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King MR, Ruff KM, Pappu RV. Emergent microenvironments of nucleoli. Nucleus 2024; 15:2319957. [PMID: 38443761 PMCID: PMC10936679 DOI: 10.1080/19491034.2024.2319957] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2023] [Accepted: 02/13/2024] [Indexed: 03/07/2024] Open
Abstract
In higher eukaryotes, the nucleolus harbors at least three sub-phases that facilitate multiple functionalities including ribosome biogenesis. The three prominent coexisting sub-phases are the fibrillar center (FC), the dense fibrillar component (DFC), and the granular component (GC). Here, we review recent efforts in profiling sub-phase compositions that shed light on the types of physicochemical properties that emerge from compositional biases and territorial organization of specific types of macromolecules. We highlight roles played by molecular grammars which refers to protein sequence features including the substrate binding domains, the sequence features of intrinsically disordered regions, and the multivalence of these distinct types of domains / regions. We introduce the concept of a barcode of emergent physicochemical properties of nucleoli. Although our knowledge of the full barcode remains incomplete, we hope that the concept prompts investigations into undiscovered emergent properties and engenders an appreciation for how and why unique microenvironments control biochemical reactions.
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Affiliation(s)
- Matthew R. King
- Department of Biomedical Engineering and Center for Biomolecular Condensates, Washington University in St. Louis, Campus, MO, USA
| | - Kiersten M. Ruff
- Department of Biomedical Engineering and Center for Biomolecular Condensates, Washington University in St. Louis, Campus, MO, USA
| | - Rohit V. Pappu
- Department of Biomedical Engineering and Center for Biomolecular Condensates, Washington University in St. Louis, Campus, MO, USA
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2
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Liao M, Cao J, Chen W, Wang M, Jin Z, Ye J, Ren Y, Wei Y, Xue Y, Chen D, Zhang Y, Chen S. HMGB1 prefers to interact with structural RNAs and regulates rRNA methylation modification and translation in HeLa cells. BMC Genomics 2024; 25:345. [PMID: 38580917 PMCID: PMC10996203 DOI: 10.1186/s12864-024-10204-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2023] [Accepted: 03/08/2024] [Indexed: 04/07/2024] Open
Abstract
BACKGROUND High-mobility group B1 (HMGB1) is both a DNA binding nuclear factor modulating transcription and a crucial cytokine that mediates the response to both infectious and noninfectious inflammation such as autoimmunity, cancer, trauma, and ischemia reperfusion injury. HMGB1 has been proposed to control ribosome biogenesis, similar as the other members of a class of HMGB proteins. RESULTS Here, we report that HMGB1 selectively promotes transcription of genes involved in the regulation of transcription, osteoclast differentiation and apoptotic process. Improved RNA immunoprecipitation by UV cross-linking and deep sequencing (iRIP-seq) experiment revealed that HMGB1 selectively bound to mRNAs functioning not only in signal transduction and gene expression, but also in axon guidance, focal adhesion, and extracellular matrix organization. Importantly, HMGB1-bound reads were strongly enriched in specific structured RNAs, including the domain II of 28S rRNA, H/ACA box snoRNAs including snoRNA63 and scaRNAs. RTL-P experiment showed that overexpression of HMGB1 led to a decreased methylation modification of 28S rRNA at position Am2388, Cm2409, and Gm2411. We further showed that HMGB1 overexpression increased ribosome RNA expression levels and enhanced protein synthesis. CONCLUSION Taken together, our results support a model in which HMGB1 binds to multiple RNA species in human cancer cells, which could at least partially contribute to HMGB1-modulated rRNA modification, protein synthesis function of ribosomes, and differential gene expression including rRNA genes. These findings provide additional mechanistic clues to HMGB1 functions in cancers and cell differentiation.
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Affiliation(s)
- Meimei Liao
- Department of Ultrasound Imaging, Renmin Hospital of Wuhan University, Hubei, Wuhan, People's Republic of China
| | - Jiarui Cao
- Department of Orthopedics, Renmin Hospital of Wuhan University, Hubei, Wuhan, People's Republic of China
| | - Wen Chen
- Center for Genome Analysis, ABLife Inc., Optics Valley International Biomedical Park, East Lake High-Tech Development Zone, 388 Gaoxin 2Nd Road, Hubei, Wuhan, 430075, China
- Laboratory for Genome Regulation and Human Health, ABLife Inc., Optics Valley International Biomedical Park, East Lake High-Tech Development Zone, 388 Gaoxin 2Nd Road, Hubei, Wuhan, 430075, China
| | - Mengwei Wang
- Department of Orthopedics, Renmin Hospital of Wuhan University, Hubei, Wuhan, People's Republic of China
| | - Zhihui Jin
- Department of Orthopedics, Renmin Hospital of Wuhan University, Hubei, Wuhan, People's Republic of China
| | - Jia Ye
- Department of Orthopedics, Renmin Hospital of Wuhan University, Hubei, Wuhan, People's Republic of China
| | - Yijun Ren
- Department of Orthopedics, Renmin Hospital of Wuhan University, Hubei, Wuhan, People's Republic of China
| | - Yaxun Wei
- Center for Genome Analysis, ABLife Inc., Optics Valley International Biomedical Park, East Lake High-Tech Development Zone, 388 Gaoxin 2Nd Road, Hubei, Wuhan, 430075, China
| | - Yaqiang Xue
- Center for Genome Analysis, ABLife Inc., Optics Valley International Biomedical Park, East Lake High-Tech Development Zone, 388 Gaoxin 2Nd Road, Hubei, Wuhan, 430075, China
- Laboratory for Genome Regulation and Human Health, ABLife Inc., Optics Valley International Biomedical Park, East Lake High-Tech Development Zone, 388 Gaoxin 2Nd Road, Hubei, Wuhan, 430075, China
| | - Dong Chen
- Center for Genome Analysis, ABLife Inc., Optics Valley International Biomedical Park, East Lake High-Tech Development Zone, 388 Gaoxin 2Nd Road, Hubei, Wuhan, 430075, China
- Laboratory for Genome Regulation and Human Health, ABLife Inc., Optics Valley International Biomedical Park, East Lake High-Tech Development Zone, 388 Gaoxin 2Nd Road, Hubei, Wuhan, 430075, China
| | - Yi Zhang
- Center for Genome Analysis, ABLife Inc., Optics Valley International Biomedical Park, East Lake High-Tech Development Zone, 388 Gaoxin 2Nd Road, Hubei, Wuhan, 430075, China
- Laboratory for Genome Regulation and Human Health, ABLife Inc., Optics Valley International Biomedical Park, East Lake High-Tech Development Zone, 388 Gaoxin 2Nd Road, Hubei, Wuhan, 430075, China
| | - Sen Chen
- Department of Orthopedics, Renmin Hospital of Wuhan University, Hubei, Wuhan, People's Republic of China.
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3
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Daiß JL, Griesenbeck J, Tschochner H, Engel C. Synthesis of the ribosomal RNA precursor in human cells: mechanisms, factors and regulation. Biol Chem 2023; 404:1003-1023. [PMID: 37454246 DOI: 10.1515/hsz-2023-0214] [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: 05/12/2023] [Accepted: 07/04/2023] [Indexed: 07/18/2023]
Abstract
The ribosomal RNA precursor (pre-rRNA) comprises three of the four ribosomal RNAs and is synthesized by RNA polymerase (Pol) I. Here, we describe the mechanisms of Pol I transcription in human cells with a focus on recent insights gained from structure-function analyses. The comparison of Pol I-specific structural and functional features with those of other Pols and with the excessively studied yeast system distinguishes organism-specific from general traits. We explain the organization of the genomic rDNA loci in human cells, describe the Pol I transcription cycle regarding structural changes in the enzyme and the roles of human Pol I subunits, and depict human rDNA transcription factors and their function on a mechanistic level. We disentangle information gained by direct investigation from what had apparently been deduced from studies of the yeast enzymes. Finally, we provide information about how Pol I mutations may contribute to developmental diseases, and why Pol I is a target for new cancer treatment strategies, since increased rRNA synthesis was correlated with rapidly expanding cell populations.
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Affiliation(s)
- Julia L Daiß
- Regensburg Center for Biochemistry, University of Regensburg, D-93053 Regensburg, Germany
| | - Joachim Griesenbeck
- Regensburg Center for Biochemistry, University of Regensburg, D-93053 Regensburg, Germany
| | - Herbert Tschochner
- Regensburg Center for Biochemistry, University of Regensburg, D-93053 Regensburg, Germany
| | - Christoph Engel
- Regensburg Center for Biochemistry, University of Regensburg, D-93053 Regensburg, Germany
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4
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Moss T, LeDoux MS, Crane-Robinson C. HMG-boxes, ribosomopathies and neurodegenerative disease. Front Genet 2023; 14:1225832. [PMID: 37600660 PMCID: PMC10435976 DOI: 10.3389/fgene.2023.1225832] [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: 05/19/2023] [Accepted: 07/19/2023] [Indexed: 08/22/2023] Open
Abstract
The UBTF E210K neuroregression syndrome is a predominantly neurological disorder caused by recurrent de novo dominant variants in Upstream Binding Factor, that is, essential for transcription of the ribosomal RNA genes. This unusual form of ribosomopathy is characterized by a slow decline in cognition, behavior, and sensorimotor functioning during the critical period of development. UBTF (or UBF) is a multi-HMGB-box protein that acts both as an epigenetic factor to establish "open" chromatin on the ribosomal genes and as a basal transcription factor in their RNA Polymerase I transcription. Here we review the possible mechanistic connections between the UBTF variants, ribosomal RNA gene transcription and the neuroregression syndrome, and suggest that DNA topology may play an important role.
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Affiliation(s)
- Tom Moss
- Laboratory of Growth and Development, St-Patrick Research Group in Basic Oncology, Cancer Division of the Quebec University Hospital Research Centre, Québec, QC, Canada
- Department of Molecular Biology, Medical Biochemistry and Pathology, Faculty of Medicine, Laval University, Québec, QC, Canada
| | - Mark S. LeDoux
- Department of Psychology, University of Memphis, Memphis, TN, United States
- Veracity Neuroscience LLC, Memphis, TN, United States
| | - Colyn Crane-Robinson
- Biophysics Laboratories, School of Biology, University of Portsmouth, Portsmouth, United Kingdom
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5
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Harold C. All these screens that we've done: how functional genetic screens have informed our understanding of ribosome biogenesis. Biosci Rep 2023; 43:BSR20230631. [PMID: 37335083 PMCID: PMC10329186 DOI: 10.1042/bsr20230631] [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: 04/09/2023] [Revised: 06/08/2023] [Accepted: 06/19/2023] [Indexed: 06/21/2023] Open
Abstract
Ribosome biogenesis is the complex and essential process that ultimately leads to the synthesis of cellular proteins. Understanding each step of this essential process is imperative to increase our understanding of basic biology, but also more critically, to provide novel therapeutic avenues for genetic and developmental diseases such as ribosomopathies and cancers which can arise when this process is impaired. In recent years, significant advances in technology have made identifying and characterizing novel human regulators of ribosome biogenesis via high-content, high-throughput screens. Additionally, screening platforms have been used to discover novel therapeutics for cancer. These screens have uncovered a wealth of knowledge regarding novel proteins involved in human ribosome biogenesis, from the regulation of the transcription of the ribosomal RNA to global protein synthesis. Specifically, comparing the discovered proteins in these screens showed interesting connections between large ribosomal subunit (LSU) maturation factors and earlier steps in ribosome biogenesis, as well as overall nucleolar integrity. In this review, a discussion of the current standing of screens for human ribosome biogenesis factors through the lens of comparing the datasets and discussing the biological implications of the areas of overlap will be combined with a look toward other technologies and how they can be adapted to discover more factors involved in ribosome synthesis, and answer other outstanding questions in the field.
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Affiliation(s)
- Cecelia M. Harold
- Department of Genetics, Yale School of Medicine, New Haven, CT, U.S.A
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6
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Dodero-Rojas E, Mello MF, Brahmachari S, Oliveira Junior AB, Contessoto VG, Onuchic JN. PyMEGABASE: Predicting cell-type-specific structural annotations of chromosomes using the epigenome. J Mol Biol 2023:168180. [PMID: 37302549 DOI: 10.1016/j.jmb.2023.168180] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2022] [Revised: 06/03/2023] [Accepted: 06/06/2023] [Indexed: 06/13/2023]
Abstract
The folding patterns of interphase genomes in higher eukaryotes, as obtained from DNA-proximity-ligation or Hi-C experiments, are used to classify loci into structural classes called compartments and subcompartments. These structurally annotated (sub)compartments are known to exhibit specific epigenomic characteristics and cell-type-specific variations. To explore the relationship between genome structure and the epigenome, we present PyMEGABASE (PYMB), a maximum-entropy-based neural network model that predicts (sub)compartment annotations of a locus based solely on the local epigenome, such as ChIP-Seq of histone post-translational modifications. PYMB builds upon our previous model while improving robustness, capability to handle diverse inputs and user-friendly implementation. We employed PYMB to predict subcompartments for over a hundred human cell types available in ENCODE, shedding light on the links between subcompartments, cell identity, and epigenomic signals. The fact that PYMB, trained on data for human cells, can accurately predict compartments in mice suggests that the model is learning underlying physicochemical principles transferable across cell types and species. Reliable at higher resolutions (up to 5 kbp), PYMB is used to investigate compartment-specific gene expression. Not only can PYMB generate (sub)compartment information without Hi-C experiments, but its predictions are also interpretable. Analyzing PYMB's trained parameters, we explore the importance of various epigenomic marks in each subcompartment prediction. Furthermore, the predictions of the model can be used as input for OpenMiChroM software, which has been calibrated to generate three-dimensional structures of the genome. Detailed documentation of PYMB is available at https://pymegabase.readthedocs.io, including an installation guide using pip or conda, and Jupyter/Colab notebook tutorials.
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Affiliation(s)
| | - Matheus F Mello
- Center for Theoretical Biological Physics, Rice University, Houston, TX, USA
| | | | | | | | - José N Onuchic
- Center for Theoretical Biological Physics, Rice University, Houston, TX, USA; Department of Physics & Astronomy, Rice University, Houston, TX, USA; Department of Chemistry, Rice University, Houston, TX, USA; Department of Biosciences, Rice University, Houston, TX, USA.
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7
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Casciaro M, Vincelli D, Ferraro M, Mirabile G, Pace E, Martino B, Tonacci A, Gangemi S, Pioggia G, Allegra A. The role of High-mobility group box-1 and Psoriasin in multiple myeloma: Analysis of a population affected by monoclonal gammopathies and review of the literature. Pathol Res Pract 2023; 247:154562. [PMID: 37216746 DOI: 10.1016/j.prp.2023.154562] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/06/2023] [Accepted: 05/18/2023] [Indexed: 05/24/2023]
Abstract
Multiple myeloma (MM) is a plasma cells neoplasm which is often preceded by a preneoplastic condition called monoclonal gammopathy of unknown significance (MGUS). A protein called High-mobility group box-1 (HMGB-1) controls transcription and genomic stability. Both pro- and anti-tumor properties of HMGB1 have been described during tumor growth. The S100 protein family includes a protein known as psoriasin. Poorer prognosis and survival were linked to higher psoriasin expression in cancer patients. The goal of the current investigation was to compare the plasma levels of HMGB-1 and psoriasin in patients with MM and MGUS significance, as well as in a group of healthy controls. According to our research, patients with MGUS have higher HMGHB-1 concentrations than healthy controls (846.7 ± 287.6 pg/ml vs. 176.9 ± 204.8 pg/ml for controls, p < 0.001). Similarly, we found a huge difference in HMGB-1 levels for MM patients with respect to controls (928.0 ± 551.4 pg/ml vs. 176.9 ± 204.8 pg/ml; p = 0.001). No difference was found as for the Psoriasin levels in the three groups considered. Additionally, we tried to evaluate the knowledge already present in the literature about putative mechanisms of action for these molecules in the onset and development of these disorders.
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Affiliation(s)
- Marco Casciaro
- Allergy and Clinical Immunology Unit, Department of Clinical and Experimental Medicine, University of Messina, 98125 Messina, Italy
| | - Donatella Vincelli
- Division of Hematology, Azienda Ospedaliera "Bianchi Melacrino Morelli", 89133 Reggio Calabria, Italy
| | - Maria Ferraro
- Institute of Traslational Pharmacology (IFT), National Research Council of Italy (CNR), 90146 Palermo, Italy
| | - Giuseppe Mirabile
- Division of Hematology, Department of Human Pathology in Adulthood and Childhood "Gaetano Barresi", University of Messina, 98125 Messina, Italy
| | - Elisabetta Pace
- Institute of Traslational Pharmacology (IFT), National Research Council of Italy (CNR), 90146 Palermo, Italy
| | - Bruno Martino
- Division of Hematology, Azienda Ospedaliera "Bianchi Melacrino Morelli", 89133 Reggio Calabria, Italy
| | - Alessandro Tonacci
- Institute of Clinical Physiology, National Research Council of Italy (IFC-CNR), Via G. Moruzzi 1, 56124 Pisa, Italy
| | - Sebastiano Gangemi
- Allergy and Clinical Immunology Unit, Department of Clinical and Experimental Medicine, University of Messina, 98125 Messina, Italy
| | - Giovanni Pioggia
- Institute for Biomedical Research and Innovation (IRIB), National Research Council of Italy (CNR), 98164 Messina, Italy
| | - Alessandro Allegra
- Division of Hematology, Department of Human Pathology in Adulthood and Childhood "Gaetano Barresi", University of Messina, 98125 Messina, Italy.
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8
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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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9
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Brown IN, Lafita-Navarro MC, Conacci-Sorrell M. Regulation of Nucleolar Activity by MYC. Cells 2022; 11:cells11030574. [PMID: 35159381 PMCID: PMC8834138 DOI: 10.3390/cells11030574] [Citation(s) in RCA: 6] [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: 01/07/2022] [Revised: 02/02/2022] [Accepted: 02/03/2022] [Indexed: 01/20/2023] Open
Abstract
The nucleolus harbors the machinery necessary to produce new ribosomes which are critical for protein synthesis. Nucleolar size, shape, and density are highly dynamic and can be adjusted to accommodate ribosome biogenesis according to the needs for protein synthesis. In cancer, cells undergo continuous proliferation; therefore, nucleolar activity is elevated due to their high demand for protein synthesis. The transcription factor and universal oncogene MYC promotes nucleolar activity by enhancing the transcription of ribosomal DNA (rDNA) and ribosomal proteins. This review summarizes the importance of nucleolar activity in mammalian cells, MYC’s role in nucleolar regulation in cancer, and discusses how a better understanding (and the potential inhibition) of aberrant nucleolar activity in cancer cells could lead to novel therapeutics.
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Affiliation(s)
- Isabella N. Brown
- Department of Cell Biology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA;
| | - M. Carmen Lafita-Navarro
- Department of Cell Biology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA;
- Correspondence: (M.C.L.-N.); (M.C.-S.)
| | - Maralice Conacci-Sorrell
- Department of Cell Biology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA;
- Hamon Center for Regenerative Science and Medicine, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
- Harold C. Simmons Comprehensive Cancer Center, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
- Correspondence: (M.C.L.-N.); (M.C.-S.)
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10
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Ribosomal RNA Transcription Regulation in Breast Cancer. Genes (Basel) 2021; 12:genes12040502. [PMID: 33805424 PMCID: PMC8066022 DOI: 10.3390/genes12040502] [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: 03/10/2021] [Revised: 03/26/2021] [Accepted: 03/29/2021] [Indexed: 12/24/2022] Open
Abstract
Ribosome biogenesis is a complex process that is responsible for the formation of ribosomes and ultimately global protein synthesis. The first step in this process is the synthesis of the ribosomal RNA in the nucleolus, transcribed by RNA Polymerase I. Historically, abnormal nucleolar structure is indicative of poor cancer prognoses. In recent years, it has been shown that ribosome biogenesis, and rDNA transcription in particular, is dysregulated in cancer cells. Coupled with advancements in screening technology that allowed for the discovery of novel drugs targeting RNA Polymerase I, this transcriptional machinery is an increasingly viable target for cancer therapies. In this review, we discuss ribosome biogenesis in breast cancer and the different cellular pathways involved. Moreover, we discuss current therapeutics that have been found to affect rDNA transcription and more novel drugs that target rDNA transcription machinery as a promising avenue for breast cancer treatment.
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11
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Analysis of the P 53N a Novel Protein Encoded on Chromosome 22q12.1-12.3 in Glioblastomas and Ependymomas Specimens. J Mol Neurosci 2021; 71:1714-1722. [PMID: 33595778 DOI: 10.1007/s12031-021-01808-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2020] [Accepted: 02/01/2021] [Indexed: 10/22/2022]
Abstract
The P53N gene maps precisely to human chromosome sub-band 22q12.1-12.3, a region where loss of heterozygosity has been reported in 30% of astrocytic tumors and associated with progression to anaplasia. Moreover, a putative tumor suppressor gene has been indicated on 22q11 region involved in pathogenesis of ependymal tumors. Our objectives to examine the expression level of novel membrane-associated protein (termed P53N) encoded by a novel human gene on chromosome 22q12.1-12.3 in glioblastomas and ependymomas. Serial analysis of gene expression (SAGE) and immunofluorescence analysis of the P53N in the brain tumor tissues were performed. Our analysis revealed that there was high expression of the P53N mRNA in brain ependymoma and brain well-differentiated astrocytoma libraries. The P53N protein. P53N protein contains a high mobility group (HMG) domain at amino acid positions 301 to 360 expressed highly in glioblastoma and ependymoma specimens. Anti-P53N carboxyl-terminal peptide antibody localized the P53N protein to the cytoplasmic membranes of protoplasmic astrocytes in the glioblastoma and ependymoma specimens. These results are in good agreement with the SAGE analysis and the predicted transmembrane topology for the P53N protein and support a possible transmembrane model in which the P53N contains a predicted transmembrane region with its amino terminus localized to the inside of the cytoplasmic membrane.
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12
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Wang S, Wong CC, Zhang Y, Huang J, Li C, Zhai J, Wang G, Wei H, Zhang X, He HH, Yu J. ZNF545 loss promotes ribosome biogenesis and protein translation to initiate colorectal tumorigenesis in mice. Oncogene 2021; 40:6590-6600. [PMID: 34615997 PMCID: PMC8639438 DOI: 10.1038/s41388-021-01938-8] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2020] [Revised: 06/21/2021] [Accepted: 07/01/2021] [Indexed: 11/25/2022]
Abstract
Ribosome biogenesis plays a pivotal role in tumorigenesis by supporting robust protein translation. We investigate the functional and molecular mechanism of Zinc finger protein 545 (ZNF545), a transcriptional repressor for ribosomal RNA (rRNA), in colorectal cancer (CRC). ZNF545 was silenced in CRC compared to adjacent normal tissues (P < 0.0001), implying a tumor-suppressive role. Colon-specific Znf545 knockout in mice accelerated CRC in ApcMin/+ and azoxymethane/dextran sulfate sodium-induced CRC. Mechanistically, we demonstrated that ZNF545 uses its two zinc finger clusters to bind to minimal rDNA promoter, where it assembled transcriptional repressor complex by interacting with KAP1. Znf545 deletion in mouse embryonic fibroblasts not only increased rRNA transcription rate and the nucleolar size and number but also altered the nucleolar composition and architecture with an increased number of fibrillar centers surrounded by net-like dense fibrillar components. Consequently, Znf545 deletion promoted the gene expression of translation machinery, protein translation, and cell growth. Consistent with its tumor-suppressive role, ZNF545 overexpression in CRC cells induced growth arrest and apoptosis. Finally, administration of rRNA synthesis inhibitor, CX-5461, inhibited CRC development in Znf545Δ/ΔApcMin/+ mice. In conclusion, ZNF545 suppresses CRC through repressing rRNA transcription and protein translation. Targeting rRNA biosynthesis in ZNF545-silenced tumors is a potential therapeutic strategy for CRC.
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Affiliation(s)
- Shiyan Wang
- grid.10784.3a0000 0004 1937 0482Institute of Digestive Disease and Department of Medicine and Therapeutics, State Key Laboratory of Digestive Disease, Li Ka Shing Institute of Health Sciences, CUHK-Shenzhen Research Institute, The Chinese University of Hong Kong, Hong Kong, China
| | - Chi Chun Wong
- grid.10784.3a0000 0004 1937 0482Institute of Digestive Disease and Department of Medicine and Therapeutics, State Key Laboratory of Digestive Disease, Li Ka Shing Institute of Health Sciences, CUHK-Shenzhen Research Institute, The Chinese University of Hong Kong, Hong Kong, China
| | - Yanquan Zhang
- grid.10784.3a0000 0004 1937 0482Institute of Digestive Disease and Department of Medicine and Therapeutics, State Key Laboratory of Digestive Disease, Li Ka Shing Institute of Health Sciences, CUHK-Shenzhen Research Institute, The Chinese University of Hong Kong, Hong Kong, China
| | - Junzhe Huang
- grid.10784.3a0000 0004 1937 0482Institute of Digestive Disease and Department of Medicine and Therapeutics, State Key Laboratory of Digestive Disease, Li Ka Shing Institute of Health Sciences, CUHK-Shenzhen Research Institute, The Chinese University of Hong Kong, Hong Kong, China
| | - Chuangen Li
- grid.10784.3a0000 0004 1937 0482Institute of Digestive Disease and Department of Medicine and Therapeutics, State Key Laboratory of Digestive Disease, Li Ka Shing Institute of Health Sciences, CUHK-Shenzhen Research Institute, The Chinese University of Hong Kong, Hong Kong, China
| | - Jianning Zhai
- grid.10784.3a0000 0004 1937 0482Institute of Digestive Disease and Department of Medicine and Therapeutics, State Key Laboratory of Digestive Disease, Li Ka Shing Institute of Health Sciences, CUHK-Shenzhen Research Institute, The Chinese University of Hong Kong, Hong Kong, China
| | - Guoping Wang
- grid.10784.3a0000 0004 1937 0482Institute of Digestive Disease and Department of Medicine and Therapeutics, State Key Laboratory of Digestive Disease, Li Ka Shing Institute of Health Sciences, CUHK-Shenzhen Research Institute, The Chinese University of Hong Kong, Hong Kong, China
| | - Hong Wei
- grid.12981.330000 0001 2360 039XPrecision Medicine Institute, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
| | - Xueji Zhang
- grid.263488.30000 0001 0472 9649School of Biomedical Engineering, Health Science Centre, Shenzhen University, Shenzhen, China
| | - Housheng Hansen He
- grid.17063.330000 0001 2157 2938Department of Medical Biophysics, Princess Margaret Cancer Centre, University Health Network, University of Toronto, Ontario, Canada
| | - Jun Yu
- grid.10784.3a0000 0004 1937 0482Institute of Digestive Disease and Department of Medicine and Therapeutics, State Key Laboratory of Digestive Disease, Li Ka Shing Institute of Health Sciences, CUHK-Shenzhen Research Institute, The Chinese University of Hong Kong, Hong Kong, China
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13
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Akishina AA, Kuvaeva EE, Vorontsova YE, Simonova OB. NAP Family Histone Chaperones: Characterization and Role in Ontogenesis. Russ J Dev Biol 2020. [DOI: 10.1134/s1062360420060028] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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14
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Justilien V, Lewis KC, Meneses KM, Jamieson L, Murray NR, Fields AP. Protein kinase Cι promotes UBF1-ECT2 binding on ribosomal DNA to drive rRNA synthesis and transformed growth of non-small-cell lung cancer cells. J Biol Chem 2020; 295:8214-8226. [PMID: 32350115 DOI: 10.1074/jbc.ra120.013175] [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: 02/21/2020] [Revised: 04/23/2020] [Indexed: 01/31/2023] Open
Abstract
Epithelial cell-transforming sequence 2 (ECT2) is a guanine nucleotide exchange factor for Rho GTPases that is overexpressed in many cancers and involved in signal transduction pathways that promote cancer cell proliferation, invasion, and tumorigenesis. Recently, we demonstrated that a significant pool of ECT2 localizes to the nucleolus of non-small-cell lung cancer (NSCLC) cells, where it binds the transcription factor upstream binding factor 1 (UBF1) on the promoter regions of ribosomal DNA (rDNA) and activates rDNA transcription, transformed cell growth, and tumor formation. Here, we investigated the mechanism by which ECT2 engages UBF1 on rDNA promoters. Results from ECT2 mutagenesis indicated that the tandem BRCT domain of ECT2 mediates binding to UBF1. Biochemical and MS-based analyses revealed that protein kinase Cι (PKCι) directly phosphorylates UBF1 at Ser-412, thereby generating a phosphopeptide-binding epitope that binds the ECT2 BRCT domain. Lentiviral shRNA knockdown and reconstitution experiments revealed that both a functional ECT2 BRCT domain and the UBF1 Ser-412 phosphorylation site are required for UBF1-mediated ECT2 recruitment to rDNA, elevated rRNA synthesis, and transformed growth. Our findings provide critical molecular insight into ECT2-mediated regulation of rDNA transcription in cancer cells and offer a rationale for therapeutic targeting of UBF1- and ECT2-stimulated rDNA transcription for the management of NSCLC.
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Affiliation(s)
- Verline Justilien
- Department of Cancer Biology, Mayo Clinic Comprehensive Cancer Center, Jacksonville, Florida, USA
| | - Kayla C Lewis
- Department of Cancer Biology, Mayo Clinic Comprehensive Cancer Center, Jacksonville, Florida, USA
| | - Kayleah M Meneses
- Department of Cancer Biology, Mayo Clinic Comprehensive Cancer Center, Jacksonville, Florida, USA
| | - Lee Jamieson
- Department of Cancer Biology, Mayo Clinic Comprehensive Cancer Center, Jacksonville, Florida, USA
| | - Nicole R Murray
- Department of Cancer Biology, Mayo Clinic Comprehensive Cancer Center, Jacksonville, Florida, USA
| | - Alan P Fields
- Department of Cancer Biology, Mayo Clinic Comprehensive Cancer Center, Jacksonville, Florida, USA
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15
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Ferreira R, Schneekloth JS, Panov KI, Hannan KM, Hannan RD. Targeting the RNA Polymerase I Transcription for Cancer Therapy Comes of Age. Cells 2020; 9:cells9020266. [PMID: 31973211 PMCID: PMC7072222 DOI: 10.3390/cells9020266] [Citation(s) in RCA: 84] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2019] [Revised: 01/14/2020] [Accepted: 01/15/2020] [Indexed: 12/24/2022] Open
Abstract
Transcription of the ribosomal RNA genes (rDNA) that encode the three largest ribosomal RNAs (rRNA), is mediated by RNA Polymerase I (Pol I) and is a key regulatory step for ribosomal biogenesis. Although it has been reported over a century ago that the number and size of nucleoli, the site of ribosome biogenesis, are increased in cancer cells, the significance of this observation for cancer etiology was not understood. The realization that the increase in rRNA expression has an active role in cancer progression, not only through increased protein synthesis and thus proliferative capacity but also through control of cellular check points and chromatin structure, has opened up new therapeutic avenues for the treatment of cancer through direct targeting of Pol I transcription. In this review, we discuss the rational of targeting Pol I transcription for the treatment of cancer; review the current cancer therapeutics that target Pol I transcription and discuss the development of novel Pol I-specific inhibitors, their therapeutic potential, challenges and future prospects.
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Affiliation(s)
- Rita Ferreira
- ACRF Department of Cancer Biology and Therapeutics, The John Curtin School of Medical Research, Australian National University, Acton 2601, NSW, Australia; (K.I.P.); (K.M.H.); (R.D.H.)
- Correspondence:
| | - John S. Schneekloth
- Chemical Biology Laboratory, Center for Cancer Research, National Cancer Institute, Frederick, MD 21702, USA;
| | - Konstantin I. Panov
- ACRF Department of Cancer Biology and Therapeutics, The John Curtin School of Medical Research, Australian National University, Acton 2601, NSW, Australia; (K.I.P.); (K.M.H.); (R.D.H.)
- CCRCB and School of Biological Sciences, Queen’s University Belfast Medical Biology Centre, School of Biological Sciences, Queen’s University Belfast, Belfast BT9 7BL, UK
| | - Katherine M. Hannan
- ACRF Department of Cancer Biology and Therapeutics, The John Curtin School of Medical Research, Australian National University, Acton 2601, NSW, Australia; (K.I.P.); (K.M.H.); (R.D.H.)
- Department of Biochemistry and Molecular Biology, University of Melbourne, Parkville, VIC 3010, Australia
| | - Ross D. Hannan
- ACRF Department of Cancer Biology and Therapeutics, The John Curtin School of Medical Research, Australian National University, Acton 2601, NSW, Australia; (K.I.P.); (K.M.H.); (R.D.H.)
- Department of Biochemistry and Molecular Biology, University of Melbourne, Parkville, VIC 3010, Australia
- Peter MacCallum Cancer Centre, 305 Grattan St, Melbourne, VIC 3000, Australia
- Department of Biochemistry and Molecular Biology, Monash University, Clayton, VIC 3800, Australia
- School of Biomedical Sciences, University of Queensland, Brisbane, QLD 4072, Australia
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16
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Gaviraghi M, Vivori C, Tonon G. How Cancer Exploits Ribosomal RNA Biogenesis: A Journey beyond the Boundaries of rRNA Transcription. Cells 2019; 8:cells8091098. [PMID: 31533350 PMCID: PMC6769540 DOI: 10.3390/cells8091098] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2019] [Revised: 09/13/2019] [Accepted: 09/15/2019] [Indexed: 02/06/2023] Open
Abstract
The generation of new ribosomes is a coordinated process essential to sustain cell growth. As such, it is tightly regulated according to cell needs. As cancer cells require intense protein translation to ensure their enhanced growth rate, they exploit various mechanisms to boost ribosome biogenesis. In this review, we will summarize how oncogenes and tumor suppressors modulate the biosynthesis of the RNA component of ribosomes, starting from the description of well-characterized pathways that converge on ribosomal RNA transcription while including novel insights that reveal unexpected regulatory networks hacked by cancer cells to unleash ribosome production.
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Affiliation(s)
- Marco Gaviraghi
- Experimental Imaging Center; Ospedale San Raffaele, 20132 Milan, Italy.
- Functional Genomics of Cancer Unit, Division of Experimental Oncology, Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS) San Raffaele Scientific Institute, 20132 Milan, Italy.
| | - Claudia Vivori
- Centre for Genomic Regulation (CRG), The Barcelona Institute for Science and Technology, 08003 Barcelona, Spain.
| | - Giovanni Tonon
- Functional Genomics of Cancer Unit, Division of Experimental Oncology, Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS) San Raffaele Scientific Institute, 20132 Milan, Italy.
- Center for Translational Genomics and Bioinformatics, Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS) San Raffaele Scientific Institute, 20132 Milan, Italy.
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17
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Mechanistic insights in transcription-coupled nucleotide excision repair of ribosomal DNA. Proc Natl Acad Sci U S A 2018; 115:E6770-E6779. [PMID: 29967171 DOI: 10.1073/pnas.1716581115] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Nucleotide excision repair (NER) guarantees genome integrity against UV light-induced DNA damage. After UV irradiation, cells have to cope with a general transcriptional block. To ensure UV lesions repair specifically on transcribed genes, NER is coupled with transcription in an extremely organized pathway known as transcription-coupled repair. In highly metabolic cells, more than 60% of total cellular transcription results from RNA polymerase I activity. Repair of the mammalian transcribed ribosomal DNA has been scarcely studied. UV lesions severely block RNA polymerase I activity and the full transcription-coupled repair machinery corrects damage on actively transcribed ribosomal DNAs. After UV irradiation, RNA polymerase I is more bound to the ribosomal DNA and both are displaced to the nucleolar periphery. Importantly, the reentry of RNA polymerase I and the ribosomal DNA is dependent on the presence of UV lesions on DNA and independent of transcription restart.
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18
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Sorrentino A, Rienzo M, Ciccodicola A, Casamassimi A, Abbondanza C. Human PRDM2: Structure, function and pathophysiology. BIOCHIMICA ET BIOPHYSICA ACTA. GENE REGULATORY MECHANISMS 2018; 1861:S1874-9399(18)30071-3. [PMID: 29883756 DOI: 10.1016/j.bbagrm.2018.06.002] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/15/2018] [Revised: 06/04/2018] [Accepted: 06/04/2018] [Indexed: 12/22/2022]
Abstract
PRDM2/RIZ is a member of a superfamily of histone/protein methyltransferases (PRDMs), which are characterized by the conserved N-terminal PR domain, with methyltransferase activity and zinc finger arrays at the C-terminus. Similar to other family members, two main protein types, known as RIZ1 and RIZ2, are produced from the PRDM2 locus differing by the presence or absence of the PR domain. The imbalance in their respective amounts may be an important cause of malignancy, with the PR-positive isoform commonly lost or downregulated and the PR-negative isoform always being present at higher levels in cancer cells. Interestingly, the RIZ1 isoform also represents an important target of estradiol action downstream of the interaction with hormone receptor. Furthermore, the imbalance between the two products could also be a molecular basis for other human diseases. Thus, understanding the molecular mechanisms underlying PRDM2 function could be useful in the pathophysiological context, with a potential to exploit this information in clinical practice.
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Affiliation(s)
- A Sorrentino
- Department of Precision Medicine, University of Campania "Luigi Vanvitelli", Naples, Italy; Department of Science and Technology, University of Naples "Parthenope", Naples, Italy
| | - M Rienzo
- Department of Environmental, Biological, and Pharmaceutical Sciences and Technologies, University of Campania "Luigi Vanvitelli", Caserta, Italy
| | - A Ciccodicola
- Department of Science and Technology, University of Naples "Parthenope", Naples, Italy; Institute of Genetics and Biophysics "Adriano Buzzati Traverso", CNR, Naples, Italy
| | - A Casamassimi
- Department of Precision Medicine, University of Campania "Luigi Vanvitelli", Naples, Italy
| | - C Abbondanza
- Department of Precision Medicine, University of Campania "Luigi Vanvitelli", Naples, Italy.
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19
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Li D, Zhang J, Wang M, Li X, Gong H, Tang H, Chen L, Wan L, Liu Q. Activity dependent LoNA regulates translation by coordinating rRNA transcription and methylation. Nat Commun 2018; 9:1726. [PMID: 29712923 PMCID: PMC5928123 DOI: 10.1038/s41467-018-04072-4] [Citation(s) in RCA: 60] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2017] [Accepted: 03/28/2018] [Indexed: 12/27/2022] Open
Abstract
The ribosome is indispensable for precisely controlling the capacity of protein synthesis. However, how translational machinery is coordinated to meet the translational demands remains elusive. Here, we identify a nucleolar-specific lncRNA (LoNA), its 5' portion binds and sequesters nucleolin to suppress rRNA transcription, and its snoRNA like 3' end recruits and diminishes fibrillarin activity to reduce rRNA methylation. Activity-dependent decrease of LoNA leads to elevated rRNA and ribosome levels, an increased proportion of polysomes, mRNA polysome loading, and protein translation. In addition, transport of ribosomes to synapses is particularly promoted, resulting in increased levels of AMPA/NMDA receptor, enhanced synaptic plasticity, long-term potentiation and consolidated memory. Strikingly, hippocampal LoNA deficiency not only enhances long-term memory in WT mice, but also restores impaired memory function in APP/PS1 transgenic mice. Together, these findings reveal the multifaceted role of LoNA in modulating ribosome biogenesis to meet the translational demands of long-term memory.
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MESH Headings
- 5' Untranslated Regions
- Amyloid beta-Protein Precursor/genetics
- Amyloid beta-Protein Precursor/metabolism
- Animals
- Cell Line, Tumor
- Chromosomal Proteins, Non-Histone/genetics
- Chromosomal Proteins, Non-Histone/metabolism
- Hippocampus/cytology
- Hippocampus/metabolism
- Long-Term Potentiation/genetics
- Memory, Long-Term/physiology
- Methylation
- Mice
- Mice, Inbred C57BL
- Mice, Transgenic
- Neurons/cytology
- Neurons/metabolism
- Phosphoproteins/genetics
- Phosphoproteins/metabolism
- Presenilin-1/genetics
- Presenilin-1/metabolism
- Protein Biosynthesis
- RNA, Long Noncoding/genetics
- RNA, Long Noncoding/metabolism
- RNA, Ribosomal/genetics
- RNA, Ribosomal/metabolism
- RNA, Small Nucleolar/genetics
- RNA, Small Nucleolar/metabolism
- RNA-Binding Proteins/genetics
- RNA-Binding Proteins/metabolism
- Receptors, AMPA/genetics
- Receptors, AMPA/metabolism
- Receptors, N-Methyl-D-Aspartate/genetics
- Receptors, N-Methyl-D-Aspartate/metabolism
- Ribosomes/genetics
- Ribosomes/metabolism
- Synapses/genetics
- Transgenes
- Nucleolin
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Affiliation(s)
- Dingfeng Li
- Hefei National Laboratory for Physical Sciences at the Microscale, School of Life Sciences, University of Science and Technology of China, Hefei, 230026, China
- CAS Key Laboratory of Brain Function and Disease, University of Science and Technology of China, Hefei, 230026, China
- Neurodegenerative Disease Research Center, University of Science and Technology of China, Hefei, 230026, China
| | - Juan Zhang
- Hefei National Laboratory for Physical Sciences at the Microscale, School of Life Sciences, University of Science and Technology of China, Hefei, 230026, China
- CAS Key Laboratory of Brain Function and Disease, University of Science and Technology of China, Hefei, 230026, China
- Neurodegenerative Disease Research Center, University of Science and Technology of China, Hefei, 230026, China
| | - Ming Wang
- Hefei National Laboratory for Physical Sciences at the Microscale, School of Life Sciences, University of Science and Technology of China, Hefei, 230026, China
- CAS Key Laboratory of Brain Function and Disease, University of Science and Technology of China, Hefei, 230026, China
| | - Xiaohui Li
- Hefei National Laboratory for Physical Sciences at the Microscale, School of Life Sciences, University of Science and Technology of China, Hefei, 230026, China
- CAS Key Laboratory of Brain Function and Disease, University of Science and Technology of China, Hefei, 230026, China
- Neurodegenerative Disease Research Center, University of Science and Technology of China, Hefei, 230026, China
| | - Huarui Gong
- Hefei National Laboratory for Physical Sciences at the Microscale, School of Life Sciences, University of Science and Technology of China, Hefei, 230026, China
- CAS Key Laboratory of Brain Function and Disease, University of Science and Technology of China, Hefei, 230026, China
| | - Huiping Tang
- Hefei National Laboratory for Physical Sciences at the Microscale, School of Life Sciences, University of Science and Technology of China, Hefei, 230026, China
- CAS Key Laboratory of Brain Function and Disease, University of Science and Technology of China, Hefei, 230026, China
| | - Lin Chen
- Hefei National Laboratory for Physical Sciences at the Microscale, School of Life Sciences, University of Science and Technology of China, Hefei, 230026, China
- CAS Key Laboratory of Brain Function and Disease, University of Science and Technology of China, Hefei, 230026, China
| | - Lili Wan
- Department of Biochemistry and Biophysics, Howard Hughes Medical Institute, School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Qiang Liu
- Hefei National Laboratory for Physical Sciences at the Microscale, School of Life Sciences, University of Science and Technology of China, Hefei, 230026, China.
- CAS Key Laboratory of Brain Function and Disease, University of Science and Technology of China, Hefei, 230026, China.
- Neurodegenerative Disease Research Center, University of Science and Technology of China, Hefei, 230026, China.
- National Synchrotron Radiation Laboratory, University of Science and Technology of China, Hefei, 230029, China.
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20
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HMGB proteins involved in TOR signaling as general regulators of cell growth by controlling ribosome biogenesis. Curr Genet 2018; 64:1205-1213. [PMID: 29713761 DOI: 10.1007/s00294-018-0842-8] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2018] [Revised: 04/21/2018] [Accepted: 04/24/2018] [Indexed: 12/14/2022]
Abstract
The number of ribosomes and their activity need to be highly regulated because their function is crucial for the cell. Ribosome biogenesis is necessary for cell growth and proliferation in accordance with nutrient availability and other external and intracellular signals. High-mobility group B (HMGB) proteins are conserved from yeasts to human and are decisive in cellular fate. These proteins play critical functions, from the maintenance of chromatin structure, DNA repair, or transcriptional regulation, to facilitation of ribosome biogenesis. They are also involved in cancer and other pathologies. In this review, we summarize evidence of how HMGB proteins contribute to ribosome-biogenesis control, with special emphasis on a common nexus to the target of rapamycin (TOR) pathway, a signaling cascade essential for cell growth and proliferation from yeast to human. Perspectives in this field are also discussed.
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21
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Maldonado R, Filarsky M, Grummt I, Längst G. Purine- and pyrimidine-triple-helix-forming oligonucleotides recognize qualitatively different target sites at the ribosomal DNA locus. RNA (NEW YORK, N.Y.) 2018; 24:371-380. [PMID: 29222118 PMCID: PMC5824356 DOI: 10.1261/rna.063800.117] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/29/2017] [Accepted: 11/30/2017] [Indexed: 05/04/2023]
Abstract
Triplexes are noncanonical DNA structures, which are functionally associated with regulation of gene expression through ncRNA targeting to chromatin. Based on the rules of Hoogsteen base-pairing, polypurine sequences of a duplex can potentially form triplex structures with single-stranded oligonucleotides. Prediction of triplex-forming sequences by bioinformatics analyses have revealed enrichment of potential triplex targeting sites (TTS) at regulatory elements, mainly in promoters and enhancers, suggesting a potential function of RNA-DNA triplexes in transcriptional regulation. Here, we have quantitatively evaluated the potential of different sequences of human and mouse ribosomal RNA genes (rDNA) to form triplexes at different salt and pH conditions. We show by biochemical and biophysical approaches that some of these predicted sequences form triplexes with high affinity, following the canonical rules for triplex formation. We further show that RNA triplex-forming oligos (TFOs) are more stable than their DNA counterpart, and point mutations strongly affect triplex formation. We further show differential sequence requirements of pyrimidine and purine TFO sequences for efficient binding, depending on the G-C content of the TTS. The unexpected sequence specificity, revealing distinct sequence requirements for purine and pyrimidine TFOs, shows that in addition to the Hoogsteen pairing rules, a sequence code and mutations have to be taken into account to predict genomic TTS.
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Affiliation(s)
- Rodrigo Maldonado
- Biochemistry Centre Regensburg (BCR), Universität Regensburg, 93053 Regensburg, Germany
| | - Michael Filarsky
- Biochemistry Centre Regensburg (BCR), Universität Regensburg, 93053 Regensburg, Germany
| | - Ingrid Grummt
- Division of Molecular Biology of the Cell II, German Cancer Research Center (DKFZ), DKFZ-ZMBH Alliance, 69120 Heidelberg, Germany
| | - Gernot Längst
- Biochemistry Centre Regensburg (BCR), Universität Regensburg, 93053 Regensburg, Germany
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22
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Toro C, Hori RT, Malicdan MCV, Tifft CJ, Goldstein A, Gahl WA, Adams DR, Fauni HB, Wolfe LA, Xiao J, Khan MM, Tian J, Hope KA, Reiter LT, Tremblay MG, Moss T, Franks AL, Balak C, LeDoux MS. A recurrent de novo missense mutation in UBTF causes developmental neuroregression. Hum Mol Genet 2018; 27:691-705. [PMID: 29300972 PMCID: PMC5886272 DOI: 10.1093/hmg/ddx435] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2017] [Revised: 11/29/2017] [Accepted: 12/19/2017] [Indexed: 12/17/2022] Open
Abstract
UBTF (upstream binding transcription factor) exists as two isoforms; UBTF1 regulates rRNA transcription by RNA polymerase 1, whereas UBTF2 regulates mRNA transcription by RNA polymerase 2. Herein, we describe 4 patients with very similar patterns of neuroregression due to recurrent de novo mutations in UBTF (GRCh37/hg19, NC_000017.10: g.42290219C > T, NM_014233.3: c.628G > A) resulting in the same amino acid change in both UBTF1 and UBTF2 (p.Glu210Lys [p.E210K]). Disease onset in our cohort was at 2.5 to 3 years and characterized by slow progression of global motor, cognitive and behavioral dysfunction. Notable early features included hypotonia with a floppy gait, high-pitched dysarthria and hyperactivity. Later features included aphasia, dystonia, and spasticity. Speech and ambulatory ability were lost by the early teens. Magnetic resonance imaging showed progressive generalized cerebral atrophy (supratentorial > infratentorial) with involvement of both gray and white matter. Patient fibroblasts showed normal levels of UBTF transcripts, increased expression of pre-rRNA and 18S rRNA, nucleolar abnormalities, markedly increased numbers of DNA breaks, defective cell-cycle progression, and apoptosis. Expression of mutant human UBTF1 in Drosophila neurons was lethal. Although no loss-of-function variants are reported in the Exome Aggregation Consortium (ExAC) database and Ubtf-/- is early embryonic lethal in mice, Ubtf+/- mice displayed only mild motor and behavioral dysfunction in adulthood. Our data underscore the importance of including UBTF E210K in the differential diagnosis of neuroregression and suggest that mainly gain-of-function mechanisms contribute to the pathogenesis of the UBTF E210K neuroregression syndrome.
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Affiliation(s)
- Camilo Toro
- Undiagnosed Diseases Program and Office of the Clinical Director, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
| | - Roderick T Hori
- Department of Microbiology, Immunology and Biochemistry, University of Tennessee Health Science Center, Memphis, TN, USA
| | - May Christine V Malicdan
- Undiagnosed Diseases Program and Office of the Clinical Director, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
| | - Cynthia J Tifft
- Undiagnosed Diseases Program and Office of the Clinical Director, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
| | - Amy Goldstein
- Division of Child Neurology, Department of Pediatrics, Children’s Hospital of Pittsburgh, Pittsburgh, PA, USA
| | - William A Gahl
- Undiagnosed Diseases Program and Office of the Clinical Director, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
| | - David R Adams
- Undiagnosed Diseases Program and Office of the Clinical Director, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
| | - Harper B Fauni
- Undiagnosed Diseases Program and Office of the Clinical Director, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
| | - Lynne A Wolfe
- Undiagnosed Diseases Program and Office of the Clinical Director, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
| | - Jianfeng Xiao
- Departments of Neurology and Anatomy & Neurobiology, University of Tennessee Health Science Center, Memphis, TN, USA
| | - Mohammad M Khan
- Departments of Neurology and Anatomy & Neurobiology, University of Tennessee Health Science Center, Memphis, TN, USA
| | - Jun Tian
- Departments of Neurology and Anatomy & Neurobiology, University of Tennessee Health Science Center, Memphis, TN, USA
| | - Kevin A Hope
- Integrated Program in Biological Sciences, University of Tennessee Health Science Center, Memphis, TN, USA
| | - Lawrence T Reiter
- Departments of Neurology and Anatomy & Neurobiology, University of Tennessee Health Science Center, Memphis, TN, USA
- Department of Pediatrics, University of Tennessee Health Science Center, Memphis, TN, USA
| | - Michel G Tremblay
- Laboratory of Growth and Development, St-Patrick Research Group in Basic Oncology, Cancer Division of the Quebec University Hospital Research Centre, Canada
- Department of Molecular Biology, Medical Biochemistry and Pathology, Faculty of Medicine, Laval University, QC, Canada
| | - Tom Moss
- Laboratory of Growth and Development, St-Patrick Research Group in Basic Oncology, Cancer Division of the Quebec University Hospital Research Centre, Canada
- Department of Molecular Biology, Medical Biochemistry and Pathology, Faculty of Medicine, Laval University, QC, Canada
| | - Alexis L Franks
- Division of Child Neurology, Department of Pediatrics, Children’s Hospital of Pittsburgh, Pittsburgh, PA, USA
| | - Chris Balak
- Center for Rare Childhood Disorders (C4RCD), Translational Genomics Research Institute (TGen), Phoenix, AZ, USA
| | - C4RCD Research Group
- Center for Rare Childhood Disorders (C4RCD), Translational Genomics Research Institute (TGen), Phoenix, AZ, USA
| | - Mark S LeDoux
- Departments of Neurology and Anatomy & Neurobiology, University of Tennessee Health Science Center, Memphis, TN, USA
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23
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Pfister AS, Kühl M. Of Wnts and Ribosomes. PROGRESS IN MOLECULAR BIOLOGY AND TRANSLATIONAL SCIENCE 2018; 153:131-155. [PMID: 29389514 DOI: 10.1016/bs.pmbts.2017.11.006] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Wnt proteins are secreted glycoproteins that activate different intracellular signal transduction pathways. They regulate cell proliferation and are required for proper embryonic development. Misregulation of Wnt signaling can result in various diseases including cancer. In most circumstances, cell growth is essential for cell division and thus cell proliferation. Therefore, several reports have highlighted the key role of Wnt proteins for cell growth. Ribosomes represent the cellular protein synthesis machinery and cells need to be equipped with an appropriate number of ribosomes to allow cell growth. Recent findings suggest a role for Wnt proteins in regulating ribosome biogenesis and we here summarize these findings representing a previously unknown function of Wnt proteins. Understanding this role of Wnt signaling might open new avenues to slow down proliferation by drugs for instance in cancer therapy.
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Affiliation(s)
- Astrid S Pfister
- Institute of Biochemistry and Molecular Biology, Ulm University, Ulm, Germany.
| | - Michael Kühl
- Institute of Biochemistry and Molecular Biology, Ulm University, Ulm, Germany
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Internal Associations of the Acidic Region of Upstream Binding Factor Control Its Nucleolar Localization. Mol Cell Biol 2017; 37:MCB.00218-17. [PMID: 28874518 DOI: 10.1128/mcb.00218-17] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2017] [Accepted: 08/25/2017] [Indexed: 01/24/2023] Open
Abstract
Upstream binding factor (UBF) is a member of the high-mobility group (HMG) box protein family, characterized by multiple HMG boxes and a C-terminal acidic region (AR). UBF is an essential transcription factor for rRNA genes and mediates the formation of transcriptionally active chromatin in the nucleolus. However, it remains unknown how UBF is specifically localized to the nucleolus. Here, we examined the molecular mechanisms that localize UBF to the nucleolus. We found that the first HMG box (HMG box 1), the linker region (LR), and the AR cooperatively regulate the nucleolar localization of UBF1. We demonstrated that the AR intramolecularly associates with and attenuates the DNA binding activity of HMG boxes and confers the structured DNA preference to HMG box 1. In contrast, the LR was found to serve as a nuclear localization signal and compete with HMG boxes to bind the AR, permitting nucleolar localization of UBF1. The LR sequence binds DNA and assists the stable chromatin binding of UBF. We also showed that the phosphorylation status of the AR does not clearly affect the localization of UBF1. Our results strongly suggest that associations of the AR with HMG boxes and the LR regulate UBF nucleolar localization.
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25
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Koopman P, Sinclair A, Lovell-Badge R. Of sex and determination: marking 25 years of Randy, the sex-reversed mouse. Development 2017; 143:1633-7. [PMID: 27190031 DOI: 10.1242/dev.137372] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2016] [Accepted: 03/21/2016] [Indexed: 12/31/2022]
Abstract
On Thursday 9 May 1991, the world awoke to front-page news of a breakthrough in biological research. From Washington to Wollongong, newspapers, radio and TV were abuzz with the story of a transgenic mouse in London called Randy. Why was this mouse so special? The mouse in question was a chromosomal female (XX) made male by the presence of a transgene containing the Y chromosome gene Sry This sex-reversal provided clear experimental proof that Sry was the elusive mammalian sex-determining gene. Twenty-five years on, we reflect on what this discovery meant for our understanding of how males and females arise and what remains to be understood.
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Affiliation(s)
- Peter Koopman
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, Queensland 4072, Australia
| | - Andrew Sinclair
- Murdoch Children's Research Institute and Department of Paediatrics, The University of Melbourne, Royal Children's Hospital, Melbourne, Victoria 3052, Australia
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26
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Wu M, Wei W, Chen J, Cong R, Shi T, Bouvet P, Li J, Wong J, Du JX. Acidic domains differentially read histone H3 lysine 4 methylation status and are widely present in chromatin-associated proteins. SCIENCE CHINA. LIFE SCIENCES 2017; 60:138-151. [PMID: 28194553 DOI: 10.1007/s11427-016-0413-3] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/26/2016] [Accepted: 01/09/2017] [Indexed: 02/03/2023]
Abstract
Histone methylation is believed to provide binding sites for specific reader proteins, which translate histone code into biological function. Here we show that a family of acidic domain-containing proteins including nucleophosmin (NPM1), pp32, SET/TAF1β, nucleolin (NCL) and upstream binding factor (UBF) are novel H3K4me2-binding proteins. These proteins exhibit a unique pattern of interaction with methylated H3K4, as their binding is stimulated by H3K4me2 and inhibited by H3K4me1 and H3K4me3. These proteins contain one or more acidic domains consisting mainly of aspartic and/or glutamic residues that are necessary for preferential binding of H3K4me2. Furthermore, we demonstrate that the acidic domain with sufficient length alone is capable of binding H3K4me2 in vitro and in vivo. NPM1, NCL and UBF require their acidic domains for association with and transcriptional activation of rDNA genes. Interestingly, by defining acidic domain as a sequence with at least 20 acidic residues in 50 continuous amino acids, we identified 655 acidic domain-containing protein coding genes in the human genome and Gene Ontology (GO) analysis showed that many of the acidic domain proteins have chromatin-related functions. Our data suggest that acidic domain is a novel histone binding motif that can differentially read the status of H3K4 methylation and is broadly present in chromatin-associated proteins.
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Affiliation(s)
- Meng Wu
- Shanghai Key Laboratory of Regulatory Biology, the Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Shanghai, 200241, China
| | - Wei Wei
- Shanghai Key Laboratory of Regulatory Biology, the Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Shanghai, 200241, China
| | - Jiwei Chen
- Shanghai Key Laboratory of Regulatory Biology, the Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Shanghai, 200241, China
| | - Rong Cong
- Université de Lyon, Ecole Normale Supérieure de Lyon, CNRS USR 3010, Laboratoire Joliot-Curie, Lyon, 69364, France
| | - Tieliu Shi
- Shanghai Key Laboratory of Regulatory Biology, the Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Shanghai, 200241, China
| | - Philippe Bouvet
- Université de Lyon, Ecole Normale Supérieure de Lyon, CNRS USR 3010, Laboratoire Joliot-Curie, Lyon, 69364, France
- Université de Lyon, Centre de Recherche en Cancérologie de Lyon, Cancer Cell Plasticity Department, UMR INSERM 1052 CNRS 5286, Centre Léon Bérard, Lyon, France
| | - Jiwen Li
- Shanghai Key Laboratory of Regulatory Biology, the Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Shanghai, 200241, China
| | - Jiemin Wong
- Shanghai Key Laboratory of Regulatory Biology, the Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Shanghai, 200241, China.
- Collaborative Innovation Center for Cancer Medicine, Sun Yat-Sen University Cancer Center, Guangzhou, 510060, China.
| | - James X Du
- Shanghai Key Laboratory of Regulatory Biology, the Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Shanghai, 200241, China.
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Kargı A, Demirpençe Ö, Gündüz Ş, Göktaş S, Alikanoǧlu AS, Yıldırım M. Serum levels of HMGB1 have a diagnostic role in metastatic renal cell cancer. Cancer Biomark 2017; 17:17-20. [PMID: 27062570 DOI: 10.3233/cbm-160611] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
RCC constitutes approximately 90% of all renal malignancies and 2-3% of all malignant tumours in adults. In spite of the improvement in radiologic methods, nearly 30% of the early metastatic RCC patients are incidentally diagnosed. HMGB1 is an extracellular signalling molecule that plays a role both in inflammation and carcinogenesis. Patients who were followed in Medical Oncology Departments of Denizli Government Hospital and Antalya Education and Research Hospital with a histopathological diagnosis of RCC between years 2010-2012 were enrolled in this study. HMGB1 levels were also assessed in a manually performed quantitative sandwich-enzyme-linked immunosorbent assay (ELISA) assay kit. In our study, we showed that the serum level of HMGB1, whether 149.9 pg/ml or not is important in differential diagnosis between patient and control group.
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28
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Gogoi B, Gogoi D, Silla Y, Kakoti BB, Bhau BS. Network pharmacology-based virtual screening of natural products from Clerodendrum species for identification of novel anti-cancer therapeutics. MOLECULAR BIOSYSTEMS 2017; 13:406-416. [DOI: 10.1039/c6mb00807k] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
In the present work, latest network pharmacological approach has been used for the screening of natural anticancer compounds from Clerodendrum species.
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Affiliation(s)
- Barbi Gogoi
- Plant Genomic Laboratory
- Medicinal Aromatic & Economic Plants (MAEP) Group
- Biological Sciences & Technology Division (BSTD)
- CSIR-North East Institute of Science and Technology
- Jorhat-785006
| | - Dhrubajyoti Gogoi
- DBT-BIF
- Centre for Biotechnology and Bioinformatics
- Dibrugarh University
- Dibrugarh
- India
| | - Yumnam Silla
- Biotechnology Group
- Biological Sciences & Technology Division (BSTD)
- CSIR-North East Institute of Science and Technology
- Jorhat-785006
- India
| | | | - Brijmohan Singh Bhau
- Plant Genomic Laboratory
- Medicinal Aromatic & Economic Plants (MAEP) Group
- Biological Sciences & Technology Division (BSTD)
- CSIR-North East Institute of Science and Technology
- Jorhat-785006
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29
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Cai S, Liu X, Zhang C, Xing B, Du X. Autoacetylation of NAT10 is critical for its function in rRNA transcription activation. Biochem Biophys Res Commun 2016; 483:624-629. [PMID: 27993683 DOI: 10.1016/j.bbrc.2016.12.092] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2016] [Accepted: 12/13/2016] [Indexed: 01/13/2023]
Abstract
NAT10, an important member of GNAT family, harbors histone acetyltransferase and participates in many cellular processes such as ribosome production and cell cycle. Here, we report that NAT10 is acetylated in vivo and autoacetylated in vitro. The lysine residue at 426 (K426) is the acetylation site of NAT10. K426R mutant of NAT10 fails to activate rRNA transcription. NAT10 K426R loses its capability of acetylating UBF though it still binds UBF, which fails to recruit PAF53 and RNA polymerase I to rDNA, eventually resulting in inhibition of pre-rRNA transcription. Therefore, acetylation of K426 in NAT10 is required for its function in activating rRNA transcription. These findings identify a new post-translational modification on NAT10 which regulates its function.
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Affiliation(s)
- Shiying Cai
- Department of Cell Biology, School of Basic Medical Sciences, Peking University Health Science Center, Beijing 100191, China
| | - Xiaofeng Liu
- Department of Cell Biology, School of Basic Medical Sciences, Peking University Health Science Center, Beijing 100191, China
| | - Chunfeng Zhang
- Department of Medical Genetics, School of Basic Medical Sciences, Peking University Health Science Center, Beijing 100191, China
| | - Baocai Xing
- Hepatopancreatobiliary Surgery Department I, Key Laboratory of Carcinogenesis and Translational Research, Ministry of Education, Peking University School of Oncology, Beijing Cancer Hospital and Institute, No. 52, Fu-Cheng Road, Beijing 100142, China
| | - Xiaojuan Du
- Department of Cell Biology, School of Basic Medical Sciences, Peking University Health Science Center, Beijing 100191, China.
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30
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Ugrinova I, Pasheva E. HMGB1 Protein: A Therapeutic Target Inside and Outside the Cell. ADVANCES IN PROTEIN CHEMISTRY AND STRUCTURAL BIOLOGY 2016; 107:37-76. [PMID: 28215228 DOI: 10.1016/bs.apcsb.2016.10.001] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
High-mobility group box 1 protein (HMGB1) is a nonhistone chromosomal protein discovered more than 30 years ago. It is an abundant nuclear protein that has a dual function-in the nucleus, it binds DNA and participates in practically all DNA-dependent processes serving as an architectural factor. Outside the cell, HMGB1 plays a different role-it acts as an alarmine that activates a large number of HMGB1-"competent" cells and mediates a broad range of physiological and pathological responses. This universality makes it an attractive target for innovative therapeutic strategies in the treatment of various diseases. Here we present an overview of the major nuclear and extracellular properties of HMGB1 and describe its interaction with different molecular partners as specific receptors or inhibitors, which are important for its role as a target in multiple diseases. We highlight its pivotal role as a target for cancer treatment at two aspects: first in terms of its substantial impact on the repair capacity of cancer cells, thus affecting the effectiveness of chemotherapy with the antitumor drug cis-platinum and, second, the possibility to be targeted by microRNAs influencing different pathways of human diseases, thus making it a promising candidate for a new strategy for therapeutic interventions against various pathological conditions but mainly cancer.
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Affiliation(s)
- I Ugrinova
- "Roumen Tsanev" Institute of Molecular Biology, Bulgarian Academy of Sciences, Sofia, Bulgaria.
| | - E Pasheva
- "Roumen Tsanev" Institute of Molecular Biology, Bulgarian Academy of Sciences, Sofia, Bulgaria
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31
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Neben CL, Lay FD, Mao X, Tuzon CT, Merrill AE. Ribosome biogenesis is dynamically regulated during osteoblast differentiation. Gene 2016; 612:29-35. [PMID: 27847259 DOI: 10.1016/j.gene.2016.11.010] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2016] [Revised: 11/04/2016] [Accepted: 11/07/2016] [Indexed: 01/19/2023]
Abstract
Changes in ribosome biogenesis are tightly linked to cell growth, proliferation, and differentiation. The rate of ribosome biogenesis is established by RNA Pol I-mediated transcription of ribosomal RNA (rRNA). Thus, rRNA gene transcription is a key determinant of cell behavior. Here, we show that ribosome biogenesis is dynamically regulated during osteoblast differentiation. Upon osteoinduction, osteoprogenitor cells transiently silence a subset of rRNA genes through a reversible mechanism that is initiated through biphasic nucleolar depletion of UBF1 and then RNA Pol I. Nucleolar depletion of UBF1 is coincident with an increase in the number of silent but transcriptionally permissible rRNA genes. This increase in the number of silent rRNA genes reduces levels of ribosome biogenesis and subsequently, protein synthesis. Together these findings demonstrate that fluctuations in rRNA gene transcription are determined by nucleolar occupancy of UBF1 and closely coordinated with the early events necessary for acquisition of the osteoblast cell fate.
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Affiliation(s)
- Cynthia L Neben
- Center for Craniofacial Molecular Biology, Ostrow School of Dentistry, University of Southern California, Los Angeles, CA 90033, United States; Department of Biochemistry and Molecular Biology, Keck School of Medicine, University of Southern California, Los Angeles, CA 90033, United States
| | - Fides D Lay
- Department of Biochemistry and Molecular Biology, Keck School of Medicine, University of Southern California, Los Angeles, CA 90033, United States
| | - Xiaojing Mao
- Center for Craniofacial Molecular Biology, Ostrow School of Dentistry, University of Southern California, Los Angeles, CA 90033, United States; Department of Biochemistry and Molecular Biology, Keck School of Medicine, University of Southern California, Los Angeles, CA 90033, United States
| | - Creighton T Tuzon
- Center for Craniofacial Molecular Biology, Ostrow School of Dentistry, University of Southern California, Los Angeles, CA 90033, United States; Department of Biochemistry and Molecular Biology, Keck School of Medicine, University of Southern California, Los Angeles, CA 90033, United States
| | - Amy E Merrill
- Center for Craniofacial Molecular Biology, Ostrow School of Dentistry, University of Southern California, Los Angeles, CA 90033, United States; Department of Biochemistry and Molecular Biology, Keck School of Medicine, University of Southern California, Los Angeles, CA 90033, United States.
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32
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Abstract
Post-translational modifications (PTMs) add regulatory features to proteins that help establish the complex functional networks that make up higher organisms. Advances in analytical detection methods have led to the identification of more than 200 types of PTMs. However, some modifications are unstable under the present detection methods, anticipating the existence of further modifications and a much more complex map of PTMs. An example is the recently discovered protein modification polyphosphorylation. Polyphosphorylation is mediated by inorganic polyphosphate (polyP) and represents the covalent attachment of this linear polymer of orthophosphate to lysine residues in target proteins. This modification has eluded MS analysis as both polyP itself and the phosphoramidate bonds created upon its reaction with lysine residues are highly unstable in acidic conditions. Polyphosphorylation detection was only possible through extensive biochemical characterization. Two targets have been identified: nuclear signal recognition 1 (Nsr1) and its interacting partner, topoisomerase 1 (Top1). Polyphosphorylation occurs within a conserved N-terminal polyacidic serine (S) and lysine (K) rich (PASK) cluster. It negatively regulates Nsr1-Top1 interaction and impairs Top1 enzymatic activity, namely relaxing supercoiled DNA. Modulation of cellular levels of polyP regulates Top1 activity by modifying its polyphosphorylation status. Here we discuss the significance of the recently identified new role of inorganic polyP.
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33
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Zhang Y, Najmi SM, Schneider DA. Transcription factors that influence RNA polymerases I and II: To what extent is mechanism of action conserved? BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2016; 1860:246-255. [PMID: 27989933 DOI: 10.1016/j.bbagrm.2016.10.010] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/05/2016] [Revised: 10/07/2016] [Accepted: 10/25/2016] [Indexed: 01/05/2023]
Abstract
In eukaryotic cells, nuclear RNA synthesis is accomplished by at least three unique, multisubunit RNA polymerases. The roles of these enzymes are generally partitioned into the synthesis of the three major classes of RNA: rRNA, mRNA, and tRNA for RNA polymerases I, II, and III respectively. Consistent with their unique cellular roles, each enzyme has a complement of specialized transcription factors and enzymatic properties. However, not all transcription factors have evolved to affect only one eukaryotic RNA polymerase. In fact, many factors have been shown to influence the activities of multiple nuclear RNA polymerases. This review focuses on a subset of these factors, specifically addressing the mechanisms by which these proteins influence RNA polymerases I and II.
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Affiliation(s)
- Yinfeng Zhang
- Department of Biochemistry and Molecular Genetics, University of Alabama at Birmingham, Birmingham, AL 35294
| | - Saman M Najmi
- Department of Biochemistry and Molecular Genetics, University of Alabama at Birmingham, Birmingham, AL 35294
| | - David A Schneider
- Department of Biochemistry and Molecular Genetics, University of Alabama at Birmingham, Birmingham, AL 35294
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Regulation of energy homeostasis by the ubiquitin-independent REGγ proteasome. Nat Commun 2016; 7:12497. [PMID: 27511885 PMCID: PMC4987533 DOI: 10.1038/ncomms12497] [Citation(s) in RCA: 49] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2016] [Accepted: 07/07/2016] [Indexed: 12/30/2022] Open
Abstract
Maintenance of energy homeostasis is essential for cell survival. Here, we report that the ATP- and ubiquitin-independent REGγ-proteasome system plays a role in maintaining energy homeostasis and cell survival during energy starvation via repressing rDNA transcription, a major intracellular energy-consuming process. Mechanistically, REGγ-proteasome limits cellular rDNA transcription and energy consumption by targeting the rDNA transcription activator SirT7 for ubiquitin-independent degradation under normal conditions. Moreover, energy starvation induces an AMPK-directed SirT7 phosphorylation and subsequent REGγ-dependent SirT7 subcellular redistribution and degradation, thereby further reducing rDNA transcription to save energy to overcome cell death. Energy starvation is a promising strategy for cancer therapy. Our report also shows that REGγ knockdown markedly improves the anti-tumour activity of energy metabolism inhibitors in mice. Our results underscore a control mechanism for an ubiquitin-independent process in maintaining energy homeostasis and cell viability under starvation conditions, suggesting that REGγ-proteasome inhibition has a potential to provide tumour-starving benefits. In conditions of energy stress cells reduce transcription of ribosomal RNA (rRNA) to maintain cell survival. Here, the authors show that energy stress induces an AMPK-dependent phosphorylation of Sirt7, which promotes its ubiquitin-independent degradation by REGγ, resulting in the down-regulation of rRNA transcription and cell survival.
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35
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Abstract
Nucleoli form around tandem arrays of a ribosomal gene repeat, termed nucleolar organizer regions (NORs). During metaphase, active NORs adopt a characteristic undercondensed morphology. Recent evidence indicates that the HMG-box-containing DNA-binding protein UBF (upstream binding factor) is directly responsible for this morphology and provides a mitotic bookmark to ensure rapid nucleolar formation beginning in telophase in human cells. This is likely to be a widely employed strategy, as UBF is present throughout metazoans. In higher eukaryotes, NORs are typically located within regions of chromosomes that form perinucleolar heterochromatin during interphase. Typically, the genomic architecture of NORs and the chromosomal regions within which they lie is very poorly described, yet recent evidence points to a role for context in their function. In Arabidopsis, NOR silencing appears to be controlled by sequences outside the rDNA (ribosomal DNA) array. Translocations reveal a role for context in the expression of the NOR on the X chromosome in Drosophila Recent work has begun on characterizing the genomic architecture of human NORs. A role for distal sequences located in perinucleolar heterochromatin has been inferred, as they exhibit a complex transcriptionally active chromatin structure. Links between rDNA genomic stability and aging in Saccharomyces cerevisiae are now well established, and indications are emerging that this is important in aging and replicative senescence in higher eukaryotes. This, combined with the fact that rDNA arrays are recombinational hot spots in cancer cells, has focused attention on DNA damage responses in NORs. The introduction of DNA double-strand breaks into rDNA arrays leads to a dramatic reorganization of nucleolar structure. Damaged rDNA repeats move from the nucleolar interior to form caps at the nucleolar periphery, presumably to facilitate repair, suggesting that the chromosomal context of human NORs contributes to their genomic stability. The inclusion of NORs and their surrounding chromosomal environments in future genome drafts now becomes a priority.
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Affiliation(s)
- Brian McStay
- Centre for Chromosome Biology, School of Natural Sciences, National University of Ireland, Galway, Ireland
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36
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Koné MC, Fleurot R, Chebrout M, Debey P, Beaujean N, Bonnet-Garnier A. Three-Dimensional Distribution of UBF and Nopp140 in Relationship to Ribosomal DNA Transcription During Mouse Preimplantation Development. Biol Reprod 2016; 94:95. [PMID: 26984997 DOI: 10.1095/biolreprod.115.136366] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2015] [Accepted: 03/08/2016] [Indexed: 12/31/2022] Open
Abstract
The nucleolus is a dynamic nuclear compartment that is mostly involved in ribosome subunit biogenesis; however, it may also play a role in many other biological processes, such as stress response and the cell cycle. Mainly using electron microscopy, several studies have tried to decipher how active nucleoli are set up during early development in mice. In this study, we analyzed nucleologenesis during mouse early embryonic development using 3D-immunofluorescent detection of UBF and Nopp140, two proteins associated with different nucleolar compartments. UBF is a transcription factor that helps maintain the euchromatic state of ribosomal genes; Nopp140 is a phosphoprotein that has been implicated in pre-rRNA processing. First, using detailed image analyses and the in situ proximity ligation assay technique, we demonstrate that UBF and Nopp140 dynamic redistribution between the two-cell and blastocyst stages (time of implantation) is correlated with morphological and structural modifications that occur in embryonic nucleolar compartments. Our results also support the hypothesis that nucleoli develop at the periphery of nucleolar precursor bodies. Finally, we show that the RNA polymerase I inhibitor CX-5461: 1) disrupts transcriptional activity, 2) alters preimplantation development, and 3) leads to a complete reorganization of UBF and Nopp140 distribution. Altogether, our results underscore that highly dynamic changes are occurring in the nucleoli of embryos and confirm a close link between ribosomal gene transcription and nucleologenesis during the early stages of development.
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Affiliation(s)
| | - Renaud Fleurot
- UMR BDR, INRA, ENVA, Université Paris Saclay, Jouy en Josas, France
| | - Martine Chebrout
- UMR BDR, INRA, ENVA, Université Paris Saclay, Jouy en Josas, France
| | - Pascale Debey
- Sorbonne-Universités, MNHN, CNRS, INSERM, Structure et instabilité des génomes, Paris, France
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Ouellet Lavallée G, Pearson A. Upstream binding factor inhibits herpes simplex virus replication. Virology 2015; 483:108-16. [PMID: 25965800 DOI: 10.1016/j.virol.2015.04.003] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2014] [Revised: 01/09/2015] [Accepted: 04/02/2015] [Indexed: 12/16/2022]
Abstract
Herpes simplex virus 1 (HSV-1) infection induces changes to the host cell nucleus including relocalization of the cellular protein Upstream Binding Factor (UBF) from the nucleolus to viral replication compartments (VRCs). Herein, we tested the hypothesis that UBF is recruited to VRCs to promote viral DNA replication. Surprisingly, infection of UBF-depleted HeLa cells with HSV-1 or HSV-2 produced higher viral titers compared to controls. Reduced expression of UBF also led to a progressive increase in the relative amount of HSV-1 DNA versus controls, and increased levels of HSV-1 ICP27 and TK mRNA and protein, regardless of whether viral DNA replication was inhibited or not. Our results suggest that UBF can inhibit gene expression from viral DNA prior to its replication. A similar but smaller effect on viral titers was observed in human foreskin fibroblasts. This is the first report of UBF having a restrictive effect on replication of a virus.
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Azevedo C, Livermore T, Saiardi A. Protein Polyphosphorylation of Lysine Residues by Inorganic Polyphosphate. Mol Cell 2015; 58:71-82. [DOI: 10.1016/j.molcel.2015.02.010] [Citation(s) in RCA: 80] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2014] [Revised: 12/02/2014] [Accepted: 02/03/2015] [Indexed: 10/23/2022]
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Thapar R. Structure-specific nucleic acid recognition by L-motifs and their diverse roles in expression and regulation of the genome. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2015; 1849:677-87. [PMID: 25748361 DOI: 10.1016/j.bbagrm.2015.02.006] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/18/2014] [Revised: 02/05/2015] [Accepted: 02/24/2015] [Indexed: 01/08/2023]
Abstract
The high-mobility group (HMG) domain containing proteins regulate transcription, DNA replication and recombination. They adopt L-shaped folds and are structure-specific DNA binding motifs. Here, I define the L-motif super-family that consists of DNA-binding HMG-box proteins and the L-motif of the histone mRNA binding domain of stem-loop binding protein (SLBP). The SLBP L-motif and HMG-box domains adopt similar L-shaped folds with three α-helices and two or three small hydrophobic cores that stabilize the overall fold, but have very different and distinct modes of nucleic acid recognition. A comparison of the structure, dynamics, protein-protein and nucleic acid interactions, and regulation by PTMs of the SLBP and the HMG-box L-motifs reveals the versatile and diverse modes by which L-motifs utilize their surfaces for structure-specific recognition of nucleic acids to regulate gene expression.
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Affiliation(s)
- Roopa Thapar
- BioSciences at Rice-Biochemistry and Cell Biology, Rice University, Houston, TX 77251-1892, USA.
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40
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The nucleolus—guardian of cellular homeostasis and genome integrity. Chromosoma 2014; 122:487-97. [PMID: 24022641 DOI: 10.1007/s00412-013-0430-0] [Citation(s) in RCA: 144] [Impact Index Per Article: 14.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2013] [Accepted: 08/05/2013] [Indexed: 01/25/2023]
Abstract
All organisms sense and respond to conditions that stress their homeostasis by downregulating the synthesis of rRNA and ribosome biogenesis, thus designating the nucleolus as the central hub in coordinating the cellular stress response. One of the most intriguing roles of the nucleolus, long regarded as a mere ribosome-producing factory, is its participation in monitoring cellular stress signals and transmitting them to the RNA polymerase I (Pol I) transcription machinery. As rRNA synthesis is a most energy-consuming process, switching off transcription of rRNA genes is an effective way of saving the energy required to maintain cellular homeostasis during acute stress. The Pol I transcription machinery is the key convergence point that collects and integrates a vast array of information from cellular signaling cascades to regulate ribosome production which, in turn, guides cell growth and proliferation. This review focuses on the mechanisms that link cell physiology to rDNA silencing, a prerequisite for nucleolar integrity and cell survival.
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Identification of temozolomide resistance factors in glioblastoma via integrative miRNA/mRNA regulatory network analysis. Sci Rep 2014; 4:5260. [PMID: 24919120 PMCID: PMC4052714 DOI: 10.1038/srep05260] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2014] [Accepted: 05/23/2014] [Indexed: 12/21/2022] Open
Abstract
Drug resistance is a major issue in the treatment of glioblastoma. Almost all glioblastomas are intrinsically resistant to chemotherapeutic temozolomide (TMZ) or develop resistance during treatment. The interaction networks of microRNAs (miRNAs) and mRNAs likely regulate most biological processes and can be employed to better understand complex processes including drug resistance in cancer. In this study, we examined if integrative miRNA/mRNA network analysis using the web-service tool mirConnX could be used to identify drug resistance factors in glioblastoma. We used TMZ-resistant glioblastoma cells and their integrated miRNA/mRNA networks to identify TMZ-sensitizing factors. TMZ resistance was previously induced in glioblastoma cell lines U87, Hs683, and LNZ308. miRNA/mRNA expression profiling of these cells and integration of the profiles using mirConnX resulted in the identification of plant homeodomain (PHD)-like finger 6 (PHF6) as a potential TMZ-sensitizing factor in resistant glioblastoma cells. Analysis of PHF6 expression showed significant upregulation in glioblastoma as compared to normal tissue. Interference with PHF6 expression in three TMZ-resistant subclones significantly enhanced TMZ-induced cell kill in two of these cell lines. Altogether, these results demonstrate that mirConnX is a feasible and useful tool to investigate miRNA/mRNA interactions in TMZ-resistant cells and has potential to identify drug resistance factors in glioblastoma.
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Süren D, Yıldırım M, Demirpençe Ö, Kaya V, Alikanoğlu AS, Bülbüller N, Yıldız M, Sezer C. The role of high mobility group box 1 (HMGB1) in colorectal cancer. Med Sci Monit 2014; 20:530-7. [PMID: 24681824 PMCID: PMC3976146 DOI: 10.12659/msm.890531] [Citation(s) in RCA: 55] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Background HMGB1, the most important member of the high mobility group box protein family, is a nuclear protein with different functions in the cell; it has a role in cancer progression, angiogenesis, invasion, and metastasis development. We studied the expression of HMGB1 and whether it is a prognostic factor in colorectal carcinoma. Material/Methods The study included 110 cases that were histopathologically diagnosed with colorectal carcinoma from the tissue samples acquired by surgical resection and biopsy in Antalya Education and Research Hospital between 2008 and 2012. HMGB1 expression was examined via immunohistochemical method. Results HMGB1 expression was evaluated as negative in 32 (44.4%) of the patients and as positive in 40 (55.6%) patients. There was no relation between the HMGB1 expression and sex, age, tumor invasion depth, and histological type. However, a significant relation was detected between the HMGB1 expression and lymph node status, metastasis status, and stage (p:<0.001, p:<0.001, p:<0.001, respectively). Similar results were obtained for the relations between the HMGB1 and histological grade, perineural invasion, lymphovascular invasion, and lymphocytic response (p<0.001, p<0.001, p<0.001, and p<0.001, respectively). Conclusions The results of our study demonstrate that HMGB1 overexpression has a significant role in tumor progression (especially migration of tumor cells) and tumor ability to metastasize in colorectal cancers; thus, it corroborates the idea that it might be an important prognostic factor.
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Affiliation(s)
- Dinç Süren
- Department of Medical Oncology, Ministry of Health Batman Regional Government Hospital, Batman, Turkey
| | - Mustafa Yıldırım
- Department of Pathology, Antalya Education and Research Hospital, Antalya, Turkey
| | - Özlem Demirpençe
- Department of Biochemistry, Dicle University, Medical Faculty, Diyarbakır, Turkey
| | - Vildan Kaya
- Department of Radiation Oncology, Süleyman Demirel University, Medical Faculty, Isparta, Turkey
| | | | - Nurullah Bülbüller
- Department of General Surgey, Antalya Education and Research Hospital, Antalya, Turkey
| | - Mustafa Yıldız
- Department of Medical Oncology, Antalya Education and Research Hospital, Antalya, Turkey
| | - Cem Sezer
- Department of Pathology, Antalya Education and Research Hospital, Antalya, Turkey
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Grob A, McStay B. Construction of synthetic nucleoli and what it tells us about propagation of sub-nuclear domains through cell division. Cell Cycle 2014; 13:2501-8. [PMID: 25486191 PMCID: PMC4614152 DOI: 10.4161/15384101.2014.949124] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2014] [Revised: 07/16/2014] [Accepted: 07/16/2014] [Indexed: 11/19/2022] Open
Abstract
The cell nucleus is functionally compartmentalized into numerous membraneless and dynamic, yet defined, bodies. The cell cycle inheritance of these nuclear bodies (NBs) is poorly understood at the molecular level. In higher eukaryotes, their propagation is challenged by cell division through an "open" mitosis, where the nuclear envelope disassembles along with most NBs. A deeper understanding of the mechanisms involved can be achieved using the engineering principles of synthetic biology to construct artificial NBs. Successful biogenesis of such synthetic NBs demonstrates knowledge of the basic mechanisms involved. Application of this approach to the nucleolus, a paradigm of nuclear organization, has highlighted a key role for mitotic bookmarking in the cell cycle propagation of NBs.
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Key Words
- 1°, primary
- 2°, secondary
- CBs, Cajal bodies
- CDK, cyclin-dependent kinase
- DFC, dense fibrillar component
- DJ, distal junction
- FCs, fibrillar centers
- GC, granular component
- HLBs, histone locus bodies
- HMG, high mobility group
- IGS, intergenic spacers
- NBs, nuclear bodies
- NORs, nucleolar organizer regions
- Nucleolar Organizer Region (NOR)
- PJ, proximal junction
- PML, promyelocytic leukemia
- PNBs, pre-nucleolar bodies
- TFs, transcription factors
- UBF
- UBF, Upstream binding factor
- XEn, Xenopus enhancer
- cell cycle
- mitotic bookmarking
- neo-NOR
- neonucleoli
- nuclear bodies
- nucleolus
- pol, RNA polymerase
- pre-rRNA, precursor rRNA
- pseudo-NOR
- rDNA, ribosomal genes
- rRNA, ribosomal RNA; RNP, ribonucleoprotein
- synthetic biology
- t-UTPs, transcription U 3 proteins
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Affiliation(s)
- Alice Grob
- Center for Chromosome Biology; School of Natural Sciences; National University of Ireland; Galway, Ireland
| | - Brian McStay
- Center for Chromosome Biology; School of Natural Sciences; National University of Ireland; Galway, Ireland
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Tsoi H, Chan HYE. Roles of the nucleolus in the CAG RNA-mediated toxicity. Biochim Biophys Acta Mol Basis Dis 2013; 1842:779-84. [PMID: 24269666 DOI: 10.1016/j.bbadis.2013.11.015] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2013] [Revised: 11/12/2013] [Accepted: 11/13/2013] [Indexed: 10/26/2022]
Abstract
The nucleolus is a subnuclear compartment within the cell nucleus that serves as the site for ribosomal RNA (rRNA) transcription and the assembly of ribosome subunits. Apart from its classical role in ribosomal biogenesis, a number of cellular regulatory roles have recently been assigned to the nucleolus, including governing the induction of apoptosis. "Nucleolar stress" is a term that is used to describe a signaling pathway through which the nucleolus communicates with other subcellular compartments, including the mitochondria, to induce apoptosis. It is an effective mechanism for eliminating cells that are incapable of performing protein synthesis efficiently due to ribosome biogenesis defects. The down-regulation of rRNA transcription is a common cause of nucleolar function disruption that subsequently triggers nucleolar stress, and has been associated with the pathogenesis of neurological disorders such as spinocerebellar ataxias (SCAs) and Huntington's diseases (HD). This article discusses recent advances in mechanistic studies of how expanded CAG trinucleotide repeat RNA transcripts trigger nucleolar stress in SCAs, HD and other trinucleotide repeat disorders. This article is part of a Special Issue entitled: Role of the Nucleolus in Human Disease.
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Affiliation(s)
- Ho Tsoi
- Laboratory of Drosophila Research, School of Life Sciences, Faculty of Science, The Chinese University of Hong Kong, Shatin, N.T., Hong Kong, China; Biochemistry Program, School of Life Sciences, Faculty of Science, The Chinese University of Hong Kong, Shatin, N.T., Hong Kong, China
| | - Ho Yin Edwin Chan
- Laboratory of Drosophila Research, School of Life Sciences, Faculty of Science, The Chinese University of Hong Kong, Shatin, N.T., Hong Kong, China; Biochemistry Program, School of Life Sciences, Faculty of Science, The Chinese University of Hong Kong, Shatin, N.T., Hong Kong, China; Cell and Molecular Biology Program, School of Life Sciences, Faculty of Science, The Chinese University of Hong Kong, Shatin, N.T., Hong Kong, China; Molecular Biotechnology Program, School of Life Sciences, Faculty of Science, The Chinese University of Hong Kong, Shatin, N.T., Hong Kong, China.
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Ait Benkhali J, Coppin E, Brun S, Peraza-Reyes L, Martin T, Dixelius C, Lazar N, van Tilbeurgh H, Debuchy R. A network of HMG-box transcription factors regulates sexual cycle in the fungus Podospora anserina. PLoS Genet 2013; 9:e1003642. [PMID: 23935511 PMCID: PMC3730723 DOI: 10.1371/journal.pgen.1003642] [Citation(s) in RCA: 47] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2012] [Accepted: 06/03/2013] [Indexed: 12/14/2022] Open
Abstract
High-mobility group (HMG) B proteins are eukaryotic DNA-binding proteins characterized by the HMG-box functional motif. These transcription factors play a pivotal role in global genomic functions and in the control of genes involved in specific developmental or metabolic pathways. The filamentous ascomycete Podospora anserina contains 12 HMG-box genes. Of these, four have been previously characterized; three are mating-type genes that control fertilization and development of the fruit-body, whereas the last one encodes a factor involved in mitochondrial DNA stability. Systematic deletion analysis of the eight remaining uncharacterized HMG-box genes indicated that none were essential for viability, but that seven were involved in the sexual cycle. Two HMG-box genes display striking features. PaHMG5, an ortholog of SpSte11 from Schizosaccharomyces pombe, is a pivotal activator of mating-type genes in P. anserina, whereas PaHMG9 is a repressor of several phenomena specific to the stationary phase, most notably hyphal anastomoses. Transcriptional analyses of HMG-box genes in HMG-box deletion strains indicated that PaHMG5 is at the hub of a network of several HMG-box factors that regulate mating-type genes and mating-type target genes. Genetic analyses revealed that this network also controls fertility genes that are not regulated by mating-type transcription factors. This study points to the critical role of HMG-box members in sexual reproduction in fungi, as 11 out of 12 members were involved in the sexual cycle in P. anserina. PaHMG5 and SpSte11 are conserved transcriptional regulators of mating-type genes, although P. anserina and S. pombe diverged 550 million years ago. Two HMG-box genes, SOX9 and its upstream regulator SRY, also play an important role in sex determination in mammals. The P. anserina and S. pombe mating-type genes and their upstream regulatory factor form a module of HMG-box genes analogous to the SRY/SOX9 module, revealing a commonality of sex regulation in animals and fungi. Podospora anserina, a coprophilous fungus, is used extensively as a model organism to address questions of sexual development and mating-type functions. Its mating-type locus contains three HMGB genes that encode transcription factors involved in fertilization and fruit-body development. We present the functional characterization of the remaining HMGB genes, which revealed that 11 of 12 HMGB genes were involved in sexual development. An analysis of the relationships between these genes uncovered a regulatory network governing the expression of mating-type genes. PaHMG5 is a key transcription factor that operates upstream of mating-type genes in this network. A homolog of PaHMG5 performs a similar function in the fission yeast Schizosaccharomyces pombe, which diverged from P. anserina 550 million years ago. The conservation of a regulatory circuit over such a prolonged timeframe is a striking exception to the general observation that sex developmental pathways are highly variable, even across closely related lineages. A module consisting of two HMGB transcription factors (Sry and Sox9) is a key regulator of sex determination in mammals. We propose that the module containing PaHMG5 and mating-type HMGB genes is the fungal counterpart of the mammalian module, revealing a commonality of sex regulation in animals and fungi.
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Affiliation(s)
- Jinane Ait Benkhali
- Université Paris-Sud, Institut de Génétique et Microbiologie UMR8621, Orsay, France
- CNRS, Institut de Génétique et Microbiologie UMR8621, Orsay, France
| | - Evelyne Coppin
- Université Paris-Sud, Institut de Génétique et Microbiologie UMR8621, Orsay, France
- CNRS, Institut de Génétique et Microbiologie UMR8621, Orsay, France
| | - Sylvain Brun
- Université Paris-Sud, Institut de Génétique et Microbiologie UMR8621, Orsay, France
- CNRS, Institut de Génétique et Microbiologie UMR8621, Orsay, France
- Université Paris Diderot, Sorbonne Paris Cité, Institut des Energies de Demain (IED), Paris, France
| | - Leonardo Peraza-Reyes
- Université Paris-Sud, Institut de Génétique et Microbiologie UMR8621, Orsay, France
- CNRS, Institut de Génétique et Microbiologie UMR8621, Orsay, France
| | - Tom Martin
- Department of Plant Biology and Forest Genetics, Uppsala BioCenter, Swedish University of Agricultural Sciences and Linnean Center for Plant Biology, Uppsala, Sweden
| | - Christina Dixelius
- Department of Plant Biology and Forest Genetics, Uppsala BioCenter, Swedish University of Agricultural Sciences and Linnean Center for Plant Biology, Uppsala, Sweden
| | - Noureddine Lazar
- Université Paris-Sud, Institut de Biochimie et de Biophysique Moléculaire et Cellulaire, UMR8619, Orsay, France
| | - Herman van Tilbeurgh
- Université Paris-Sud, Institut de Biochimie et de Biophysique Moléculaire et Cellulaire, UMR8619, Orsay, France
| | - Robert Debuchy
- Université Paris-Sud, Institut de Génétique et Microbiologie UMR8621, Orsay, France
- CNRS, Institut de Génétique et Microbiologie UMR8621, Orsay, France
- * E-mail:
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Valdez BC, Henning D, Zhu L, Stetler DA. Silver ( AgNOR) Staining of Nucleolar Transcription Factor UBF Requires Adjacent Aspartic Acid Residues. J Histotechnol 2013. [DOI: 10.1179/his.1998.21.1.13] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/31/2022]
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Melatonin Suppresses the Expression of 45S Preribosomal RNA and Upstream Binding Factor and Enhances the Antitumor Activity of Puromycin in MDA-MB-231 Breast Cancer Cells. EVIDENCE-BASED COMPLEMENTARY AND ALTERNATIVE MEDICINE 2013; 2013:879746. [PMID: 23690862 PMCID: PMC3638601 DOI: 10.1155/2013/879746] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/12/2013] [Revised: 03/07/2013] [Accepted: 03/07/2013] [Indexed: 02/08/2023]
Abstract
Since the dysregulation of ribosome biogenesis is closely associated with tumor progression, in the current study, the critical role of ribosome biogenesis related signaling was investigated in melatonin and/or puromycin induced apoptosis in MDA-MB-231 breast cancer cells. Despite its weak cytotoxicity, melatonin from 3 mM attenuated the expression of 45S pre-ribosomal RNA (pre-rRNA), UBF as a nucleolar transcription factor, and fibrillarin at mRNA level and consistently downregulated nucleolar proteins such as UBF and fibrillarin at protein level in MDA-MB-231 cells. Furthermore, immunofluorescence assay revealed that UBF was also degraded by melatonin in MDA-MB-231 cells. In contrast, melatonin attenuated the expression of survival genes such as Bcl-xL, Mcl-1, cyclinD1, and cyclin E, suppressed the phosphorylation of AKT, mTOR, and STAT3, and cleaved PARP and activated caspase 3 only at a high concentration of 12 mM. However, combined treatment of melatonin (3 mM) and puromycin (1 μM) synergistically inhibited viability, attenuated the expression of 45S pre-rRNA and UBF, and consistently downregulated UBF, XPO1 and IPO7, procaspase 3, and Bcl-xL in MDA-MB 231 cells. Overall, these findings suggest that melatonin can be a cancer preventive agent by combination with puromycin via the inhibition of 45S pre-rRNA and UBF in MDA-MB 231 breast cancer cells.
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Stepanchick A, Zhi H, Cavanaugh AH, Rothblum K, Schneider DA, Rothblum LI. DNA binding by the ribosomal DNA transcription factor rrn3 is essential for ribosomal DNA transcription. J Biol Chem 2013; 288:9135-44. [PMID: 23393135 DOI: 10.1074/jbc.m112.444265] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The human homologue of yeast Rrn3 is an RNA polymerase I-associated transcription factor that is essential for ribosomal DNA (rDNA) transcription. The generally accepted model is that Rrn3 functions as a bridge between RNA polymerase I and the transcription factors bound to the committed template. In this model Rrn3 would mediate an interaction between the mammalian Rrn3-polymerase I complex and SL1, the rDNA transcription factor that binds to the core promoter element of the rDNA. In the course of studying the role of Rrn3 in recruitment, we found that Rrn3 was in fact a DNA-binding protein. Analysis of the sequence of Rrn3 identified a domain with sequence similarity to the DNA binding domain of heat shock transcription factor 2. Randomization, or deletion, of the amino acids in this region in Rrn3, amino acids 382-400, abrogated its ability to bind DNA, indicating that this domain was an important contributor to DNA binding by Rrn3. Control experiments demonstrated that these mutant Rrn3 constructs were capable of interacting with both rpa43 and SL1, two other activities demonstrated to be essential for Rrn3 function. However, neither of these Rrn3 mutants was capable of functioning in transcription in vitro. Moreover, although wild-type human Rrn3 complemented a yeast rrn3-ts mutant, the DNA-binding site mutant did not. These results demonstrate that DNA binding by Rrn3 is essential for transcription by RNA polymerase I.
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Affiliation(s)
- Ann Stepanchick
- Sigfried and Janet Weis Center for Research, Geisinger Clinic, Danville, PA 17821, USA
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Hamperl S, Wittner M, Babl V, Perez-Fernandez J, Tschochner H, Griesenbeck J. Chromatin states at ribosomal DNA loci. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2013; 1829:405-17. [PMID: 23291532 DOI: 10.1016/j.bbagrm.2012.12.007] [Citation(s) in RCA: 52] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/07/2012] [Revised: 11/16/2012] [Accepted: 12/21/2012] [Indexed: 12/29/2022]
Abstract
Eukaryotic transcription of ribosomal RNAs (rRNAs) by RNA polymerase I can account for more than half of the total cellular transcripts depending on organism and growth condition. To support this level of expression, eukaryotic rRNA genes are present in multiple copies. Interestingly, these genes co-exist in different chromatin states that may differ significantly in their nucleosome content and generally correlate well with transcriptional activity. Here we review how these chromatin states have been discovered and characterized focusing particularly on their structural protein components. The establishment and maintenance of rRNA gene chromatin states and their impact on rRNA synthesis are discussed. This article is part of a Special Issue entitled: Transcription by Odd Pols.
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Affiliation(s)
- Stephan Hamperl
- Lehrstuhl Biochemie III, Universität Regensburg, 93053 Regensburg, Germany
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Goodfellow SJ, Zomerdijk JCBM. Basic mechanisms in RNA polymerase I transcription of the ribosomal RNA genes. Subcell Biochem 2013; 61:211-36. [PMID: 23150253 PMCID: PMC3855190 DOI: 10.1007/978-94-007-4525-4_10] [Citation(s) in RCA: 120] [Impact Index Per Article: 10.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
RNA Polymerase (Pol) I produces ribosomal (r)RNA, an essential component of the cellular protein synthetic machinery that drives cell growth, underlying many fundamental cellular processes. Extensive research into the mechanisms governing transcription by Pol I has revealed an intricate set of control mechanisms impinging upon rRNA production. Pol I-specific transcription factors guide Pol I to the rDNA promoter and contribute to multiple rounds of transcription initiation, promoter escape, elongation and termination. In addition, many accessory factors are now known to assist at each stage of this transcription cycle, some of which allow the integration of transcriptional activity with metabolic demands. The organisation and accessibility of rDNA chromatin also impinge upon Pol I output, and complex mechanisms ensure the appropriate maintenance of the epigenetic state of the nucleolar genome and its effective transcription by Pol I. The following review presents our current understanding of the components of the Pol I transcription machinery, their functions and regulation by associated factors, and the mechanisms operating to ensure the proper transcription of rDNA chromatin. The importance of such stringent control is demonstrated by the fact that deregulated Pol I transcription is a feature of cancer and other disorders characterised by abnormal translational capacity.
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Affiliation(s)
- Sarah J. Goodfellow
- Wellcome Trust Centre for Gene Regulation and Expression, College of Life Sciences, University of Dundee , Dundee DD1 5EH , UK
| | - Joost C. B. M. Zomerdijk
- Wellcome Trust Centre for Gene Regulation and Expression, College of Life Sciences, University of Dundee , Dundee DD1 5EH , UK
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