensitivity to CX-5461 but also induces genome-wide instability and sensitivity to DNA damage. We propose that the proportion of active to inactive rDNA repeats may serve as a biomarker to identify cancer patients who will benefit from CX-5461 therapy in future clinical trials. The data also reinforces the notion that rDNA instability is a threat to genomic integrity and cellular homeostasis.
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Affiliation(s)
- Jinbae Son
- Peter MacCallum Cancer Centre, Melbourne, VIC, Australia
- Sir Peter MacCallum Department of Oncology, The University of Melbourne, Parkville, VIC, Australia
| | - Katherine M. Hannan
- ACRF Department of Cancer Biology and Therapeutics, The John Curtin School of Medical Research, Australian National University, Canberra, ACT, Australia
- Department of Biochemistry and Molecular Biology, The University of Melbourne, Parkville, VIC, Australia
| | - Gretchen Poortinga
- Peter MacCallum Cancer Centre, Melbourne, VIC, Australia
- Sir Peter MacCallum Department of Oncology, The University of Melbourne, Parkville, VIC, Australia
- Department of Medicine, St. Vincent’s Hospital, The University of Melbourne, Parkville, VIC, Australia
| | - Nadine Hein
- ACRF Department of Cancer Biology and Therapeutics, The John Curtin School of Medical Research, Australian National University, Canberra, ACT, Australia
| | - Donald P. Cameron
- ACRF Department of Cancer Biology and Therapeutics, The John Curtin School of Medical Research, Australian National University, Canberra, ACT, Australia
| | - Austen R. D. Ganley
- School of Biological Sciences, The University of Auckland, Auckland, New Zealand
| | - Karen E. Sheppard
- Peter MacCallum Cancer Centre, Melbourne, VIC, Australia
- Sir Peter MacCallum Department of Oncology, The University of Melbourne, Parkville, VIC, Australia
- Department of Biochemistry and Molecular Biology, The University of Melbourne, Parkville, VIC, Australia
| | - Richard B. Pearson
- Peter MacCallum Cancer Centre, Melbourne, VIC, Australia
- Sir Peter MacCallum Department of Oncology, The University of Melbourne, Parkville, VIC, Australia
- Department of Biochemistry and Molecular Biology, The University of Melbourne, Parkville, VIC, Australia
- Department of Biochemistry and Molecular Biology, Monash University, Clayton, VIC, Australia
| | - Ross D. Hannan
- Peter MacCallum Cancer Centre, Melbourne, VIC, Australia
- Sir Peter MacCallum Department of Oncology, The University of Melbourne, Parkville, VIC, Australia
- ACRF Department of Cancer Biology and Therapeutics, The John Curtin School of Medical Research, Australian National University, Canberra, ACT, Australia
- Department of Biochemistry and Molecular Biology, The University of Melbourne, Parkville, VIC, Australia
- Department of Biochemistry and Molecular Biology, Monash University, Clayton, VIC, Australia
- School of Biomedical Sciences, The University of Queensland, Brisbane, QLD, Australia
| | - Elaine Sanij
- Peter MacCallum Cancer Centre, Melbourne, VIC, Australia
- Sir Peter MacCallum Department of Oncology, The University of Melbourne, Parkville, VIC, Australia
- Department of Clinical Pathology, The University of Melbourne, Parkville, VIC, Australia
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Kretova OV, Fedoseeva DM, Slovohotov IY, Klushevskaya ES, Kravatsky YV, Tchurikov NA. Drosophila rDNA Genes Shape the Stable Contacts with the Tlk Gene at the Expression Area of Small RNAs and Affect on Looped Domains inside the Gene. Mol Biol 2020. [DOI: 10.1134/s0026893320020089] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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Sharifi S, da Costa HFR, Bierhoff H. The circuitry between ribosome biogenesis and translation in stem cell function and ageing. Mech Ageing Dev 2020; 189:111282. [PMID: 32531294 DOI: 10.1016/j.mad.2020.111282] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2020] [Revised: 05/11/2020] [Accepted: 06/01/2020] [Indexed: 12/13/2022]
Abstract
Ribosome biogenesis takes place mainly in the nucleolus, a nuclear, non-membrane bound organelle forming around the gene arrays encoding ribosomal RNA (rRNA). Nucleolar activity comprises synthesis, processing and maturation of rRNAs, followed by their assembly with ribosomal proteins into pre-ribosomal particles. The final formation of translation-competent ribosomes in the cytoplasm is the prerequisite for protein synthesis, which is the most energy-consuming cellular process. In adult stem cells, ribosome biogenesis and protein synthesis determine the switch between the quiescent and the activated state, but also decide whether activated stem cells self-renew or differentiate. Given this major impact on cellular function, it seems likely that perturbations of the circuitry between nucleolar activity and translation lead to ageing-related stem cell deterioration. This review provides an overview of how ribosome biogenesis and translation govern stem cell function and discusses the resultant implication in stem cell ageing.
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Affiliation(s)
- Samim Sharifi
- Institute of Biochemistry and Biophysics, Center for Molecular Biomedicine (CMB), Friedrich Schiller University Jena, Hans-Knöll-Str. 2, 07745 Jena, Germany; Leibniz-Institute on Aging - Fritz Lipmann Institute (FLI), Beutenbergstrasse 11, 07745 Jena, Germany
| | - Hugo Filipe Rangel da Costa
- Institute of Biochemistry and Biophysics, Center for Molecular Biomedicine (CMB), Friedrich Schiller University Jena, Hans-Knöll-Str. 2, 07745 Jena, Germany
| | - Holger Bierhoff
- Institute of Biochemistry and Biophysics, Center for Molecular Biomedicine (CMB), Friedrich Schiller University Jena, Hans-Knöll-Str. 2, 07745 Jena, Germany; Leibniz-Institute on Aging - Fritz Lipmann Institute (FLI), Beutenbergstrasse 11, 07745 Jena, Germany.
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Li D, Wang J. Ribosome heterogeneity in stem cells and development. J Cell Biol 2020; 219:e202001108. [PMID: 32330234 PMCID: PMC7265316 DOI: 10.1083/jcb.202001108] [Citation(s) in RCA: 45] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2020] [Revised: 04/03/2020] [Accepted: 04/06/2020] [Indexed: 02/08/2023] Open
Abstract
Translation control is critical to regulate protein expression. By directly adjusting protein levels, cells can quickly respond to dynamic transitions during stem cell differentiation and embryonic development. Ribosomes are multisubunit cellular assemblies that mediate translation. Previously seen as invariant machines with the same composition of components in all conditions, recent studies indicate that ribosomes are heterogeneous and that different ribosome types can preferentially translate specific subsets of mRNAs. Such heterogeneity and specialized translation functions are very important in stem cells and development, as they allow cells to quickly respond to stimuli through direct changes of protein abundance. In this review, we discuss ribosome heterogeneity that arises from multiple features of rRNAs, including rRNA variants and rRNA modifications, and ribosomal proteins, including their stoichiometry, compositions, paralogues, and posttranslational modifications. We also discuss alterations of ribosome-associated proteins (RAPs), with a particular focus on their consequent specialized translational control in stem cells and development.
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Affiliation(s)
- Dan Li
- Department of Cell, Developmental and Regenerative Biology, The Black Family Stem Cell Institute, Icahn School of Medicine at Mount Sinai, New York, NY
- The Graduate School of Biomedical Sciences, Icahn School of Medicine at Mount Sinai, New York, NY
| | - Jianlong Wang
- Department of Cell, Developmental and Regenerative Biology, The Black Family Stem Cell Institute, Icahn School of Medicine at Mount Sinai, New York, NY
- The Graduate School of Biomedical Sciences, Icahn School of Medicine at Mount Sinai, New York, NY
- Department of Medicine, Columbia Center for Human Development, Columbia University Irving Medical Center, New York, NY
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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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Yildirim O, Izgu EC, Damle M, Chalei V, Ji F, Sadreyev RI, Szostak JW, Kingston RE. S-phase Enriched Non-coding RNAs Regulate Gene Expression and Cell Cycle Progression. Cell Rep 2020; 31:107629. [PMID: 32402276 PMCID: PMC7954657 DOI: 10.1016/j.celrep.2020.107629] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2019] [Revised: 02/20/2020] [Accepted: 04/20/2020] [Indexed: 12/13/2022] Open
Abstract
Many proteins that are needed for progression through S-phase are produced from transcripts that peak in the S-phase, linking temporal expression of those proteins to the time that they are required in cell cycle. Here, we explore the potential roles of long non-coding RNAs in cell cycle progression. We use a sensitive click-chemistry approach to isolate nascent RNAs in a human cell line, and we identify more than 900 long non-coding RNAs (lncRNAs) whose synthesis peaks during the S-phase. More than 200 of these are long intergenic non-coding RNAs (lincRNAs) with S-phase-specific expression. We characterize three of these lincRNAs by knockdown and find that all three lincRNAs are required for appropriate S-phase progression. We infer that non-coding RNAs are key regulatory effectors during the cell cycle, acting on distinct regulatory networks, and herein, we provide a large catalog of candidate cell-cycle regulatory RNAs.
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Affiliation(s)
- Ozlem Yildirim
- Department of Molecular Biology, Massachusetts General Hospital, Boston, MA 02114, USA; Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
| | - Enver C Izgu
- Department of Molecular Biology, Massachusetts General Hospital, Boston, MA 02114, USA; Department of Genetics, Harvard Medical School, Boston, MA 02115, USA; Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, NJ 08854, USA
| | - Manashree Damle
- Department of Molecular Biology, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Vladislava Chalei
- Department of Molecular Biology, Massachusetts General Hospital, Boston, MA 02114, USA; Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
| | - Fei Ji
- Department of Molecular Biology, Massachusetts General Hospital, Boston, MA 02114, USA; Department of Pathology, Massachusetts General Hospital and Harvard Medical School, Boston, MA 02114, USA
| | - Ruslan I Sadreyev
- Department of Molecular Biology, Massachusetts General Hospital, Boston, MA 02114, USA; Department of Pathology, Massachusetts General Hospital and Harvard Medical School, Boston, MA 02114, USA
| | - Jack W Szostak
- Department of Molecular Biology, Massachusetts General Hospital, Boston, MA 02114, USA; Department of Genetics, Harvard Medical School, Boston, MA 02115, USA; Center for Computational and Integrative Biology, Massachusetts General Hospital, Boston, MA 02114, USA; Howard Hughes Medical Institute, Chevy Chase, MD, USA
| | - Robert E Kingston
- Department of Molecular Biology, Massachusetts General Hospital, Boston, MA 02114, USA; Department of Genetics, Harvard Medical School, Boston, MA 02115, USA.
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50
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Kretova OV, Fedoseeva DM, Kravatsky YV, Klushevskaya ES, Alembekov IR, Slovohotov IY, Tchurikov NA. Contact Sites of rDNA Clusters with FANK1 Gene Correspond to Repressed Chromatin. Mol Biol 2020. [DOI: 10.1134/s0026893320020077] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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