1
|
Song Y, Cui J, Zhu J, Kim B, Kuo ML, Potts PR. RNATACs: Multispecific small molecules targeting RNA by induced proximity. Cell Chem Biol 2024; 31:1101-1117. [PMID: 38876100 DOI: 10.1016/j.chembiol.2024.05.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2024] [Revised: 05/09/2024] [Accepted: 05/22/2024] [Indexed: 06/16/2024]
Abstract
RNA-targeting small molecules (rSMs) have become an attractive modality to tackle traditionally undruggable proteins and expand the druggable space. Among many innovative concepts, RNA-targeting chimeras (RNATACs) represent a new class of multispecific, induced proximity small molecules that act by chemically bringing RNA targets into proximity with an endogenous RNA effector, such as a ribonuclease (RNase). Depending on the RNA effector, RNATACs can alter the stability, localization, translation, or splicing of the target RNA. Although still in its infancy, this new modality has the potential for broad applications in the future to treat diseases with high unmet need. In this review, we discuss potential advantages of RNATACs, recent progress in the field, and challenges to this cutting-edge technology.
Collapse
Affiliation(s)
- Yan Song
- Induced Proximity Platform, Amgen Research, Thousand Oaks, CA 91320, USA.
| | - Jia Cui
- Induced Proximity Platform, Amgen Research, Thousand Oaks, CA 91320, USA
| | - Jiaqiang Zhu
- Induced Proximity Platform, Amgen Research, Thousand Oaks, CA 91320, USA
| | - Boseon Kim
- Induced Proximity Platform, Amgen Research, Thousand Oaks, CA 91320, USA
| | - Mei-Ling Kuo
- Induced Proximity Platform, Amgen Research, Thousand Oaks, CA 91320, USA
| | - Patrick Ryan Potts
- Induced Proximity Platform, Amgen Research, Thousand Oaks, CA 91320, USA.
| |
Collapse
|
2
|
Możdżan M, Węgiel A, Biskup L, Brzezińska O, Makowska J. Anti-Th/To Antibodies in Scleroderma: Good Prognosis or Serious Concern? J Clin Med 2024; 13:3022. [PMID: 38892733 PMCID: PMC11172938 DOI: 10.3390/jcm13113022] [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: 04/15/2024] [Revised: 05/10/2024] [Accepted: 05/16/2024] [Indexed: 06/21/2024] Open
Abstract
Systemic sclerosis (SSc) represents a rare and intricate autoimmune connective tissue disease, the pathophysiology of which has not been fully understood. Its key features include progressive fibrosis of the skin and internal organs, vasculopathy and aberrant immune activation. While various anti-nuclear antibodies can serve as biomarkers for the classification and prognosis of SSc, their direct role in organ dysfunction remains unclear. Anti-Th/To antibodies are present in approximately 5% of SSc patients, and are particularly prevalent among those with the limited subtype of the disease. Although the presence of these autoantibodies is associated with a mild course of the disease, there is a strong connection between them and severe clinical manifestations of SSc, including interstitial lung disease, pulmonary arterial hypertension and gastrointestinal involvement. Also, the additional clinical correlations, particularly with malignancies, need further research. Moreover, the disease's course seems to be influenced by antibodies, specific serum cytokines and TLR signaling pathways. Understanding the relationships between presence of anti-Th/To, its molecular aspects and response to treatment options is crucial for the development of novel, personalized therapeutic techniques and should undergo profound analysis in future studies.
Collapse
Affiliation(s)
- Maria Możdżan
- Department of Rheumatology, Medical University of Lodz, 90-549 Lodz, Poland; (A.W.); (L.B.); (O.B.)
| | | | | | | | - Joanna Makowska
- Department of Rheumatology, Medical University of Lodz, 90-549 Lodz, Poland; (A.W.); (L.B.); (O.B.)
| |
Collapse
|
3
|
Rossmanith W, Giegé P, Hartmann RK. Discovery, structure, mechanisms, and evolution of protein-only RNase P enzymes. J Biol Chem 2024; 300:105731. [PMID: 38336295 PMCID: PMC10941002 DOI: 10.1016/j.jbc.2024.105731] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2023] [Revised: 01/22/2024] [Accepted: 01/24/2024] [Indexed: 02/12/2024] Open
Abstract
The endoribonuclease RNase P is responsible for tRNA 5' maturation in all domains of life. A unique feature of RNase P is the variety of enzyme architectures, ranging from dual- to multi-subunit ribonucleoprotein forms with catalytic RNA subunits to protein-only enzymes, the latter occurring as single- or multi-subunit forms or homo-oligomeric assemblies. The protein-only enzymes evolved twice: a eukaryal protein-only RNase P termed PRORP and a bacterial/archaeal variant termed homolog of Aquifex RNase P (HARP); the latter replaced the RNA-based enzyme in a small group of thermophilic bacteria but otherwise coexists with the ribonucleoprotein enzyme in a few other bacteria as well as in those archaea that also encode a HARP. Here we summarize the history of the discovery of protein-only RNase P enzymes and review the state of knowledge on structure and function of bacterial HARPs and eukaryal PRORPs, including human mitochondrial RNase P as a paradigm of multi-subunit PRORPs. We also describe the phylogenetic distribution and evolution of PRORPs, as well as possible reasons for the spread of PRORPs in the eukaryal tree and for the recruitment of two additional protein subunits to metazoan mitochondrial PRORP. We outline potential applications of PRORPs in plant biotechnology and address diseases associated with mutations in human mitochondrial RNase P genes. Finally, we consider possible causes underlying the displacement of the ancient RNA enzyme by a protein-only enzyme in a small group of bacteria.
Collapse
Affiliation(s)
- Walter Rossmanith
- Center for Anatomy & Cell Biology, Medical University of Vienna, Vienna, Austria.
| | - Philippe Giegé
- Institute for Plant Molecular Biology, IBMP-CNRS, University of Strasbourg, Strasbourg, France.
| | - Roland K Hartmann
- Institute of Pharmaceutical Chemistry, Philipps-University Marburg, Marburg, Germany.
| |
Collapse
|
4
|
Dodel M, Guiducci G, Dermit M, Krishnamurthy S, Alard EL, Capraro F, Rekad Z, Stojic L, Mardakheh FK. TREX reveals proteins that bind to specific RNA regions in living cells. Nat Methods 2024; 21:423-434. [PMID: 38374261 PMCID: PMC10927567 DOI: 10.1038/s41592-024-02181-1] [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: 08/21/2023] [Accepted: 01/16/2024] [Indexed: 02/21/2024]
Abstract
Different regions of RNA molecules can often engage in specific interactions with distinct RNA-binding proteins (RBPs), giving rise to diverse modalities of RNA regulation and function. However, there are currently no methods for unbiased identification of RBPs that interact with specific RNA regions in living cells and under endogenous settings. Here we introduce TREX (targeted RNase H-mediated extraction of crosslinked RBPs)-a highly sensitive approach for identifying proteins that directly bind to specific RNA regions in living cells. We demonstrate that TREX outperforms existing methods in identifying known interactors of U1 snRNA, and reveals endogenous region-specific interactors of NORAD long noncoding RNA. Using TREX, we generated a comprehensive region-by-region interactome for 45S rRNA, uncovering both established and previously unknown interactions that regulate ribosome biogenesis. With its applicability to different cell types, TREX is an RNA-centric tool for unbiased positional mapping of endogenous RNA-protein interactions in living cells.
Collapse
Affiliation(s)
- Martin Dodel
- Centre for Cancer Cell and Molecular Biology, Barts Cancer Institute, Queen Mary University of London, London, UK
| | - Giulia Guiducci
- Centre for Cancer Cell and Molecular Biology, Barts Cancer Institute, Queen Mary University of London, London, UK
| | - Maria Dermit
- Centre for Cancer Cell and Molecular Biology, Barts Cancer Institute, Queen Mary University of London, London, UK
| | - Sneha Krishnamurthy
- Centre for Cancer Cell and Molecular Biology, Barts Cancer Institute, Queen Mary University of London, London, UK
| | - Emilie L Alard
- Centre for Cancer Cell and Molecular Biology, Barts Cancer Institute, Queen Mary University of London, London, UK
| | - Federica Capraro
- Centre for Cancer Cell and Molecular Biology, Barts Cancer Institute, Queen Mary University of London, London, UK
- Randall Centre for Cell and Molecular Biophysics, King's College London, London, UK
| | - Zeinab Rekad
- Centre for Cancer Cell and Molecular Biology, Barts Cancer Institute, Queen Mary University of London, London, UK
| | - Lovorka Stojic
- Centre for Cancer Cell and Molecular Biology, Barts Cancer Institute, Queen Mary University of London, London, UK.
| | - Faraz K Mardakheh
- Centre for Cancer Cell and Molecular Biology, Barts Cancer Institute, Queen Mary University of London, London, UK.
| |
Collapse
|
5
|
Zhou B, Wan F, Lei KX, Lan P, Wu J, Lei M. Coevolution of RNA and protein subunits in RNase P and RNase MRP, two RNA processing enzymes. J Biol Chem 2024; 300:105729. [PMID: 38336296 PMCID: PMC10966300 DOI: 10.1016/j.jbc.2024.105729] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2023] [Revised: 01/12/2024] [Accepted: 01/16/2024] [Indexed: 02/12/2024] Open
Abstract
RNase P and RNase mitochondrial RNA processing (MRP) are ribonucleoproteins (RNPs) that consist of a catalytic RNA and a varying number of protein cofactors. RNase P is responsible for precursor tRNA maturation in all three domains of life, while RNase MRP, exclusive to eukaryotes, primarily functions in rRNA biogenesis. While eukaryotic RNase P is associated with more protein cofactors and has an RNA subunit with fewer auxiliary structural elements compared to its bacterial cousin, the double-anchor precursor tRNA recognition mechanism has remarkably been preserved during evolution. RNase MRP shares evolutionary and structural similarities with RNase P, preserving the catalytic core within the RNA moiety inherited from their common ancestor. By incorporating new protein cofactors and RNA elements, RNase MRP has established itself as a distinct RNP capable of processing ssRNA substrates. The structural information on RNase P and MRP helps build an evolutionary trajectory, depicting how emerging protein cofactors harmonize with the evolution of RNA to shape different functions for RNase P and MRP. Here, we outline the structural and functional relationship between RNase P and MRP to illustrate the coevolution of RNA and protein cofactors, a key driver for the extant, diverse RNP world.
Collapse
Affiliation(s)
- Bin Zhou
- Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China; Shanghai Institute of Precision Medicine, Shanghai, China
| | - Futang Wan
- Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China; Shanghai Institute of Precision Medicine, Shanghai, China
| | - Kevin X Lei
- Shanghai High School International Division, Shanghai, China
| | - Pengfei Lan
- Shanghai Institute of Precision Medicine, Shanghai, China; Renji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China.
| | - Jian Wu
- Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China; Shanghai Institute of Precision Medicine, Shanghai, China.
| | - Ming Lei
- Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China; Shanghai Institute of Precision Medicine, Shanghai, China; State Key Laboratory of Oncogenes and Related Genes, Shanghai Jiao Tong University School of Medicine, Shanghai, China.
| |
Collapse
|
6
|
Bryant CJ, McCool MA, Rosado González G, Abriola L, Surovtseva Y, Baserga S. Discovery of novel microRNA mimic repressors of ribosome biogenesis. Nucleic Acids Res 2024; 52:1988-2011. [PMID: 38197221 PMCID: PMC10899765 DOI: 10.1093/nar/gkad1235] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2023] [Revised: 12/03/2023] [Accepted: 12/16/2023] [Indexed: 01/11/2024] Open
Abstract
While microRNAs and other non-coding RNAs are the next frontier of novel regulators of mammalian ribosome biogenesis (RB), a systematic exploration of microRNA-mediated RB regulation has not yet been undertaken. We carried out a high-content screen in MCF10A cells for changes in nucleolar number using a library of 2603 mature human microRNA mimics. Following a secondary screen for nucleolar rRNA biogenesis inhibition, we identified 72 novel microRNA negative regulators of RB after stringent hit calling. Hits included 27 well-conserved microRNAs present in MirGeneDB, and were enriched for mRNA targets encoding proteins with nucleolar localization or functions in cell cycle regulation. Rigorous selection and validation of a subset of 15 microRNA hits unexpectedly revealed that most of them caused dysregulated pre-rRNA processing, elucidating a novel role for microRNAs in RB regulation. Almost all hits impaired global protein synthesis and upregulated CDKN1A (p21) levels, while causing diverse effects on RNA Polymerase 1 (RNAP1) transcription and TP53 protein levels. We provide evidence that the MIR-28 siblings, hsa-miR-28-5p and hsa-miR-708-5p, potently target the ribosomal protein mRNA RPS28 via tandem primate-specific 3' UTR binding sites, causing a severe pre-18S pre-rRNA processing defect. Our work illuminates novel microRNA attenuators of RB, forging a promising new path for microRNA mimic chemotherapeutics.
Collapse
Affiliation(s)
- Carson J Bryant
- Department of Molecular Biophysics and Biochemistry, Yale School of Medicine, New Haven, CT, 06520, USA
| | - Mason A McCool
- Department of Molecular Biophysics and Biochemistry, Yale School of Medicine, New Haven, CT, 06520, USA
| | | | - Laura Abriola
- Yale Center for Molecular Discovery, Yale University, West Haven, CT, 06516, USA
| | - Yulia V Surovtseva
- Yale Center for Molecular Discovery, Yale University, West Haven, CT, 06516, USA
| | - Susan J Baserga
- Department of Molecular Biophysics and Biochemistry, Yale School of Medicine, New Haven, CT, 06520, USA
- Department of Genetics, Yale School of Medicine, New Haven, CT, 06520, USA
- Department of Therapeutic Radiology, Yale School of Medicine, New Haven, CT, 06520, USA
| |
Collapse
|
7
|
Da Costa L, Mohandas N, David-NGuyen L, Platon J, Marie I, O'Donohue MF, Leblanc T, Gleizes PE. Diamond-Blackfan anemia, the archetype of ribosomopathy: How distinct is it from the other constitutional ribosomopathies? Blood Cells Mol Dis 2024:102838. [PMID: 38413287 DOI: 10.1016/j.bcmd.2024.102838] [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: 11/15/2023] [Revised: 02/16/2024] [Accepted: 02/16/2024] [Indexed: 02/29/2024]
Abstract
Diamond-Blackfan anemia (DBA) was the first ribosomopathy described in humans. DBA is a congenital hypoplastic anemia, characterized by macrocytic aregenerative anemia, manifesting by differentiation blockage between the BFU-e/CFU-e developmental erythroid progenitor stages. In 50 % of the DBA cases, various malformations are noted. Strikingly, for a hematological disease with a relative erythroid tropism, DBA is due to ribosomal haploinsufficiency in 24 different ribosomal protein (RP) genes. A few other genes have been described in DBA-like disorders, but they do not fit into the classical DBA phenotype (Sankaran et al., 2012; van Dooijeweert et al., 2022; Toki et al., 2018; Kim et al., 2017 [1-4]). Haploinsufficiency in a RP gene leads to defective ribosomal RNA (rRNA) maturation, which is a hallmark of DBA. However, the mechanistic understandings of the erythroid tropism defect in DBA are still to be fully defined. Erythroid defect in DBA has been recently been linked in a non-exclusive manner to a number of mechanisms that include: 1) a defect in translation, in particular for the GATA1 erythroid gene; 2) a deficit of HSP70, the GATA1 chaperone, and 3) free heme toxicity. In addition, p53 activation in response to ribosomal stress is involved in DBA pathophysiology. The DBA phenotype may thus result from the combined contributions of various actors, which may explain the heterogenous phenotypes observed in DBA patients, even within the same family.
Collapse
Affiliation(s)
- L Da Costa
- Service d'Hématologie Biologique (Hematology Diagnostic Lab), AP-HP, Hôpital Bicêtre, F-94270 Le Kremlin-Bicêtre, France; University of Paris Saclay, F-94270 Le Kremlin-Bicêtre, France; University of Paris Cité, F-75010 Paris, France; University of Picardie Jules Verne, F-80000 Amiens, France; Inserm U1170, IGR, F-94805 Villejuif/HEMATIM UR4666, F-80000 Amiens, France; Laboratory of Excellence for Red Cells, LABEX GR-Ex, F-75015 Paris, France.
| | | | - Ludivine David-NGuyen
- Service d'Hématologie Biologique (Hematology Diagnostic Lab), AP-HP, Hôpital Bicêtre, F-94270 Le Kremlin-Bicêtre, France
| | - Jessica Platon
- Inserm U1170, IGR, F-94805 Villejuif/HEMATIM UR4666, F-80000 Amiens, France
| | - Isabelle Marie
- Service d'Hématologie Biologique (Hematology Diagnostic Lab), AP-HP, Hôpital Bicêtre, F-94270 Le Kremlin-Bicêtre, France
| | - Marie Françoise O'Donohue
- Molecular, Cellular and Developmental biology department (MCD), Centre de Biologie Intégrative (CBI), Université de Toulouse, CNRS, UPS, Toulouse, France
| | - Thierry Leblanc
- Service d'immuno-hématologie pédiatrique, Hôpital Robert-Debré, F-75019 Paris, France
| | - Pierre-Emmanuel Gleizes
- Molecular, Cellular and Developmental biology department (MCD), Centre de Biologie Intégrative (CBI), Université de Toulouse, CNRS, UPS, Toulouse, France
| |
Collapse
|
8
|
Sizer RE, Butterfield SP, Hancocks LA, Gato De Sousa L, White RJ. Selective Occupation by E2F and RB of Loci Expressed by RNA Polymerase III. Cancers (Basel) 2024; 16:481. [PMID: 38339234 PMCID: PMC10854548 DOI: 10.3390/cancers16030481] [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: 12/19/2023] [Revised: 01/15/2024] [Accepted: 01/15/2024] [Indexed: 02/12/2024] Open
Abstract
In all cases tested, TFIIIB is responsible for recruiting pol III to its genetic templates. In mammalian cells, RB binds TFIIIB and prevents its interactions with both promoter DNA and pol III, thereby suppressing transcription. As TFIIIB is not recruited to its target genes when bound by RB, the mechanism predicts that pol III-dependent templates will not be occupied by RB; this contrasts with the situation at most genes controlled by RB, where it can be tethered by promoter-bound sequence-specific DNA-binding factors such as E2F. Contrary to this prediction, however, ChIP-seq data reveal the presence of RB in multiple cell types and the related protein p130 at many loci that rely on pol III for their expression, including RMRP, RN7SL, and a variety of tRNA genes. The sets of genes targeted varies according to cell type and growth state. In such cases, recruitment of RB and p130 can be explained by binding of E2F1, E2F4 and/or E2F5. Genes transcribed by pol III had not previously been identified as common targets of E2F family members. The data provide evidence that E2F may allow for the selective regulation of specific non-coding RNAs by RB, in addition to its influence on overall pol III output through its interaction with TFIIIB.
Collapse
Affiliation(s)
| | | | | | | | - Robert J. White
- Department of Biology, University of York, York YO10 5DD, UK; (R.E.S.)
| |
Collapse
|
9
|
Böğürcü-Seidel N, Ritschel N, Acker T, Németh A. Beyond ribosome biogenesis: noncoding nucleolar RNAs in physiology and tumor biology. Nucleus 2023; 14:2274655. [PMID: 37906621 PMCID: PMC10730139 DOI: 10.1080/19491034.2023.2274655] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2023] [Accepted: 10/19/2023] [Indexed: 11/02/2023] Open
Abstract
The nucleolus, the largest subcompartment of the nucleus, stands out from the nucleoplasm due to its exceptionally high local RNA and low DNA concentrations. Within this central hub of nuclear RNA metabolism, ribosome biogenesis is the most prominent ribonucleoprotein (RNP) biogenesis process, critically determining the structure and function of the nucleolus. However, recent studies have shed light on other roles of the nucleolus, exploring the interplay with various noncoding RNAs that are not directly involved in ribosome synthesis. This review focuses on this intriguing topic and summarizes the techniques to study and the latest findings on nucleolar long noncoding RNAs (lncRNAs) as well as microRNAs (miRNAs) in the context of nucleolus biology beyond ribosome biogenesis. We particularly focus on the multifaceted roles of the nucleolus and noncoding RNAs in physiology and tumor biology.
Collapse
Affiliation(s)
| | - Nadja Ritschel
- Institute of Neuropathology, Justus Liebig University Giessen, Giessen, Germany
| | - Till Acker
- Institute of Neuropathology, Justus Liebig University Giessen, Giessen, Germany
| | - Attila Németh
- Institute of Neuropathology, Justus Liebig University Giessen, Giessen, Germany
| |
Collapse
|
10
|
Bryant CJ, McCool MA, Rosado-González GT, Abriola L, Surovtseva YV, Baserga SJ. Discovery of novel microRNA mimic repressors of ribosome biogenesis. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.02.17.526327. [PMID: 36824951 PMCID: PMC9949135 DOI: 10.1101/2023.02.17.526327] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/20/2023]
Abstract
While microRNAs and other non-coding RNAs are the next frontier of novel regulators of mammalian ribosome biogenesis (RB), a systematic exploration of microRNA-mediated RB regulation has not yet been undertaken. We carried out a high-content screen in MCF10A cells for changes in nucleolar number using a library of 2,603 mature human microRNA mimics. Following a secondary screen for nucleolar rRNA biogenesis inhibition, we identified 72 novel microRNA negative regulators of RB after stringent hit calling. Hits included 27 well-conserved microRNAs present in MirGeneDB, and were enriched for mRNA targets encoding proteins with nucleolar localization or functions in cell cycle regulation. Rigorous selection and validation of a subset of 15 microRNA hits unexpectedly revealed that most of them caused dysregulated pre-rRNA processing, elucidating a novel role for microRNAs in RB regulation. Almost all hits impaired global protein synthesis and upregulated CDKN1A ( p21 ) levels, while causing diverse effects on RNA Polymerase 1 (RNAP1) transcription and TP53 protein levels. We discovered that the MIR-28 siblings, hsa-miR-28-5p and hsa-miR-708-5p, directly and potently target the ribosomal protein mRNA RPS28 via tandem primate-specific 3' UTR binding sites, causing a severe pre-18S pre-rRNA processing defect. Our work illuminates novel microRNA attenuators of RB, forging a promising new path for microRNA mimic chemotherapeutics.
Collapse
|
11
|
Limouse C, Smith OK, Jukam D, Fryer KA, Greenleaf WJ, Straight AF. Global mapping of RNA-chromatin contacts reveals a proximity-dominated connectivity model for ncRNA-gene interactions. Nat Commun 2023; 14:6073. [PMID: 37770513 PMCID: PMC10539311 DOI: 10.1038/s41467-023-41848-9] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2023] [Accepted: 09/19/2023] [Indexed: 09/30/2023] Open
Abstract
Non-coding RNAs (ncRNAs) are transcribed throughout the genome and provide regulatory inputs to gene expression through their interaction with chromatin. Yet, the genomic targets and functions of most ncRNAs are unknown. Here we use chromatin-associated RNA sequencing (ChAR-seq) to map the global network of ncRNA interactions with chromatin in human embryonic stem cells and the dynamic changes in interactions during differentiation into definitive endoderm. We uncover general principles governing the organization of the RNA-chromatin interactome, demonstrating that nearly all ncRNAs exclusively interact with genes in close three-dimensional proximity to their locus and provide a model predicting the interactome. We uncover RNAs that interact with many loci across the genome and unveil thousands of unannotated RNAs that dynamically interact with chromatin. By relating the dynamics of the interactome to changes in gene expression, we demonstrate that activation or repression of individual genes is unlikely to be controlled by a single ncRNA.
Collapse
Affiliation(s)
- Charles Limouse
- Department of Biochemistry, Stanford University, Stanford, California, USA
| | - Owen K Smith
- Department of Chemical and Systems Biology, Stanford University, Stanford, California, USA
| | - David Jukam
- Department of Biochemistry, Stanford University, Stanford, California, USA
| | - Kelsey A Fryer
- Department of Biochemistry, Stanford University, Stanford, California, USA
- Department of Genetics, Stanford University, Stanford, California, USA
| | | | - Aaron F Straight
- Department of Biochemistry, Stanford University, Stanford, California, USA.
| |
Collapse
|
12
|
Zhou S, Van Bortle K. The Pol III transcriptome: Basic features, recurrent patterns, and emerging roles in cancer. WILEY INTERDISCIPLINARY REVIEWS. RNA 2023; 14:e1782. [PMID: 36754845 PMCID: PMC10498592 DOI: 10.1002/wrna.1782] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/06/2022] [Revised: 01/13/2023] [Accepted: 01/18/2023] [Indexed: 02/10/2023]
Abstract
The RNA polymerase III (Pol III) transcriptome is universally comprised of short, highly structured noncoding RNA (ncRNA). Through RNA-protein interactions, the Pol III transcriptome actuates functional activities ranging from nuclear gene regulation (7SK), splicing (U6, U6atac), and RNA maturation and stability (RMRP, RPPH1, Y RNA), to cytoplasmic protein targeting (7SL) and translation (tRNA, 5S rRNA). In higher eukaryotes, the Pol III transcriptome has expanded to include additional, recently evolved ncRNA species that effectively broaden the footprint of Pol III transcription to additional cellular activities. Newly evolved ncRNAs function as riboregulators of autophagy (vault), immune signaling cascades (nc886), and translation (Alu, BC200, snaR). Notably, upregulation of Pol III transcription is frequently observed in cancer, and multiple ncRNA species are linked to both cancer progression and poor survival outcomes among cancer patients. In this review, we outline the basic features and functions of the Pol III transcriptome, and the evidence for dysregulation and dysfunction for each ncRNA in cancer. When taken together, recurrent patterns emerge, ranging from shared functional motifs that include molecular scaffolding and protein sequestration, overlapping protein interactions, and immunostimulatory activities, to the biogenesis of analogous small RNA fragments and noncanonical miRNAs, augmenting the function of the Pol III transcriptome and further broadening its role in cancer. This article is categorized under: RNA in Disease and Development > RNA in Disease RNA Processing > Processing of Small RNAs RNA Interactions with Proteins and Other Molecules > Protein-RNA Interactions: Functional Implications.
Collapse
Affiliation(s)
- Sihang Zhou
- Department of Cell and Developmental Biology, University of Illinois Urbana-Champaign, Urbana, Illinois, USA
| | - Kevin Van Bortle
- Department of Cell and Developmental Biology, University of Illinois Urbana-Champaign, Urbana, Illinois, USA
- Cancer Center at Illinois, University of Illinois Urbana-Champaign, Urbana, Illinois, USA
| |
Collapse
|
13
|
Elkholi IE, Boulais J, Thibault MP, Phan HD, Robert A, Lai LB, Faubert D, Smith MJ, Gopalan V, Côté JF. Mapping the MOB proteins' proximity network reveals a unique interaction between human MOB3C and the RNase P complex. J Biol Chem 2023; 299:105123. [PMID: 37536630 PMCID: PMC10480535 DOI: 10.1016/j.jbc.2023.105123] [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: 05/09/2023] [Revised: 07/20/2023] [Accepted: 07/23/2023] [Indexed: 08/05/2023] Open
Abstract
Distinct functions mediated by members of the monopolar spindle-one-binder (MOB) family of proteins remain elusive beyond the evolutionarily conserved and well-established roles of MOB1 (MOB1A/B) in regulating tissue homeostasis within the Hippo pathway. Since MOB proteins are adaptors, understanding how they engage in protein-protein interactions and help assemble complexes is essential to define the full scope of their biological functions. To address this, we undertook a proximity-dependent biotin identification approach to define the interactomes of all seven human MOB proteins in HeLa and human embryonic kidney 293 cell lines. We uncovered >200 interactions, of which at least 70% are unreported on BioGrid. The generated dataset reliably recalled the bona fide interactors of the well-studied MOBs. We further defined the common and differential interactome between different MOBs on a subfamily and an individual level. We discovered a unique association between MOB3C and 7 of 10 protein subunits of the RNase P complex, an endonuclease that catalyzes tRNA 5' maturation. As a proof of principle for the robustness of the generated dataset, we validated the specific interaction of MOB3C with catalytically active RNase P by using affinity purification-mass spectrometry and pre-tRNA cleavage assays of MOB3C pulldowns. In summary, our data provide novel insights into the biology of MOB proteins and reveal the first interactors of MOB3C, components of the RNase P complex, and hence an exciting nexus with RNA biology.
Collapse
Affiliation(s)
- Islam E Elkholi
- Montreal Clinical Research Institute (IRCM), Montreal, Quebec, Canada; Molecular Biology Programs, Université de Montréal, Montreal, Quebec, Canada; Department of Anatomy and Cell Biology, McGill University, Montreal, Quebec, Canada.
| | - Jonathan Boulais
- Montreal Clinical Research Institute (IRCM), Montreal, Quebec, Canada
| | | | - Hong-Duc Phan
- Department of Chemistry & Biochemistry, Center for RNA Biology, The Ohio State University, Columbus, Ohio, USA
| | - Amélie Robert
- Montreal Clinical Research Institute (IRCM), Montreal, Quebec, Canada
| | - Lien B Lai
- Department of Chemistry & Biochemistry, Center for RNA Biology, The Ohio State University, Columbus, Ohio, USA
| | - Denis Faubert
- Montreal Clinical Research Institute (IRCM), Montreal, Quebec, Canada
| | - Matthew J Smith
- Institute for Research in Immunology and Cancer, Université de Montréal, Montreal, Quebec, Canada
| | - Venkat Gopalan
- Department of Chemistry & Biochemistry, Center for RNA Biology, The Ohio State University, Columbus, Ohio, USA
| | - Jean-Franҫois Côté
- Montreal Clinical Research Institute (IRCM), Montreal, Quebec, Canada; Molecular Biology Programs, Université de Montréal, Montreal, Quebec, Canada; Department of Anatomy and Cell Biology, McGill University, Montreal, Quebec, Canada; Department of Biochemistry and Molecular Medicine, Université de Montréal, Montreal, Quebec, Canada.
| |
Collapse
|
14
|
Hecker M, Fitzner B, Boxberger N, Putscher E, Engelmann R, Bergmann W, Müller M, Ludwig-Portugall I, Schwartz M, Meister S, Dudesek A, Winkelmann A, Koczan D, Zettl UK. Transcriptome alterations in peripheral blood B cells of patients with multiple sclerosis receiving immune reconstitution therapy. J Neuroinflammation 2023; 20:181. [PMID: 37533036 PMCID: PMC10394872 DOI: 10.1186/s12974-023-02859-x] [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: 10/12/2022] [Accepted: 07/25/2023] [Indexed: 08/04/2023] Open
Abstract
BACKGROUND Multiple sclerosis (MS) is a chronic, inflammatory and neurodegenerative disease that leads to irreversible damage to the brain and spinal cord. The goal of so-called "immune reconstitution therapies" (IRTs) is to achieve long-term disease remission by eliminating a pathogenic immune repertoire through intense short-term immune cell depletion. B cells are major targets for effective immunotherapy in MS. OBJECTIVES The aim of this study was to analyze the gene expression pattern of B cells before and during IRT (i.e., before B-cell depletion and after B-cell repopulation) to better understand the therapeutic effects and to identify biomarker candidates of the clinical response to therapy. METHODS B cells were obtained from blood samples of patients with relapsing-remitting MS (n = 50), patients with primary progressive MS (n = 13) as well as healthy controls (n = 28). The patients with relapsing MS received either monthly infusions of natalizumab (n = 29) or a pulsed IRT with alemtuzumab (n = 15) or cladribine (n = 6). B-cell subpopulation frequencies were determined by flow cytometry, and transcriptome profiling was performed using Clariom D arrays. Differentially expressed genes (DEGs) between the patient groups and controls were examined with regard to their functions and interactions. We also tested for differences in gene expression between patients with and without relapse following alemtuzumab administration. RESULTS Patients treated with alemtuzumab or cladribine showed on average a > 20% lower proportion of memory B cells as compared to before IRT. This was paralleled by profound transcriptome shifts, with > 6000 significant DEGs after adjustment for multiple comparisons. The top DEGs were found to regulate apoptosis, cell adhesion and RNA processing, and the most highly connected nodes in the network of encoded proteins were ESR2, PHB and RC3H1. Higher mRNA levels of BCL2, IL13RA1 and SLC38A11 were seen in patients with relapse despite IRT, though these differences did not pass the false discovery rate correction. CONCLUSIONS We show that B cells circulating in the blood of patients with MS undergoing IRT present a distinct gene expression signature, and we delineated the associated biological processes and gene interactions. Moreover, we identified genes whose expression may be an indicator of relapse risk, but further studies are needed to verify their potential value as biomarkers.
Collapse
Affiliation(s)
- Michael Hecker
- Division of Neuroimmunology, Department of Neurology, Rostock University Medical Center, Gehlsheimer Str. 20, 18147, Rostock, Germany.
| | - Brit Fitzner
- Division of Neuroimmunology, Department of Neurology, Rostock University Medical Center, Gehlsheimer Str. 20, 18147, Rostock, Germany
| | - Nina Boxberger
- Division of Neuroimmunology, Department of Neurology, Rostock University Medical Center, Gehlsheimer Str. 20, 18147, Rostock, Germany
| | - Elena Putscher
- Division of Neuroimmunology, Department of Neurology, Rostock University Medical Center, Gehlsheimer Str. 20, 18147, Rostock, Germany
| | - Robby Engelmann
- Clinic III (Hematology, Oncology and Palliative Medicine), Special Hematology Laboratory, Rostock University Medical Center, Ernst-Heydemann-Str. 6, 18057, Rostock, Germany
| | - Wendy Bergmann
- Core Facility for Cell Sorting and Cell Analysis, Rostock University Medical Center, Schillingallee 70, 18057, Rostock, Germany
| | - Michael Müller
- Core Facility for Cell Sorting and Cell Analysis, Rostock University Medical Center, Schillingallee 70, 18057, Rostock, Germany
| | | | - Margit Schwartz
- Division of Neuroimmunology, Department of Neurology, Rostock University Medical Center, Gehlsheimer Str. 20, 18147, Rostock, Germany
| | - Stefanie Meister
- Division of Neuroimmunology, Department of Neurology, Rostock University Medical Center, Gehlsheimer Str. 20, 18147, Rostock, Germany
| | - Ales Dudesek
- Division of Neuroimmunology, Department of Neurology, Rostock University Medical Center, Gehlsheimer Str. 20, 18147, Rostock, Germany
| | - Alexander Winkelmann
- Division of Neuroimmunology, Department of Neurology, Rostock University Medical Center, Gehlsheimer Str. 20, 18147, Rostock, Germany
| | - Dirk Koczan
- Institute of Immunology, Rostock University Medical Center, Schillingallee 70, 18057, Rostock, Germany
| | - Uwe Klaus Zettl
- Division of Neuroimmunology, Department of Neurology, Rostock University Medical Center, Gehlsheimer Str. 20, 18147, Rostock, Germany
| |
Collapse
|
15
|
Ivanov KI, Samuilova OV, Zamyatnin AA. The emerging roles of long noncoding RNAs in lymphatic vascular development and disease. Cell Mol Life Sci 2023; 80:197. [PMID: 37407839 PMCID: PMC10322780 DOI: 10.1007/s00018-023-04842-4] [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: 11/08/2022] [Revised: 06/06/2023] [Accepted: 06/19/2023] [Indexed: 07/07/2023]
Abstract
Recent advances in RNA sequencing technologies helped uncover what was once uncharted territory in the human genome-the complex and versatile world of long noncoding RNAs (lncRNAs). Previously thought of as merely transcriptional "noise", lncRNAs have now emerged as essential regulators of gene expression networks controlling development, homeostasis and disease progression. The regulatory functions of lncRNAs are broad and diverse, and the underlying molecular mechanisms are highly variable, acting at the transcriptional, post-transcriptional, translational, and post-translational levels. In recent years, evidence has accumulated to support the important role of lncRNAs in the development and functioning of the lymphatic vasculature and associated pathological processes such as tumor-induced lymphangiogenesis and cancer metastasis. In this review, we summarize the current knowledge on the role of lncRNAs in regulating the key genes and pathways involved in lymphatic vascular development and disease. Furthermore, we discuss the potential of lncRNAs as novel therapeutic targets and outline possible strategies for the development of lncRNA-based therapeutics to treat diseases of the lymphatic system.
Collapse
Affiliation(s)
- Konstantin I Ivanov
- Research Center for Translational Medicine, Sirius University of Science and Technology, Sochi, Russian Federation.
- Department of Microbiology, University of Helsinki, Helsinki, Finland.
| | - Olga V Samuilova
- Department of Biochemistry, Sechenov First Moscow State Medical University, Moscow, Russian Federation
- HSE University, Moscow, Russian Federation
| | - Andrey A Zamyatnin
- Research Center for Translational Medicine, Sirius University of Science and Technology, Sochi, Russian Federation
- Faculty of Bioengineering and Bioinformatics, Lomonosov Moscow State University, Moscow, Russian Federation
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, Russian Federation
- Faculty of Health and Medical Sciences, University of Surrey, Guildford, UK
| |
Collapse
|
16
|
Schneider C, Bohnsack KE. Caught in the act-Visualizing ribonucleases during eukaryotic ribosome assembly. WILEY INTERDISCIPLINARY REVIEWS. RNA 2023; 14:e1766. [PMID: 36254602 DOI: 10.1002/wrna.1766] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/14/2022] [Revised: 09/22/2022] [Accepted: 09/24/2022] [Indexed: 07/20/2023]
Abstract
Ribosomes are essential macromolecular machines responsible for translating the genetic information encoded in mRNAs into proteins. Ribosomes are composed of ribosomal RNAs and proteins (rRNAs and RPs) and the rRNAs fulfill both catalytic and architectural functions. Excision of the mature eukaryotic rRNAs from their precursor transcript is achieved through a complex series of endoribonucleolytic cleavages and exoribonucleolytic processing steps that are precisely coordinated with other aspects of ribosome assembly. Many ribonucleases involved in pre-rRNA processing have been identified and pre-rRNA processing pathways are relatively well defined. However, momentous advances in cryo-electron microscopy have recently enabled structural snapshots of various pre-ribosomal particles from budding yeast (Saccharomyces cerevisiae) and human cells to be captured and, excitingly, these structures not only allow pre-rRNAs to be observed before and after cleavage events, but also enable ribonucleases to be visualized on their target RNAs. These structural views of pre-rRNA processing in action allow a new layer of understanding of rRNA maturation and how it is coordinated with other aspects of ribosome assembly. They illuminate mechanisms of target recognition by the diverse ribonucleases involved and reveal how the cleavage/processing activities of these enzymes are regulated. In this review, we discuss the new insights into pre-rRNA processing gained by structural analyses and the growing understanding of the mechanisms of ribonuclease regulation. This article is categorized under: Translation > Ribosome Biogenesis RNA Processing > rRNA Processing.
Collapse
Affiliation(s)
- Claudia Schneider
- Biosciences Institute, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne, UK
| | - Katherine E Bohnsack
- Department of Molecular Biology, University Medical Center Göttingen, Göttingen, Germany
| |
Collapse
|
17
|
Challakkara MF, Chhabra R. snoRNAs in hematopoiesis and blood malignancies: A comprehensive review. J Cell Physiol 2023; 238:1207-1225. [PMID: 37183323 DOI: 10.1002/jcp.31032] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2023] [Revised: 03/29/2023] [Accepted: 04/04/2023] [Indexed: 05/16/2023]
Abstract
Small nucleolar RNAs (snoRNAs) are noncoding RNA molecules of highly variable size, usually ranging from 60 to 150 nucleotides. They are classified into H/ACA box snoRNAs, C/D box snoRNAs, and scaRNAs. Their functional profile includes biogenesis of ribosomes, processing of rRNAs, 2'-O-methylation and pseudouridylation of RNAs, alternative splicing and processing of mRNAs and the generation of small RNA molecules like miRNA. The snoRNAs have been observed to have an important role in hematopoiesis and malignant hematopoietic conditions including leukemia, lymphoma, and multiple myeloma. Blood malignancies arise in immune system cells or the bone marrow due to chromosome abnormalities. It has been estimated that annually over 1.25 million cases of blood cancer occur worldwide. The snoRNAs often show a differential expression profile in blood malignancies. Recent reports associate the abnormal expression of snoRNAs with the inhibition of apoptosis, uncontrolled cell proliferation, angiogenesis, and metastasis. This implies that targeting snoRNAs could be a potential way to treat hematologic malignancies. In this review, we describe the various functions of snoRNAs, their role in hematopoiesis, and the consequences of their dysregulation in blood malignancies. We also evaluate the potential of the dysregulated snoRNAs as biomarkers and therapeutic targets for blood malignancies.
Collapse
Affiliation(s)
- Mohamed Fahad Challakkara
- Department of Biochemistry, School of Basic Sciences, Central University of Punjab, Bathinda, Punjab, India
| | - Ravindresh Chhabra
- Department of Biochemistry, School of Basic Sciences, Central University of Punjab, Bathinda, Punjab, India
| |
Collapse
|
18
|
Parker MD, Karbstein K. Quality control ensures fidelity in ribosome assembly and cellular health. J Cell Biol 2023; 222:213871. [PMID: 36790396 PMCID: PMC9960125 DOI: 10.1083/jcb.202209115] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2022] [Revised: 01/09/2023] [Accepted: 02/02/2023] [Indexed: 02/16/2023] Open
Abstract
The coordinated integration of ribosomal RNA and protein into two functional ribosomal subunits is safeguarded by quality control checkpoints that ensure ribosomes are correctly assembled and functional before they engage in translation. Quality control is critical in maintaining the integrity of ribosomes and necessary to support healthy cell growth and prevent diseases associated with mistakes in ribosome assembly. Its importance is demonstrated by the finding that bypassing quality control leads to misassembled, malfunctioning ribosomes with altered translation fidelity, which change gene expression and disrupt protein homeostasis. In this review, we outline our understanding of quality control within ribosome synthesis and how failure to enforce quality control contributes to human disease. We first provide a definition of quality control to guide our investigation, briefly present the main assembly steps, and then examine stages of assembly that test ribosome function, establish a pass-fail system to evaluate these functions, and contribute to altered ribosome performance when bypassed, and are thus considered "quality control."
Collapse
Affiliation(s)
- Melissa D. Parker
- The Skaggs Graduate School of Chemical and Biological Sciences, The Scripps Research Institute, La Jolla, CA, USA,University of Florida—Scripps Biomedical Research, Jupiter, FL, USA
| | - Katrin Karbstein
- The Skaggs Graduate School of Chemical and Biological Sciences, The Scripps Research Institute, La Jolla, CA, USA,University of Florida—Scripps Biomedical Research, Jupiter, FL, USA,Howard Hughes Medical Institute Faculty Scholar, Howard Hughes Medical Institute, Chevy Chase, MD, USA,Correspondence to Katrin Karbstein:
| |
Collapse
|
19
|
Dörner K, Ruggeri C, Zemp I, Kutay U. Ribosome biogenesis factors-from names to functions. EMBO J 2023; 42:e112699. [PMID: 36762427 PMCID: PMC10068337 DOI: 10.15252/embj.2022112699] [Citation(s) in RCA: 37] [Impact Index Per Article: 37.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2022] [Revised: 12/13/2022] [Accepted: 01/19/2023] [Indexed: 02/11/2023] Open
Abstract
The assembly of ribosomal subunits is a highly orchestrated process that involves a huge cohort of accessory factors. Most eukaryotic ribosome biogenesis factors were first identified by genetic screens and proteomic approaches of pre-ribosomal particles in Saccharomyces cerevisiae. Later, research on human ribosome synthesis not only demonstrated that the requirement for many of these factors is conserved in evolution, but also revealed the involvement of additional players, reflecting a more complex assembly pathway in mammalian cells. Yet, it remained a challenge for the field to assign a function to many of the identified factors and to reveal their molecular mode of action. Over the past decade, structural, biochemical, and cellular studies have largely filled this gap in knowledge and led to a detailed understanding of the molecular role that many of the players have during the stepwise process of ribosome maturation. Such detailed knowledge of the function of ribosome biogenesis factors will be key to further understand and better treat diseases linked to disturbed ribosome assembly, including ribosomopathies, as well as different types of cancer.
Collapse
Affiliation(s)
- Kerstin Dörner
- Department of Biology, Institute of Biochemistry, ETH Zurich, Zurich, Switzerland.,Molecular Life Sciences Ph.D. Program, Zurich, Switzerland
| | - Chiara Ruggeri
- Department of Biology, Institute of Biochemistry, ETH Zurich, Zurich, Switzerland.,RNA Biology Ph.D. Program, Zurich, Switzerland
| | - Ivo Zemp
- Department of Biology, Institute of Biochemistry, ETH Zurich, Zurich, Switzerland
| | - Ulrike Kutay
- Department of Biology, Institute of Biochemistry, ETH Zurich, Zurich, Switzerland
| |
Collapse
|
20
|
Jeandard D, Smirnova A, Fasemore AM, Coudray L, Entelis N, Förstner K, Tarassov I, Smirnov A. CoLoC-seq probes the global topology of organelle transcriptomes. Nucleic Acids Res 2022; 51:e16. [PMID: 36537202 PMCID: PMC9943681 DOI: 10.1093/nar/gkac1183] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2022] [Accepted: 11/28/2022] [Indexed: 12/24/2022] Open
Abstract
Proper RNA localisation is essential for physiological gene expression. Various kinds of genome-wide approaches permit to comprehensively profile subcellular transcriptomes. Among them, cell fractionation methods, that couple RNase treatment of isolated organelles to the sequencing of protected transcripts, remain most widely used, mainly because they do not require genetic modification of the studied system and can be easily implemented in any cells or tissues, including in non-model species. However, they suffer from numerous false-positives since incompletely digested contaminant RNAs can still be captured and erroneously identified as resident transcripts. Here we introduce Controlled Level of Contamination coupled to deep sequencing (CoLoC-seq) as a new subcellular transcriptomics approach that efficiently bypasses this caveat. CoLoC-seq leverages classical enzymatic kinetics and tracks the depletion dynamics of transcripts in a gradient of an exogenously added RNase, with or without organellar membranes. By means of straightforward mathematical modelling, CoLoC-seq infers the localisation topology of RNAs and robustly distinguishes between genuinely resident, luminal transcripts and merely abundant surface-attached contaminants. Our generic approach performed well on human mitochondria and is in principle applicable to other membrane-bounded organelles, including plastids, compartments of the vacuolar system, extracellular vesicles, and viral particles.
Collapse
Affiliation(s)
| | | | | | - Léna Coudray
- UMR7156 – Génétique Moléculaire, Génomique, Microbiologie (GMGM), University of Strasbourg, CNRS, Strasbourg, F-67000, France
| | - Nina Entelis
- UMR7156 – Génétique Moléculaire, Génomique, Microbiologie (GMGM), University of Strasbourg, CNRS, Strasbourg, F-67000, France
| | - Konrad U Förstner
- ZB MED – Information Centre for Life Sciences, Cologne, D-50931, Germany,TH Köln – University of Applied Sciences, Faculty of Information Science and Communication Studies, Institute of Information Science, Cologne, D-50678, Germany
| | - Ivan Tarassov
- UMR7156 – Génétique Moléculaire, Génomique, Microbiologie (GMGM), University of Strasbourg, CNRS, Strasbourg, F-67000, France
| | | |
Collapse
|
21
|
Tang J, Tian X, Min J, Hu M, Hong L. RPP40 is a prognostic biomarker and correlated with tumor microenvironment in uterine corpus endometrial carcinoma. Front Oncol 2022; 12:957472. [PMID: 36091104 PMCID: PMC9448918 DOI: 10.3389/fonc.2022.957472] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2022] [Accepted: 07/26/2022] [Indexed: 11/26/2022] Open
Abstract
Ribonuclease P/MRP Subunit P40 (RPP40), a component of ribonuclease P and multimeric ribonuclease P complex, was reported as one of the promoting factors for the chemoresistance of acute myeloid leukemia and a recurrence predictor of early-stage triple-negative breast cancer. However, the functional role of RPP40 in uterine corpus endometrial carcinoma (UCEC) is unclear. In this study, comprehensive bioinformatic analyses were conducted to explore the predictive role of RPP40 on UCEC diagnosis and prognosis, as well as the underlying mechanism. Differential analyses of multiple databases showed that both messenger RNA (mRNA) and the protein expression of RPP40 were significantly upregulated in UCEC tumor tissues. Furthermore, the RPP40 mRNA expression level was significantly correlated with the clinicopathological characteristics of UCEC patients, including the clinical stage, primary therapy outcome, histological type, histologic grade, overall survival event, disease-specific survival event, and progression-free interval event. Receiver operating characteristic (ROC) analysis showed that RPP40 was a reliable predictor for UCEC diagnosis with an area under the curve (AUC) of 0.775, a sensitivity of 0.829, and a specificity of 0.719. Kaplan–Meier, Cox regression, and nomogram analyses showed that high RPP40 expression was an independent prognostic factor for the 1-year, 3-year, and 5-year survival of UCEC patients. In addition, the enrichment analysis of RPP40-associated differentially expressed genes and correlation analyses showed that the expression of RPP40 was correlated with the regulation of extracellular matrix and immune cell infiltration. In conclusion, the upregulation of RPP40 is significantly correlated with the poor survival and tumor microenvironment of UCEC, suggesting that RPP40 is a promising biomarker of poor prognosis and a potential target of chemotherapy or immunotherapy in UCEC.
Collapse
Affiliation(s)
- Jianming Tang
- Department of Obstetrics and Gynecology, Renmin Hospital of Wuhan University, Wuhan, China
| | - Xiaoli Tian
- Department of Pathology, Renmin Hospital of Wuhan University, Wuhan, China
| | - Jie Min
- Department of Obstetrics and Gynecology, Renmin Hospital of Wuhan University, Wuhan, China
| | - Ming Hu
- Department of Obstetrics and Gynecology, Renmin Hospital of Wuhan University, Wuhan, China
| | - Li Hong
- Department of Obstetrics and Gynecology, Renmin Hospital of Wuhan University, Wuhan, China
- *Correspondence: Li Hong,
| |
Collapse
|
22
|
Lindahl L. Increasing Complexity of Ribosomes and Their Biogenesis. Int J Mol Sci 2022; 23:ijms23158264. [PMID: 35897840 PMCID: PMC9332792 DOI: 10.3390/ijms23158264] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2022] [Accepted: 06/29/2022] [Indexed: 12/04/2022] Open
Affiliation(s)
- Lasse Lindahl
- Department of Biological Sciences, University of Maryland, Baltimore County, 1000 Hilltop Circle, Baltimore, MD 21250, USA
| |
Collapse
|
23
|
Kufukihara R, Tanaka N, Takamatsu K, Niwa N, Fukumoto K, Yasumizu Y, Takeda T, Matsumoto K, Morita S, Kosaka T, Aimono E, Nishihara H, Mizuno R, Oya M. Hybridisation chain reaction-based visualisation and screening for lncRNA profiles in clear-cell renal-cell carcinoma. Br J Cancer 2022; 127:1133-1141. [PMID: 35764788 DOI: 10.1038/s41416-022-01895-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2021] [Revised: 06/03/2022] [Accepted: 06/09/2022] [Indexed: 11/09/2022] Open
Abstract
BACKGROUND Analysis of long noncoding RNA (lncRNA) localisation at both the tissue and subcellular levels can provide important insights into the cell types that are important for their function. METHODS By applying new fluorescent in situ hybridisation technique called hybridisation chain reaction (HCR), we achieved a high-throughput lncRNA visualisation and evaluation of clinical samples. RESULTS Assessing 1728 pairs of 16 lncRNAs and clear-cell renal-cell carcinoma (ccRCC) specimens, three lncRNAs (TUG1, HOTAIR and CDKN2B-AS1) were associated with ccRCC prognosis. Furthermore, we derived a new lncRNA risk group of ccRCC prognosis by combining the expression levels of these three lncRNAs. Examining genomic alterations underlying this classification revealed prominent features of tumours that could serve as potential biomarkers for targeting lncRNAs. We then derived combination of HCR with expansion microscopy and visualised nanoscale-resolution HCR signals in cell nuclei, uncovering intracellular colocalization of three lncRNA (TUG1, HOTAIR and CDKN2B-AS1) signals such as those located intra- or out of the nucleus or nucleolus in cancer cells. CONCLUSION LncRNAs are expected to be desirable noncoding targets for cancer diagnosis or treatments. HCR involves plural probes consisting of small DNA oligonucleotides, clinically enabling us to detect cancerous lncRNA signals simply and rapidly at a lower cost.
Collapse
Affiliation(s)
- Ryohei Kufukihara
- Department of Urology, Keio University School of Medicine, 160-8582, Tokyo, Japan
| | - Nobuyuki Tanaka
- Department of Urology, Keio University School of Medicine, 160-8582, Tokyo, Japan.
| | - Kimiharu Takamatsu
- Department of Urology, Keio University School of Medicine, 160-8582, Tokyo, Japan
| | - Naoya Niwa
- Department of Urology, Keio University School of Medicine, 160-8582, Tokyo, Japan
| | - Keishiro Fukumoto
- Department of Urology, Keio University School of Medicine, 160-8582, Tokyo, Japan
| | - Yota Yasumizu
- Department of Urology, Keio University School of Medicine, 160-8582, Tokyo, Japan
| | - Toshikazu Takeda
- Department of Urology, Keio University School of Medicine, 160-8582, Tokyo, Japan
| | - Kazuhiro Matsumoto
- Department of Urology, Keio University School of Medicine, 160-8582, Tokyo, Japan
| | - Shinya Morita
- Department of Urology, Keio University School of Medicine, 160-8582, Tokyo, Japan
| | - Takeo Kosaka
- Department of Urology, Keio University School of Medicine, 160-8582, Tokyo, Japan
| | - Eriko Aimono
- Genomics Unit, Keio Cancer Center, Keio University School of Medicine, Tokyo, Japan
| | - Hiroshi Nishihara
- Genomics Unit, Keio Cancer Center, Keio University School of Medicine, Tokyo, Japan
| | - Ryuichi Mizuno
- Department of Urology, Keio University School of Medicine, 160-8582, Tokyo, Japan
| | - Mototsugu Oya
- Department of Urology, Keio University School of Medicine, 160-8582, Tokyo, Japan
| |
Collapse
|
24
|
Del Borrello G, Miano M, Micalizzi C, Lupia M, Ceccherini I, Grossi A, Cavalli A, Gustincich S, Rusmini M, Faraci M, Dell'Orso G, Ramenghi U, Mesini A, Ricci E, Schiavone M, Di Iorgi N, Dufour C. Sirolimus Restores Erythropoiesis and Controls Immune Dysregulation in a Child With Cartilage-Hair Hypoplasia: A Case Report. Front Immunol 2022; 13:893000. [PMID: 35663969 PMCID: PMC9160192 DOI: 10.3389/fimmu.2022.893000] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2022] [Accepted: 04/19/2022] [Indexed: 12/22/2022] Open
Abstract
Cartilage-hair hypoplasia (CHH) is a syndromic immunodeficiency characterized by metaphyseal dysplasia, cancer predisposition, and varying degrees of anemia. It may present as severe combined immunodeficiency in infancy, or slowly progress until fully manifesting in late adolescence/adulthood. No targeted treatment is currently available, and patients are usually managed with supportive measures, or are offered a bone marrow transplant if the clinical phenotype is severe and a suitable donor is available. We report the case of a young girl presenting with transfusion-dependent erythropoietic failure and immunological features resembling autoimmune lymphoproliferative syndrome who responded well to empirical sirolimus. She later developed a marked growth delay, which was ultimately attributed to metaphyseal dysplasia. A diagnosis of CHH was reached through whole-genome sequencing (WGS), after a less sensitive genetic diagnostic strategy failed. The patient eventually underwent a haploidentical bone marrow transplant due to progressive combined immunodeficiency manifested as cryptococcal meningoencephalitis. This case illustrates the potential role of sirolimus in correcting anemia and partially controlling the immune aberrations associated with CHH, and serves as a reminder of the invaluable role of WGS in diagnosing patients with complex and atypical presentations.
Collapse
Affiliation(s)
- Giovanni Del Borrello
- Hematology Unit, Istituto di Ricerca e Cura a Carattere Scintifico (IRCCS) Istituto Giannina Gaslini, Genoa, Italy
| | - Maurizio Miano
- Hematology Unit, Istituto di Ricerca e Cura a Carattere Scintifico (IRCCS) Istituto Giannina Gaslini, Genoa, Italy
| | - Concetta Micalizzi
- Hematology Unit, Istituto di Ricerca e Cura a Carattere Scintifico (IRCCS) Istituto Giannina Gaslini, Genoa, Italy
| | - Michela Lupia
- Hematology Unit, Istituto di Ricerca e Cura a Carattere Scintifico (IRCCS) Istituto Giannina Gaslini, Genoa, Italy
| | - Isabella Ceccherini
- Unitá Operativa Semplice Dipartimentale (UOSD) Genetics and Genomics of Rare Diseases, Istituto di Ricerca e Cura a Carattere Scintifico (IRCCS) Istituto Giannina Gaslini, Genoa, Italy
| | - Alice Grossi
- Unitá Operativa Semplice Dipartimentale (UOSD) Genetics and Genomics of Rare Diseases, Istituto di Ricerca e Cura a Carattere Scintifico (IRCCS) Istituto Giannina Gaslini, Genoa, Italy
| | | | | | - Marta Rusmini
- Unitá Operativa Semplice Dipartimentale (UOSD) Genetics and Genomics of Rare Diseases, Istituto di Ricerca e Cura a Carattere Scintifico (IRCCS) Istituto Giannina Gaslini, Genoa, Italy
| | - Maura Faraci
- Hematopoietic Stem Cell Transplantation Unit, Istituto di Ricerca e Cura a Carattere Scintifico (IRCCS) Istituto Giannina Gaslini, Genoa, Italy
| | - Gianluca Dell'Orso
- Hematopoietic Stem Cell Transplantation Unit, Istituto di Ricerca e Cura a Carattere Scintifico (IRCCS) Istituto Giannina Gaslini, Genoa, Italy
| | - Ugo Ramenghi
- Haematology Unit, Regina Margherita Hospital, Turin, Italy.,Department of Public Health and Pediatrics, School of Medicine, University of Turin, Turin, Italy
| | - Alessio Mesini
- Covid Hospital, Unità Operativa di Malattie Infettive, Dipartimento di Scienze Pediatriche, Istituto di Ricerca e Cura a Carattere Scintifico (IRCCS) Istituto Giannina Gaslini, Genoa, Italy
| | - Erica Ricci
- Covid Hospital, Unità Operativa di Malattie Infettive, Dipartimento di Scienze Pediatriche, Istituto di Ricerca e Cura a Carattere Scintifico (IRCCS) Istituto Giannina Gaslini, Genoa, Italy
| | | | - Natascia Di Iorgi
- Department of Neuroscience, Rehabilitation, Ophthalmology, Genetics, Maternal and Child Health, University of Genova, Genoa, Italy.,Department of Pediatrics, Istituto di Ricerca e Cura a Carattere Scintifico (IRCCS) Istituto Giannina Gaslini, Genoa, Italy
| | - Carlo Dufour
- Hematology Unit, Istituto di Ricerca e Cura a Carattere Scintifico (IRCCS) Istituto Giannina Gaslini, Genoa, Italy
| |
Collapse
|
25
|
Van Bortle K, Marciano DP, Liu Q, Chou T, Lipchik AM, Gollapudi S, Geller BS, Monte E, Kamakaka RT, Snyder MP. A cancer-associated RNA polymerase III identity drives robust transcription and expression of snaR-A noncoding RNA. Nat Commun 2022; 13:3007. [PMID: 35637192 PMCID: PMC9151912 DOI: 10.1038/s41467-022-30323-6] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2021] [Accepted: 04/13/2022] [Indexed: 11/09/2022] Open
Abstract
RNA polymerase III (Pol III) includes two alternate isoforms, defined by mutually exclusive incorporation of subunit POLR3G (RPC7α) or POLR3GL (RPC7β), in mammals. The contributions of POLR3G and POLR3GL to transcription potential has remained poorly defined. Here, we discover that loss of subunit POLR3G is accompanied by a restricted repertoire of genes transcribed by Pol III. Particularly sensitive is snaR-A, a small noncoding RNA implicated in cancer proliferation and metastasis. Analysis of Pol III isoform biases and downstream chromatin features identifies loss of POLR3G and snaR-A during differentiation, and conversely, re-establishment of POLR3G gene expression and SNAR-A gene features in cancer contexts. Our results support a model in which Pol III identity functions as an important transcriptional regulatory mechanism. Upregulation of POLR3G, which is driven by MYC, identifies a subgroup of patients with unfavorable survival outcomes in specific cancers, further implicating the POLR3G-enhanced transcription repertoire as a potential disease factor. RNA polymerase III changes its subunit composition during mammalian development. Here the authors report that loss of subunit POLR3G, which re-emerges in cancer, promotes expression of small NF90-associated RNA (snaR-A), a noncoding RNA implicated in cell proliferation and metastasis.
Collapse
|
26
|
Abstract
It has long been proposed that nuclear RNAs might play an important role in organizing the structure of the nucleus. Initial experiments performed more than 30 years ago found that global disruption of RNA led to visible rearrangements of nuclear organization. Yet, this idea remained controversial for many years, in large part because it was unclear what specific RNAs might be involved, and which specific nuclear structures might be dependent on RNA. Over the past few years, the contributions of RNA to organizing nuclear structures have become clearer with the discovery that many nuclear bodies are enriched for specific noncoding RNAs (ncRNAs); in specific cases, ncRNAs have been shown to be essential for establishment and maintenance of these nuclear structures. More recently, many different ncRNAs have been shown to play critical roles in initiating the three-dimensional (3D) spatial organization of DNA, RNA, and protein molecules in the nucleus. These examples, combined with global imaging and genomic experiments, have begun to paint a picture of a broader role for RNA in nuclear organization and to uncover a unifying mechanism that may explain why RNA is a uniquely suited molecule for this role. In this review, we provide an overview of the history of RNA and nuclear structure and discuss key examples of RNA-mediated bodies, the global roles of ncRNAs in shaping nuclear structure, and emerging insights into mechanisms of RNA-mediated nuclear organization.
Collapse
Affiliation(s)
- Sofia A Quinodoz
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, California 91125, USA
| | - Mitchell Guttman
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, California 91125, USA
| |
Collapse
|
27
|
Malcolm JR, Leese NK, Lamond-Warner PI, Brackenbury WJ, White RJ. Widespread association of ERα with RMRP and tRNA genes in MCF-7 cells and breast cancers. Gene X 2022; 821:146280. [PMID: 35143945 PMCID: PMC8942118 DOI: 10.1016/j.gene.2022.146280] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2021] [Revised: 01/21/2022] [Accepted: 02/03/2022] [Indexed: 12/04/2022] Open
Abstract
Estrogen receptor (ER) interacts with hundreds of tRNA genes (tDNAs) in MCF-7 cells. Hundreds of tDNAs are also targeted in primary breast tumours and metastases. Canonical estrogen response element is not found near top tDNA targets of ER. ER also targets non-coding breast cancer driver gene RMRP. ER also targets RN7SL1 gene that promotes breast cancer progression.
tRNA gene transcription by RNA polymerase III (Pol III) is a tightly regulated process, but dysregulated Pol III transcription is widely observed in cancers. Approximately 75% of all breast cancers are positive for expression of Estrogen Receptor alpha (ERα), which acts as a key driver of disease. MCF-7 cells rapidly upregulate tRNA gene transcription in response to estrogen and ChIP-PCR demonstrated ERα enrichment at tRNALeu and 5S rRNA genes in this breast cancer cell line. While these data implicate the ERα as a Pol III transcriptional regulator, how widespread this regulation is across the 631 tRNA genes has yet to be revealed. Through analyses of ERα ChIP-seq datasets, we show that ERα interacts with hundreds of tRNA genes, not only in MCF-7 cells, but also in primary human breast tumours and distant metastases. The extent of ERα association with tRNA genes varies between breast cancer cell lines and does not correlate with levels of ERα binding to its canonical target gene GREB1. Amongst other Pol III-transcribed genes, ERα is consistently enriched at the long non-coding RNA gene RMRP, a positive regulator of cell cycle progression that is subject to focal amplification in tumours. Another Pol III template targeted by ERα is the RN7SL1 gene, which is strongly implicated in breast cancer pathology by inducing inflammatory responses in tumours. Our data indicate that Pol III-transcribed non-coding genes should be added to the list of ERα targets in breast cancer.
Collapse
Affiliation(s)
- Jodie R Malcolm
- Department of Biology, The University of York, Heslington Road, YO10 5DD, United Kingdom
| | - Natasha K Leese
- Department of Biology, The University of York, Heslington Road, YO10 5DD, United Kingdom
| | | | - William J Brackenbury
- Department of Biology, The University of York, Heslington Road, YO10 5DD, United Kingdom
| | - Robert J White
- Department of Biology, The University of York, Heslington Road, YO10 5DD, United Kingdom.
| |
Collapse
|
28
|
Köferle A, Schlattl A, Hörmann A, Thatikonda V, Popa A, Spreitzer F, Ravichandran MC, Supper V, Oberndorfer S, Puchner T, Wieshofer C, Corcokovic M, Reiser C, Wöhrle S, Popow J, Pearson M, Martinez J, Weitzer S, Mair B, Neumüller RA. Interrogation of cancer gene dependencies reveals paralog interactions of autosome and sex chromosome-encoded genes. Cell Rep 2022; 39:110636. [PMID: 35417719 DOI: 10.1016/j.celrep.2022.110636] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2021] [Revised: 12/22/2021] [Accepted: 03/16/2022] [Indexed: 02/07/2023] Open
Abstract
Genetic networks are characterized by extensive buffering. During tumor evolution, disruption of functional redundancies can create de novo vulnerabilities that are specific to cancer cells. Here, we systematically search for cancer-relevant paralog interactions using CRISPR screens and publicly available loss-of-function datasets. Our analysis reveals >2,000 candidate dependencies, several of which we validate experimentally, including CSTF2-CSTF2T, DNAJC15-DNAJC19, FAM50A-FAM50B, and RPP25-RPP25L. We provide evidence that RPP25L can physically and functionally compensate for the absence of RPP25 as a member of the RNase P/MRP complexes in tRNA processing. Our analysis also reveals unexpected redundancies between sex chromosome genes. We show that chrX- and chrY-encoded paralogs, such as ZFX-ZFY, DDX3X-DDX3Y, and EIF1AX-EIF1AY, are functionally linked. Tumor cell lines from male patients with loss of chromosome Y become dependent on the chrX-encoded gene. We propose targeting of chrX-encoded paralogs as a general therapeutic strategy for human tumors that have lost the Y chromosome.
Collapse
Affiliation(s)
- Anna Köferle
- Boehringer Ingelheim RCV GmbH & Co KG, Doktor-Boehringer-Gasse 5-11, 1120 Vienna, Austria
| | - Andreas Schlattl
- Boehringer Ingelheim RCV GmbH & Co KG, Doktor-Boehringer-Gasse 5-11, 1120 Vienna, Austria
| | - Alexandra Hörmann
- Boehringer Ingelheim RCV GmbH & Co KG, Doktor-Boehringer-Gasse 5-11, 1120 Vienna, Austria
| | - Venu Thatikonda
- Boehringer Ingelheim RCV GmbH & Co KG, Doktor-Boehringer-Gasse 5-11, 1120 Vienna, Austria
| | - Alexandra Popa
- Boehringer Ingelheim RCV GmbH & Co KG, Doktor-Boehringer-Gasse 5-11, 1120 Vienna, Austria
| | - Fiona Spreitzer
- Boehringer Ingelheim RCV GmbH & Co KG, Doktor-Boehringer-Gasse 5-11, 1120 Vienna, Austria
| | | | - Verena Supper
- Boehringer Ingelheim RCV GmbH & Co KG, Doktor-Boehringer-Gasse 5-11, 1120 Vienna, Austria
| | - Sarah Oberndorfer
- Boehringer Ingelheim RCV GmbH & Co KG, Doktor-Boehringer-Gasse 5-11, 1120 Vienna, Austria
| | - Teresa Puchner
- Boehringer Ingelheim RCV GmbH & Co KG, Doktor-Boehringer-Gasse 5-11, 1120 Vienna, Austria
| | - Corinna Wieshofer
- Boehringer Ingelheim RCV GmbH & Co KG, Doktor-Boehringer-Gasse 5-11, 1120 Vienna, Austria
| | - Maja Corcokovic
- Boehringer Ingelheim RCV GmbH & Co KG, Doktor-Boehringer-Gasse 5-11, 1120 Vienna, Austria
| | - Christoph Reiser
- Boehringer Ingelheim RCV GmbH & Co KG, Doktor-Boehringer-Gasse 5-11, 1120 Vienna, Austria
| | - Simon Wöhrle
- Boehringer Ingelheim RCV GmbH & Co KG, Doktor-Boehringer-Gasse 5-11, 1120 Vienna, Austria
| | - Johannes Popow
- Boehringer Ingelheim RCV GmbH & Co KG, Doktor-Boehringer-Gasse 5-11, 1120 Vienna, Austria
| | - Mark Pearson
- Boehringer Ingelheim RCV GmbH & Co KG, Doktor-Boehringer-Gasse 5-11, 1120 Vienna, Austria
| | - Javier Martinez
- Max Perutz Labs, Medical University of Vienna, Vienna BioCenter (VBC), Dr. Bohr-Gasse 9/2, 1030 Vienna, Austria
| | - Stefan Weitzer
- Max Perutz Labs, Medical University of Vienna, Vienna BioCenter (VBC), Dr. Bohr-Gasse 9/2, 1030 Vienna, Austria
| | - Barbara Mair
- Boehringer Ingelheim RCV GmbH & Co KG, Doktor-Boehringer-Gasse 5-11, 1120 Vienna, Austria.
| | - Ralph A Neumüller
- Boehringer Ingelheim RCV GmbH & Co KG, Doktor-Boehringer-Gasse 5-11, 1120 Vienna, Austria.
| |
Collapse
|
29
|
Derksen M, Mertens V, Visser EA, Arts J, Vree Egberts W, Pruijn GJM. A novel experimental approach for the selective isolation and characterization of human RNase MRP. RNA Biol 2022; 19:305-312. [PMID: 35129080 PMCID: PMC8820802 DOI: 10.1080/15476286.2022.2027659] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022] Open
Abstract
RNase MRP is a ribonucleoprotein complex involved in the endoribonucleolytic cleavage of different RNAs. Mutations in the RNA component of the RNP are the cause of cartilage hair hypoplasia. Patients with cartilage hair hypoplasia are characterized by skeletal dysplasia. Biochemical purification of RNase MRP is desired to be able to study its biochemical function, composition and activity in both healthy and disease situations. Due to the high similarity with RNase P, a method to specifically isolate the RNase MRP complex is currently lacking. By fusing a streptavidin-binding RNA aptamer, the S1m-aptamer, to the RNase MRP RNA we have been able to compare the relative expression levels of wildtype and mutant MRP RNAs. Moreover, we were able to isolate active RNase MRP complexes. We observed that mutant MRP RNAs are expressed at lower levels and have lower catalytic activity compared to the wildtype RNA. The observation that a single nucleotide substitution at position 40 in the P3 domain but not in other domains of RNase MRP RNA severely reduced the binding of the Rpp25 protein subunit confirmed that the P3 region harbours the main binding site for this protein. Altogether, this study shows that the RNA aptamer tagging approach can be used to identify RNase MRP substrates, but also to study the effect of mutations on MRP RNA expression levels and RNase MRP composition and endoribonuclease activity.
Collapse
Affiliation(s)
- Merel Derksen
- Department of Biomolecular Chemistry, Institute for Molecules and Materials (IMM), Radboud University, Nijmegen, The Netherlands
| | - Vicky Mertens
- Department of Biomolecular Chemistry, Institute for Molecules and Materials (IMM), Radboud University, Nijmegen, The Netherlands
| | - Eline A. Visser
- Department of Biomolecular Chemistry, Institute for Molecules and Materials (IMM), Radboud University, Nijmegen, The Netherlands
| | - Janine Arts
- Department of Biomolecular Chemistry, Institute for Molecules and Materials (IMM), Radboud University, Nijmegen, The Netherlands
| | - Wilma Vree Egberts
- Department of Biomolecular Chemistry, Institute for Molecules and Materials (IMM), Radboud University, Nijmegen, The Netherlands
| | - Ger J. M. Pruijn
- Department of Biomolecular Chemistry, Institute for Molecules and Materials (IMM), Radboud University, Nijmegen, The Netherlands
| |
Collapse
|
30
|
Robertson N, Shchepachev V, Wright D, Turowski TW, Spanos C, Helwak A, Zamoyska R, Tollervey D. A disease-linked lncRNA mutation in RNase MRP inhibits ribosome synthesis. Nat Commun 2022; 13:649. [PMID: 35115551 PMCID: PMC8814244 DOI: 10.1038/s41467-022-28295-8] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2021] [Accepted: 01/14/2022] [Indexed: 01/02/2023] Open
Abstract
RMRP encodes a non-coding RNA forming the core of the RNase MRP ribonucleoprotein complex. Mutations cause Cartilage Hair Hypoplasia (CHH), characterized by skeletal abnormalities and impaired T cell activation. Yeast RNase MRP cleaves a specific site in the pre-ribosomal RNA (pre-rRNA) during ribosome synthesis. CRISPR-mediated disruption of RMRP in human cells lines caused growth arrest, with pre-rRNA accumulation. Here, we analyzed disease-relevant primary cells, showing that mutations in RMRP impair mouse T cell activation and delay pre-rRNA processing. Patient-derived human fibroblasts with CHH-linked mutations showed similar pre-rRNA processing delay. Human cells engineered with the most common CHH mutation (70AG in RMRP) show specifically impaired pre-rRNA processing, resulting in reduced mature rRNA and a reduced ratio of cytosolic to mitochondrial ribosomes. Moreover, the 70AG mutation caused a reduction in intact RNase MRP complexes. Together, these results indicate that CHH is a ribosomopathy.
Collapse
Affiliation(s)
- Nic Robertson
- Wellcome Centre for Cell Biology, University of Edinburgh, Edinburgh, UK
| | - Vadim Shchepachev
- The Gurdon Institute and Department of Pathology, University of Cambridge, Cambridge, UK
| | - David Wright
- Ashworth Laboratories, Institute of Immunology and Infection Research, University of Edinburgh, Edinburgh, UK
| | - Tomasz W Turowski
- Wellcome Centre for Cell Biology, University of Edinburgh, Edinburgh, UK
| | - Christos Spanos
- Wellcome Centre for Cell Biology, University of Edinburgh, Edinburgh, UK
| | - Aleksandra Helwak
- Wellcome Centre for Cell Biology, University of Edinburgh, Edinburgh, UK
| | - Rose Zamoyska
- Ashworth Laboratories, Institute of Immunology and Infection Research, University of Edinburgh, Edinburgh, UK
| | - David Tollervey
- Wellcome Centre for Cell Biology, University of Edinburgh, Edinburgh, UK.
| |
Collapse
|
31
|
De la Fuente-Hernandez MA, Sarabia-Sanchez MA, Melendez-Zajgla J, Maldonado-Lagunas V. Role of lncRNAs into Mesenchymal Stromal Cell Differentiation. Am J Physiol Cell Physiol 2022; 322:C421-C460. [PMID: 35080923 DOI: 10.1152/ajpcell.00364.2021] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Currently, findings support that 75% of the human genome is actively transcribed, but only 2% is translated into a protein, according to databases such as ENCODE (Encyclopedia of DNA Elements) [1]. The development of high-throughput sequencing technologies, computational methods for genome assembly and biological models have led to the realization of the importance of the previously unconsidered non-coding fraction of the genome. Along with this, noncoding RNAs have been shown to be epigenetic, transcriptional and post-transcriptional regulators in a large number of cellular processes [2]. Within the group of non-coding RNAs, lncRNAs represent a fascinating field of study, given the functional versatility in their mode of action on their molecular targets. In recent years, there has been an interest in learning about lncRNAs in MSC differentiation. The aim of this review is to address the signaling mechanisms where lncRNAs are involved, emphasizing their role in either stimulating or inhibiting the transition to differentiated cell. Specifically, the main types of MSC differentiation are discussed: myogenesis, osteogenesis, adipogenesis and chondrogenesis. The description of increasingly new lncRNAs reinforces their role as players in the well-studied field of MSC differentiation, allowing a step towards a better understanding of their biology and their potential application in the clinic.
Collapse
Affiliation(s)
- Marcela Angelica De la Fuente-Hernandez
- Facultad de Medicina, Posgrado en Ciencias Biológicas, Universidad Nacional Autónoma de México, Mexico City, Mexico.,Laboratorio de Epigenética, Instituto Nacional de Medicina Genómica, Mexico City, Mexico
| | - Miguel Angel Sarabia-Sanchez
- Facultad de Medicina, Posgrado en Ciencias Bioquímicas, Universidad Nacional Autónoma de México, Mexico City, Mexico
| | - Jorge Melendez-Zajgla
- Laboratorio de Genómica Funcional del Cáncer, Instituto Nacional de Medicina Genómica, Mexico City, Mexico
| | | |
Collapse
|
32
|
Hao Q, Zhou X. The emerging role of long noncoding RNA RMRP in cancer development and targeted therapy. Cancer Biol Med 2022; 19:j.issn.2095-3941.2021.0577. [PMID: 35075888 PMCID: PMC8832963 DOI: 10.20892/j.issn.2095-3941.2021.0577] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2021] [Accepted: 11/26/2021] [Indexed: 11/11/2022] Open
Affiliation(s)
- Qian Hao
- Fudan University Shanghai Cancer Center and Institutes of Biomedical Sciences, Fudan University, Shanghai 200032, China
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai 200032, China
| | - Xiang Zhou
- Fudan University Shanghai Cancer Center and Institutes of Biomedical Sciences, Fudan University, Shanghai 200032, China
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai 200032, China
- Key Laboratory of Breast Cancer in Shanghai, Fudan University Shanghai Cancer Center, Fudan University, Shanghai 200032, China
- Shanghai Key Laboratory of Medical Epigenetics, International Co-laboratory of Medical Epigenetics and Metabolism (Ministry of Science and Technology), Institutes of Biomedical Sciences, Fudan University, Shanghai 200032, China
| |
Collapse
|
33
|
Chabronova A, van den Akker GGH, Meekels-Steinbusch MMF, Friedrich F, Cremers A, Surtel DAM, Peffers MJ, van Rhijn LW, Lausch E, Zabel B, Caron MMJ, Welting TJM. Uncovering pathways regulating chondrogenic differentiation of CHH fibroblasts. Noncoding RNA Res 2022; 6:211-224. [PMID: 34988338 PMCID: PMC8688813 DOI: 10.1016/j.ncrna.2021.12.003] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2021] [Revised: 12/08/2021] [Accepted: 12/08/2021] [Indexed: 02/08/2023] Open
Abstract
Mutations in the non-coding snoRNA component of mitochondrial RNA processing endoribonuclease (RMRP) are the cause of cartilage-hair hypoplasia (CHH). CHH is a rare form of metaphyseal chondrodysplasia characterized by disproportionate short stature and abnormal growth plate development. The process of chondrogenic differentiation within growth plates of long bones is vital for longitudinal bone growth. However, molecular mechanisms behind impaired skeletal development in CHH patients remain unclear. We employed a transdifferentiation model (FDC) combined with whole transcriptome analysis to investigate the chondrogenic transdifferentiation capacity of CHH fibroblasts and to examine pathway regulation in CHH cells during chondrogenic differentiation. We established that the FDC transdifferentiation model is a relevant in vitro model of chondrogenic differentiation, with an emphasis on the terminal differentiation phase, which is crucial for longitudinal bone growth. We demonstrated that CHH fibroblasts are capable of transdifferentiating into chondrocyte-like cells, and show a reduced commitment to terminal differentiation. We also found a number of key factors of BMP, FGF, and IGF-1 signalling axes to be significantly upregulated in CHH cells during the chondrogenic transdifferentiation. Our results support postulated conclusions that RMRP has pleiotropic functions and profoundly affects multiple aspects of cell fate and signalling. Our findings shed light on the consequences of pathological CHH mutations in snoRNA RMRP during chondrogenic differentiation and the relevance and roles of non-coding RNAs in genetic diseases in general.
Collapse
Affiliation(s)
- Alzbeta Chabronova
- Laboratory for Experimental Orthopedics, Department of Orthopedic Surgery, MUMC+, 6202, AZ, Maastricht, the Netherlands
| | - Guus G H van den Akker
- Laboratory for Experimental Orthopedics, Department of Orthopedic Surgery, MUMC+, 6202, AZ, Maastricht, the Netherlands
| | - Mandy M F Meekels-Steinbusch
- Laboratory for Experimental Orthopedics, Department of Orthopedic Surgery, MUMC+, 6202, AZ, Maastricht, the Netherlands
| | - Franziska Friedrich
- Department of Pediatrics, Medical Center, University of Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Andy Cremers
- Laboratory for Experimental Orthopedics, Department of Orthopedic Surgery, MUMC+, 6202, AZ, Maastricht, the Netherlands
| | - Don A M Surtel
- Laboratory for Experimental Orthopedics, Department of Orthopedic Surgery, MUMC+, 6202, AZ, Maastricht, the Netherlands
| | - Mandy J Peffers
- Institute of Life Course and Medical Sciences, University of Liverpool, William Henry Duncan Building, 6 West Derby Street, Liverpool, L7 8TX, UK
| | - Lodewijk W van Rhijn
- Laboratory for Experimental Orthopedics, Department of Orthopedic Surgery, MUMC+, 6202, AZ, Maastricht, the Netherlands
| | - Ekkehart Lausch
- Department of Pediatrics, Medical Center, University of Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Bernhard Zabel
- Medical Faculty, Otto van Guericke University of Magdeburg, 39106, Magdeburg, Germany
| | - Marjolein M J Caron
- Laboratory for Experimental Orthopedics, Department of Orthopedic Surgery, MUMC+, 6202, AZ, Maastricht, the Netherlands
| | - Tim J M Welting
- Laboratory for Experimental Orthopedics, Department of Orthopedic Surgery, MUMC+, 6202, AZ, Maastricht, the Netherlands
| |
Collapse
|
34
|
Abstract
PURPOSE OF REVIEW Translation of genetic information encoded within mRNA molecules by ribosomes into proteins is a key part of the central dogma of molecular biology. Despite the central position of the ribosome in the translation of proteins, and considering the major proteomic changes that occur in the joint during osteoarthritis development and progression, the ribosome has received very limited attention as driver of osteoarthritis pathogenesis. RECENT FINDINGS We provide an overview of the limited literature regarding this developing topic for the osteoarthritis field. Recent key findings that connect ribosome biogenesis and activity with osteoarthritis include: ribosomal RNA transcription, processing and maturation, ribosomal protein expression, protein translation capacity and preferential translation. SUMMARY The ribosome as the central cellular protein synthesis hub is largely neglected in osteoarthritis research. Findings included in this review reveal that in osteoarthritis, ribosome aberrations have been found from early-stage ribosome biogenesis, through ribosome build-up and maturation, up to preferential translation. Classically, osteoarthritis has been explained as an imbalance between joint tissue anabolism and catabolism. We postulate that osteoarthritis can be interpreted as an acquired ribosomopathy. This hypothesis fine-tunes the dogmatic anabolism/katabolism point-of-view, and may provide novel molecular opportunities for the development of osteoarthritis disease-modifying treatments.
Collapse
Affiliation(s)
- Guus G.H. van den Akker
- Laboratory for Experimental Orthopedics, Department of Orthopedic Surgery, Maastricht University
| | - Marjolein M.J. Caron
- Laboratory for Experimental Orthopedics, Department of Orthopedic Surgery, Maastricht University
| | - Mandy J. Peffers
- Institute of Life Course and Medical Sciences, University of Liverpool, Liverpool, UK
| | - Tim J.M. Welting
- Laboratory for Experimental Orthopedics, Department of Orthopedic Surgery, Maastricht University
- Laboratory for Experimental Orthopedics, Department of Orthopedic Surgery, Maastricht University Medical Center, Maastricht, the Netherlands
| |
Collapse
|
35
|
Venturi G, Zacchini F, Vaccari CL, Trerè D, Montanaro L. Primer extension coupled with fragment analysis for rapid and quantitative evaluation of 5.8S rRNA isoforms. PLoS One 2021; 16:e0261476. [PMID: 34932578 PMCID: PMC8691633 DOI: 10.1371/journal.pone.0261476] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2021] [Accepted: 12/02/2021] [Indexed: 11/30/2022] Open
Abstract
The ribosomal RNA 5.8S is one of the four rRNAs that constitute ribosomes. In human cells, like in all eukaryotes, it derives from the extensive processing of a long precursor containing the sequence of 18S, 5.8S and 28S rRNAs. It has been confirmed also in human cells the presence of three isoforms of 5.8S rRNA: one more abundant called 5.8S short, one called 5.8S long bearing 5 extra-nucleotides at its 5’ end and one 10 nucleotide shorter called 5.8S cropped. So far, little is known about 5.8S long specific role in cell biology and its function in human pathology. The lack of studies on the three 5.8S isoforms could be due to the techniques usually applied to study ribosome biogenesis, such as Northern blot with radioactively labelled probes, that require strict protective measures, and abundant and high-quality samples. To overcome this issue, we optimized a method that combines primer extension with a fluorescently labeled reverse primer designed on the 3’ of 5.8S rRNA sequence and fragment analysis. The resulting electropherogram shows the peaks corresponding to the three isoforms of 5.8S rRNA. The estimation of the area underneath the peaks allows to directly quantify the isoforms and to express their relative abundance. The relative abundance of 5.8S long and 5.8S short remains constant using scalar dilution of RNA and in samples subjected to partial degradation. 5.8S cropped abundance varies significantly in lower concentrate RNA samples. This method allows to analyze rapidly and safely the abundance of 5.8S rRNA isoforms in samples that have been so far considered not suitable such as poorly concentrated samples, RNA derived from frozen tissue or unique samples.
Collapse
Affiliation(s)
- Giulia Venturi
- Dipartimento di Medicina Specialistica, Diagnostica e Sperimentale (DIMES), Alma Mater Studiorum—Università di Bologna, Bologna, Italia
- Centro di Ricerca Biomedica Applicata–CRBA, Università̀ di Bologna, Policlinico di Sant’Orsola, Bologna, Italia
| | - Federico Zacchini
- Dipartimento di Medicina Specialistica, Diagnostica e Sperimentale (DIMES), Alma Mater Studiorum—Università di Bologna, Bologna, Italia
- Centro di Ricerca Biomedica Applicata–CRBA, Università̀ di Bologna, Policlinico di Sant’Orsola, Bologna, Italia
| | - Cinzia Lucia Vaccari
- Dipartimento di Medicina Specialistica, Diagnostica e Sperimentale (DIMES), Alma Mater Studiorum—Università di Bologna, Bologna, Italia
- Centro di Ricerca Biomedica Applicata–CRBA, Università̀ di Bologna, Policlinico di Sant’Orsola, Bologna, Italia
| | - Davide Trerè
- Dipartimento di Medicina Specialistica, Diagnostica e Sperimentale (DIMES), Alma Mater Studiorum—Università di Bologna, Bologna, Italia
- Programma Dipartimentale di Medicina di Laboratorio, IRCCS Azienda Ospedaliero-Universitaria di Bologna, Bologna, Italia
| | - Lorenzo Montanaro
- Dipartimento di Medicina Specialistica, Diagnostica e Sperimentale (DIMES), Alma Mater Studiorum—Università di Bologna, Bologna, Italia
- Centro di Ricerca Biomedica Applicata–CRBA, Università̀ di Bologna, Policlinico di Sant’Orsola, Bologna, Italia
- Programma Dipartimentale di Medicina di Laboratorio, IRCCS Azienda Ospedaliero-Universitaria di Bologna, Bologna, Italia
- * E-mail:
| |
Collapse
|
36
|
Quinodoz SA, Jachowicz JW, Bhat P, Ollikainen N, Banerjee AK, Goronzy IN, Blanco MR, Chovanec P, Chow A, Markaki Y, Thai J, Plath K, Guttman M. RNA promotes the formation of spatial compartments in the nucleus. Cell 2021; 184:5775-5790.e30. [PMID: 34739832 PMCID: PMC9115877 DOI: 10.1016/j.cell.2021.10.014] [Citation(s) in RCA: 185] [Impact Index Per Article: 61.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2020] [Revised: 08/25/2021] [Accepted: 10/13/2021] [Indexed: 12/25/2022]
Abstract
RNA, DNA, and protein molecules are highly organized within three-dimensional (3D) structures in the nucleus. Although RNA has been proposed to play a role in nuclear organization, exploring this has been challenging because existing methods cannot measure higher-order RNA and DNA contacts within 3D structures. To address this, we developed RNA & DNA SPRITE (RD-SPRITE) to comprehensively map the spatial organization of RNA and DNA. These maps reveal higher-order RNA-chromatin structures associated with three major classes of nuclear function: RNA processing, heterochromatin assembly, and gene regulation. These data demonstrate that hundreds of ncRNAs form high-concentration territories throughout the nucleus, that specific RNAs are required to recruit various regulators into these territories, and that these RNAs can shape long-range DNA contacts, heterochromatin assembly, and gene expression. These results demonstrate a mechanism where RNAs form high-concentration territories, bind to diffusible regulators, and guide them into compartments to regulate essential nuclear functions.
Collapse
Affiliation(s)
- Sofia A Quinodoz
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Joanna W Jachowicz
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Prashant Bhat
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA; David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Noah Ollikainen
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Abhik K Banerjee
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA; Keck School of Medicine, University of Southern California, Los Angeles, CA 90089, USA
| | - Isabel N Goronzy
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA; David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Mario R Blanco
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Peter Chovanec
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Amy Chow
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Yolanda Markaki
- Department of Biological Chemistry, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Jasmine Thai
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Kathrin Plath
- Department of Biological Chemistry, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Mitchell Guttman
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA.
| |
Collapse
|
37
|
Huang Y, Xie B, Cao M, Lu H, Wu X, Hao Q, Zhou X. LncRNA RNA Component of Mitochondrial RNA-Processing Endoribonuclease Promotes AKT-Dependent Breast Cancer Growth and Migration by Trapping MicroRNA-206. Front Cell Dev Biol 2021; 9:730538. [PMID: 34621748 PMCID: PMC8490808 DOI: 10.3389/fcell.2021.730538] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2021] [Accepted: 08/30/2021] [Indexed: 12/30/2022] Open
Abstract
The RNA component of mitochondrial RNA-processing endoribonuclease (RMRP) was recently shown to play a role in cancer development. However, the function and mechanism of RMRP during cancer progression remain incompletely understood. Here, we report that RMRP is amplified and highly expressed in various malignant cancers, and the high level of RMRP is significantly associated with their poor prognosis, including breast cancer. Consistent with this, ectopic RMRP promotes proliferation and migration of TP53-mutated breast cancer cells, whereas depletion of RMRP leads to inhibition of their proliferation and migration. RNA-seq analysis reveals AKT as a downstream target of RMRP. Interestingly, RMRP indirectly elevates AKT expression by preventing AKT mRNA from miR-206-mediated targeting via a competitive sequestering mechanism. Remarkably, RMRP endorses breast cancer progression in an AKT-dependent fashion, as knockdown of AKT completely abolishes RMRP-induced cancer cell growth and migration. Altogether, our results unveil a novel role of the RMRP-miR-206-AKT axis in breast cancer development, providing a potential new target for developing an anti-breast cancer therapy.
Collapse
Affiliation(s)
- Yingdan Huang
- Fudan University Shanghai Cancer Center and Institutes of Biomedical Sciences, Fudan University, Shanghai, China.,Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
| | - Bangxiang Xie
- Beijing Institute of Hepatology, Beijing You An Hospital, Capital Medical University, Beijing, China.,Beijing Engineering Research Center for Precision Medicine and Transformation of Hepatitis and Liver Cancer, Beijing, China
| | - Mingming Cao
- Fudan University Shanghai Cancer Center and Institutes of Biomedical Sciences, Fudan University, Shanghai, China.,Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
| | - Hua Lu
- Department of Biochemistry & Molecular Biology, Tulane Cancer Center, Tulane University School of Medicine, New Orleans, LA, United States
| | - Xiaohua Wu
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China.,Department of Gynecologic Oncology, Fudan University Shanghai Cancer Center, Fudan University, Shanghai, China
| | - Qian Hao
- Fudan University Shanghai Cancer Center and Institutes of Biomedical Sciences, Fudan University, Shanghai, China.,Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
| | - Xiang Zhou
- Fudan University Shanghai Cancer Center and Institutes of Biomedical Sciences, Fudan University, Shanghai, China.,Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China.,Key Laboratory of Breast Cancer in Shanghai, Fudan University Shanghai Cancer Center, Fudan University, Shanghai, China.,Shanghai Key Laboratory of Medical Epigenetics, International Co-Laboratory of Medical Epigenetics and Metabolism, Ministry of Science and Technology, Institutes of Biomedical Sciences, Fudan University, Shanghai, China
| |
Collapse
|
38
|
Birikmen M, Bohnsack KE, Tran V, Somayaji S, Bohnsack MT, Ebersberger I. Tracing Eukaryotic Ribosome Biogenesis Factors Into the Archaeal Domain Sheds Light on the Evolution of Functional Complexity. Front Microbiol 2021; 12:739000. [PMID: 34603269 PMCID: PMC8481954 DOI: 10.3389/fmicb.2021.739000] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2021] [Accepted: 08/17/2021] [Indexed: 01/23/2023] Open
Abstract
Ribosome assembly is an essential and carefully choreographed cellular process. In eukaryotes, several 100 proteins, distributed across the nucleolus, nucleus, and cytoplasm, co-ordinate the step-wise assembly of four ribosomal RNAs (rRNAs) and approximately 80 ribosomal proteins (RPs) into the mature ribosomal subunits. Due to the inherent complexity of the assembly process, functional studies identifying ribosome biogenesis factors and, more importantly, their precise functions and interplay are confined to a few and very well-established model organisms. Although best characterized in yeast (Saccharomyces cerevisiae), emerging links to disease and the discovery of additional layers of regulation have recently encouraged deeper analysis of the pathway in human cells. In archaea, ribosome biogenesis is less well-understood. However, their simpler sub-cellular structure should allow a less elaborated assembly procedure, potentially providing insights into the functional essentials of ribosome biogenesis that evolved long before the diversification of archaea and eukaryotes. Here, we use a comprehensive phylogenetic profiling setup, integrating targeted ortholog searches with automated scoring of protein domain architecture similarities and an assessment of when search sensitivity becomes limiting, to trace 301 curated eukaryotic ribosome biogenesis factors across 982 taxa spanning the tree of life and including 727 archaea. We show that both factor loss and lineage-specific modifications of factor function modulate ribosome biogenesis, and we highlight that limited sensitivity of the ortholog search can confound evolutionary conclusions. Projecting into the archaeal domain, we find that only few factors are consistently present across the analyzed taxa, and lineage-specific loss is common. While members of the Asgard group are not special with respect to their inventory of ribosome biogenesis factors (RBFs), they unite the highest number of orthologs to eukaryotic RBFs in one taxon. Using large ribosomal subunit maturation as an example, we demonstrate that archaea pursue a simplified version of the corresponding steps in eukaryotes. Much of the complexity of this process evolved on the eukaryotic lineage by the duplication of ribosomal proteins and their subsequent functional diversification into ribosome biogenesis factors. This highlights that studying ribosome biogenesis in archaea provides fundamental information also for understanding the process in eukaryotes.
Collapse
Affiliation(s)
- Mehmet Birikmen
- Applied Bioinformatics Group, Institute of Cell Biology and Neuroscience, Goethe University Frankfurt, Frankfurt, Germany
| | - Katherine E Bohnsack
- Department of Molecular Biology, University Medical Center Göttingen, Göttingen, Germany
| | - Vinh Tran
- Applied Bioinformatics Group, Institute of Cell Biology and Neuroscience, Goethe University Frankfurt, Frankfurt, Germany
| | - Sharvari Somayaji
- Applied Bioinformatics Group, Institute of Cell Biology and Neuroscience, Goethe University Frankfurt, Frankfurt, Germany
| | - Markus T Bohnsack
- Department of Molecular Biology, University Medical Center Göttingen, Göttingen, Germany.,Göttingen Center for Molecular Biosciences, Georg-August University, Göttingen, Germany
| | - Ingo Ebersberger
- Applied Bioinformatics Group, Institute of Cell Biology and Neuroscience, Goethe University Frankfurt, Frankfurt, Germany.,Senckenberg Biodiversity and Climate Research Center (S-BIK-F), Frankfurt, Germany.,LOEWE Center for Translational Biodiversity Genomics (LOEWE-TBG), Frankfurt, Germany
| |
Collapse
|
39
|
Long S. SARS-CoV-2 Subgenomic RNAs: Characterization, Utility, and Perspectives. Viruses 2021; 13:1923. [PMID: 34696353 PMCID: PMC8539008 DOI: 10.3390/v13101923] [Citation(s) in RCA: 36] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2021] [Revised: 09/12/2021] [Accepted: 09/16/2021] [Indexed: 12/11/2022] Open
Abstract
SARS-CoV-2, the etiologic agent at the root of the ongoing COVID-19 pandemic, harbors a large RNA genome from which a tiered ensemble of subgenomic RNAs (sgRNAs) is generated. Comprehensive definition and investigation of these RNA products are important for understanding SARS-CoV-2 pathogenesis. This review summarizes the recent progress on SARS-CoV-2 sgRNA identification, characterization, and application as a viral replication marker. The significance of these findings and potential future research areas of interest are discussed.
Collapse
Affiliation(s)
- Samuel Long
- Independent Researcher, Clarksburg, MD 20871, USA
| |
Collapse
|
40
|
Kang J, Brajanovski N, Chan KT, Xuan J, Pearson RB, Sanij E. Ribosomal proteins and human diseases: molecular mechanisms and targeted therapy. Signal Transduct Target Ther 2021; 6:323. [PMID: 34462428 PMCID: PMC8405630 DOI: 10.1038/s41392-021-00728-8] [Citation(s) in RCA: 125] [Impact Index Per Article: 41.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2021] [Revised: 07/12/2021] [Accepted: 07/30/2021] [Indexed: 02/07/2023] Open
Abstract
Ribosome biogenesis and protein synthesis are fundamental rate-limiting steps for cell growth and proliferation. The ribosomal proteins (RPs), comprising the structural parts of the ribosome, are essential for ribosome assembly and function. In addition to their canonical ribosomal functions, multiple RPs have extra-ribosomal functions including activation of p53-dependent or p53-independent pathways in response to stress, resulting in cell cycle arrest and apoptosis. Defects in ribosome biogenesis, translation, and the functions of individual RPs, including mutations in RPs have been linked to a diverse range of human congenital disorders termed ribosomopathies. Ribosomopathies are characterized by tissue-specific phenotypic abnormalities and higher cancer risk later in life. Recent discoveries of somatic mutations in RPs in multiple tumor types reinforce the connections between ribosomal defects and cancer. In this article, we review the most recent advances in understanding the molecular consequences of RP mutations and ribosomal defects in ribosomopathies and cancer. We particularly discuss the molecular basis of the transition from hypo- to hyper-proliferation in ribosomopathies with elevated cancer risk, a paradox termed "Dameshek's riddle." Furthermore, we review the current treatments for ribosomopathies and prospective therapies targeting ribosomal defects. We also highlight recent advances in ribosome stress-based cancer therapeutics. Importantly, insights into the mechanisms of resistance to therapies targeting ribosome biogenesis bring new perspectives into the molecular basis of cancer susceptibility in ribosomopathies and new clinical implications for cancer therapy.
Collapse
Affiliation(s)
- Jian Kang
- grid.1055.10000000403978434Division of Cancer Research, Peter MacCallum Cancer Centre, Melbourne, VIC Australia ,grid.1008.90000 0001 2179 088XSir Peter MacCallum Department of Oncology, University of Melbourne, Melbourne, VIC Australia
| | - Natalie Brajanovski
- grid.1055.10000000403978434Division of Cancer Research, Peter MacCallum Cancer Centre, Melbourne, VIC Australia
| | - Keefe T. Chan
- grid.1055.10000000403978434Division of Cancer Research, Peter MacCallum Cancer Centre, Melbourne, VIC Australia ,grid.1008.90000 0001 2179 088XSir Peter MacCallum Department of Oncology, University of Melbourne, Melbourne, VIC Australia
| | - Jiachen Xuan
- grid.1055.10000000403978434Division of Cancer Research, Peter MacCallum Cancer Centre, Melbourne, VIC Australia ,grid.1008.90000 0001 2179 088XSir Peter MacCallum Department of Oncology, University of Melbourne, Melbourne, VIC Australia
| | - Richard B. Pearson
- grid.1055.10000000403978434Division of Cancer Research, Peter MacCallum Cancer Centre, Melbourne, VIC Australia ,grid.1008.90000 0001 2179 088XSir Peter MacCallum Department of Oncology, University of Melbourne, Melbourne, VIC Australia ,grid.1002.30000 0004 1936 7857Department of Biochemistry and Molecular Biology, Monash University, Clayton, VIC Australia ,grid.1008.90000 0001 2179 088XDepartment of Biochemistry and Molecular Biology, University of Melbourne, Melbourne, VIC Australia
| | - Elaine Sanij
- grid.1055.10000000403978434Division of Cancer Research, Peter MacCallum Cancer Centre, Melbourne, VIC Australia ,grid.1008.90000 0001 2179 088XSir Peter MacCallum Department of Oncology, University of Melbourne, Melbourne, VIC Australia ,grid.1008.90000 0001 2179 088XDepartment of Clinical Pathology, University of Melbourne, Melbourne, VIC Australia ,grid.1073.50000 0004 0626 201XSt. Vincent’s Institute of Medical Research, Fitzroy, VIC Australia
| |
Collapse
|
41
|
Abstract
The tumor suppressor p53 prevents tumorigenesis, while inactivation of p53 promotes cancer development and drug resistance. Here, we identify that a long noncoding RNA, the RNA component of mitochondrial RNA-processing endoribonuclease (RMRP), promotes growth and proliferation of colorectal cancer cells by inhibiting p53 activity. Mechanistically, RMRP retains SNRPA1 in the nucleus, thus preventing its lysosomal degradation. The nuclear SNRPA1 then prompts MDM2-mediated p53 ubiquitination and degradation. Remarkably, RMRP expression is induced by poly (ADP-ribose) polymerase (PARP) inhibitors, a group of targeted anticancer drugs, through the transcription factor C/EBPβ. Targeting RMRP significantly enhances sensitivity of colorectal cancer cells to PARP inhibition by reactivating p53. Our study provides a possible mechanism underling tumor resistance to PARP inhibitors. p53 inactivation is highly associated with tumorigenesis and drug resistance. Here, we identify a long noncoding RNA, the RNA component of mitochondrial RNA-processing endoribonuclease (RMRP), as an inhibitor of p53. RMRP is overexpressed and associated with an unfavorable prognosis in colorectal cancer. Ectopic RMRP suppresses p53 activity by promoting MDM2-induced p53 ubiquitination and degradation, while depletion of RMRP activates the p53 pathway. RMRP also promotes colorectal cancer growth and proliferation in a p53-dependent fashion in vitro and in vivo. This anti-p53 action of RMRP is executed through an identified partner protein, SNRPA1. RMRP can interact with SNRPA1 and sequester it in the nucleus, consequently blocking its lysosomal proteolysis via chaperone-mediated autophagy. The nuclear SNRPA1 then interacts with p53 and enhances MDM2-induced proteasomal degradation of p53. Remarkably, ablation of SNRPA1 completely abrogates RMRP regulation of p53 and tumor cell growth, indicating that SNRPA1 is indispensable for the anti-p53 function of RMRP. Interestingly and significantly, poly (ADP-ribose) polymerase (PARP) inhibitors induce RMRP expression through the transcription factor C/EBPβ, and RMRP confers tumor resistance to PARP inhibition by preventing p53 activation. Altogether, our study demonstrates that RMRP plays an oncogenic role by inactivating p53 via SNRPA1 in colorectal cancer.
Collapse
|
42
|
Li X, Zengel JM, Lindahl L. A Novel Model for the RNase MRP-Induced Switch between the Formation of Different Forms of 5.8S rRNA. Int J Mol Sci 2021; 22:6690. [PMID: 34206573 PMCID: PMC8268776 DOI: 10.3390/ijms22136690] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2021] [Revised: 06/14/2021] [Accepted: 06/17/2021] [Indexed: 01/12/2023] Open
Abstract
Processing of the RNA polymerase I pre-rRNA transcript into the mature 18S, 5.8S, and 25S rRNAs requires removing the "spacer" sequences. The canonical pathway for the removal of the ITS1 spacer involves cleavages at the 3' end of 18S rRNA and at two sites inside ITS1. The process can generate either a long or a short 5.8S rRNA that differs in the number of ITS1 nucleotides retained at the 5.8S 5' end. Here we document a novel pathway to the long 5.8S, which bypasses cleavage within ITS1. Instead, the entire ITS1 is degraded from its 5' end by exonuclease Xrn1. Mutations in RNase MRP increase the accumulation of long relative to short 5.8S rRNA. Traditionally this is attributed to a decreased rate of RNase MRP cleavage at its target in ITS1, called A3. However, results from this work show that the MRP-induced switch between long and short 5.8S rRNA formation occurs even when the A3 site is deleted. Based on this and our published data, we propose that the link between RNase MRP and 5.8S 5' end formation involves RNase MRP cleavage at unknown sites elsewhere in pre-rRNA or in RNA molecules other than pre-rRNA.
Collapse
MESH Headings
- DNA, Ribosomal Spacer
- Endoribonucleases
- Gene Expression Regulation, Fungal
- Nucleic Acid Conformation
- RNA Processing, Post-Transcriptional
- RNA, Fungal
- RNA, Ribosomal, 5.8S/chemistry
- RNA, Ribosomal, 5.8S/genetics
- RNA, Ribosomal, 5.8S/metabolism
- Saccharomyces cerevisiae/genetics
- Saccharomyces cerevisiae/metabolism
- Saccharomyces cerevisiae Proteins/genetics
- Saccharomyces cerevisiae Proteins/metabolism
- Sequence Deletion
Collapse
Affiliation(s)
- Xiao Li
- Department of Biological Sciences, University of Maryland Baltimore County (UMBC), 1000 Hilltop Circle, Baltimore, MD 21250, USA; (X.L.); (J.M.Z.)
- Department of Biology, University of Rochester, Rochester, NY 14627, USA
| | - Janice M. Zengel
- Department of Biological Sciences, University of Maryland Baltimore County (UMBC), 1000 Hilltop Circle, Baltimore, MD 21250, USA; (X.L.); (J.M.Z.)
| | - Lasse Lindahl
- Department of Biological Sciences, University of Maryland Baltimore County (UMBC), 1000 Hilltop Circle, Baltimore, MD 21250, USA; (X.L.); (J.M.Z.)
| |
Collapse
|
43
|
Jarrous N, Mani D, Ramanathan A. Coordination of transcription and processing of tRNA. FEBS J 2021; 289:3630-3641. [PMID: 33929081 DOI: 10.1111/febs.15904] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2021] [Revised: 04/02/2021] [Accepted: 04/28/2021] [Indexed: 12/17/2022]
Abstract
Coordination of transcription and processing of RNA is a basic principle in regulation of gene expression in eukaryotes. In the case of mRNA, coordination is primarily founded on a co-transcriptional processing mechanism by which a nascent precursor mRNA undergoes maturation via cleavage and modification by the transcription machinery. A similar mechanism controls the biosynthesis of rRNA. However, the coordination of transcription and processing of tRNA, a rather short transcript, remains unknown. Here, we present a model for high molecular weight initiation complexes of human RNA polymerase III that assemble on tRNA genes and process precursor transcripts to mature forms. These multifunctional initiation complexes may support co-transcriptional processing, such as the removal of the 5' leader of precursor tRNA by RNase P. Based on this model, maturation of tRNA is predetermined prior to transcription initiation.
Collapse
Affiliation(s)
- Nayef Jarrous
- Microbiology and Molecular Genetics, Institute of Medical Research Israel-Canada, The Hebrew University-Hadassah Medical School, Jerusalem, Israel
| | - Dhivakar Mani
- Microbiology and Molecular Genetics, Institute of Medical Research Israel-Canada, The Hebrew University-Hadassah Medical School, Jerusalem, Israel
| | - Aravind Ramanathan
- Microbiology and Molecular Genetics, Institute of Medical Research Israel-Canada, The Hebrew University-Hadassah Medical School, Jerusalem, Israel
| |
Collapse
|
44
|
Bridges MC, Daulagala AC, Kourtidis A. LNCcation: lncRNA localization and function. J Cell Biol 2021; 220:e202009045. [PMID: 33464299 PMCID: PMC7816648 DOI: 10.1083/jcb.202009045] [Citation(s) in RCA: 664] [Impact Index Per Article: 221.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2020] [Revised: 12/20/2020] [Accepted: 12/23/2020] [Indexed: 12/13/2022] Open
Abstract
Subcellular localization of RNAs has gained attention in recent years as a prevalent phenomenon that influences numerous cellular processes. This is also evident for the large and relatively novel class of long noncoding RNAs (lncRNAs). Because lncRNAs are defined as RNA transcripts >200 nucleotides that do not encode protein, they are themselves the functional units, making their subcellular localization critical to their function. The discovery of tens of thousands of lncRNAs and the cumulative evidence involving them in almost every cellular activity render assessment of their subcellular localization essential to fully understanding their biology. In this review, we summarize current knowledge of lncRNA subcellular localization, factors controlling their localization, emerging themes, including the role of lncRNA isoforms and the involvement of lncRNAs in phase separation bodies, and the implications of lncRNA localization on their function and on cellular behavior. We also discuss gaps in the current knowledge as well as opportunities that these provide for novel avenues of investigation.
Collapse
Affiliation(s)
| | | | - Antonis Kourtidis
- Department of Regenerative Medicine and Cell Biology, Medical University of South Carolina, Charleston, SC
| |
Collapse
|
45
|
Kaliatsi EG, Giarimoglou N, Stathopoulos C, Stamatopoulou V. Non-Coding RNA-Driven Regulation of rRNA Biogenesis. Int J Mol Sci 2020; 21:E9738. [PMID: 33419375 PMCID: PMC7766524 DOI: 10.3390/ijms21249738] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2020] [Revised: 12/15/2020] [Accepted: 12/17/2020] [Indexed: 12/30/2022] Open
Abstract
Ribosomal RNA (rRNA) biogenesis takes place in the nucleolus, the most prominent condensate of the eukaryotic nucleus. The proper assembly and integrity of the nucleolus reflects the accurate synthesis and processing of rRNAs which in turn, as major components of ribosomes, ensure the uninterrupted flow of the genetic information during translation. Therefore, the abundant production of rRNAs in a precisely functional nucleolus is of outmost importance for the cell viability and requires the concerted action of essential enzymes, associated factors and epigenetic marks. The coordination and regulation of such an elaborate process depends on not only protein factors, but also on numerous regulatory non-coding RNAs (ncRNAs). Herein, we focus on RNA-mediated mechanisms that control the synthesis, processing and modification of rRNAs in mammals. We highlight the significance of regulatory ncRNAs in rRNA biogenesis and the maintenance of the nucleolar morphology, as well as their role in human diseases and as novel druggable molecular targets.
Collapse
Affiliation(s)
| | | | - Constantinos Stathopoulos
- Department of Biochemistry, School of Medicine, University of Patras, 26504 Patras, Greece; (E.G.K.); (N.G.)
| | - Vassiliki Stamatopoulou
- Department of Biochemistry, School of Medicine, University of Patras, 26504 Patras, Greece; (E.G.K.); (N.G.)
| |
Collapse
|
46
|
Ziv O, Price J, Shalamova L, Kamenova T, Goodfellow I, Weber F, Miska EA. The Short- and Long-Range RNA-RNA Interactome of SARS-CoV-2. Mol Cell 2020; 80:1067-1077.e5. [PMID: 33259809 PMCID: PMC7643667 DOI: 10.1016/j.molcel.2020.11.004] [Citation(s) in RCA: 128] [Impact Index Per Article: 32.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2020] [Revised: 10/05/2020] [Accepted: 10/29/2020] [Indexed: 12/16/2022]
Abstract
The Coronaviridae is a family of positive-strand RNA viruses that includes SARS-CoV-2, the etiologic agent of the COVID-19 pandemic. Bearing the largest single-stranded RNA genomes in nature, coronaviruses are critically dependent on long-distance RNA-RNA interactions to regulate the viral transcription and replication pathways. Here we experimentally mapped the in vivo RNA-RNA interactome of the full-length SARS-CoV-2 genome and subgenomic mRNAs. We uncovered a network of RNA-RNA interactions spanning tens of thousands of nucleotides. These interactions reveal that the viral genome and subgenomes adopt alternative topologies inside cells and engage in different interactions with host RNAs. Notably, we discovered a long-range RNA-RNA interaction, the FSE-arch, that encircles the programmed ribosomal frameshifting element. The FSE-arch is conserved in the related MERS-CoV and is under purifying selection. Our findings illuminate RNA structure-based mechanisms governing replication, discontinuous transcription, and translation of coronaviruses and will aid future efforts to develop antiviral strategies.
Collapse
Affiliation(s)
- Omer Ziv
- Wellcome Trust/Cancer Research UK Gurdon Institute and Department of Genetics, University of Cambridge, Cambridge CB2 1QN, UK.
| | - Jonathan Price
- Wellcome Trust/Cancer Research UK Gurdon Institute and Department of Genetics, University of Cambridge, Cambridge CB2 1QN, UK
| | - Lyudmila Shalamova
- Institute for Virology, FB10-Veterinary Medicine, Justus-Liebig University, 35392 Gießen, Germany
| | - Tsveta Kamenova
- Wellcome Trust/Cancer Research UK Gurdon Institute and Department of Genetics, University of Cambridge, Cambridge CB2 1QN, UK
| | - Ian Goodfellow
- Division of Virology, Department of Pathology, University of Cambridge, Addenbrooke's Hospital, Cambridge CB2 2QQ, UK
| | - Friedemann Weber
- Institute for Virology, FB10-Veterinary Medicine, Justus-Liebig University, 35392 Gießen, Germany.
| | - Eric A Miska
- Wellcome Trust/Cancer Research UK Gurdon Institute and Department of Genetics, University of Cambridge, Cambridge CB2 1QN, UK; Wellcome Sanger Institute, Wellcome Trust Genome Campus, Cambridge CB10 1SA, UK.
| |
Collapse
|
47
|
Abstract
In this review, Yeganeh et al. summarize different human diseases that have been linked to defects in the Pol III transcription apparatus or to Pol III products imbalance and discuss the possible underlying mechanisms. RNA polymerase (Pol) III is responsible for transcription of different noncoding genes in eukaryotic cells, whose RNA products have well-defined functions in translation and other biological processes for some, and functions that remain to be defined for others. For all of them, however, new functions are being described. For example, Pol III products have been reported to regulate certain proteins such as protein kinase R (PKR) by direct association, to constitute the source of very short RNAs with regulatory roles in gene expression, or to control microRNA levels by sequestration. Consistent with these many functions, deregulation of Pol III transcribed genes is associated with a large variety of human disorders. Here we review different human diseases that have been linked to defects in the Pol III transcription apparatus or to Pol III products imbalance and discuss the possible underlying mechanisms.
Collapse
Affiliation(s)
- Meghdad Yeganeh
- Center for Integrative Genomics, Faculty of Biology and Medicine, University of Lausanne, 1015 Lausanne, Switzerland
| | - Nouria Hernandez
- Center for Integrative Genomics, Faculty of Biology and Medicine, University of Lausanne, 1015 Lausanne, Switzerland
| |
Collapse
|
48
|
Venturi G, Montanaro L. How Altered Ribosome Production Can Cause or Contribute to Human Disease: The Spectrum of Ribosomopathies. Cells 2020; 9:E2300. [PMID: 33076379 PMCID: PMC7602531 DOI: 10.3390/cells9102300] [Citation(s) in RCA: 33] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2020] [Revised: 10/09/2020] [Accepted: 10/12/2020] [Indexed: 12/22/2022] Open
Abstract
A number of different defects in the process of ribosome production can lead to a diversified spectrum of disorders that are collectively identified as ribosomopathies. The specific factors involved may either play a role only in ribosome biogenesis or have additional extra-ribosomal functions, making it difficult to ascribe the pathogenesis of the disease specifically to an altered ribosome biogenesis, even if the latter is clearly affected. We reviewed the available literature in the field from this point of view with the aim of distinguishing, among ribosomopathies, the ones due to specific alterations in the process of ribosome production from those characterized by a multifactorial pathogenesis.
Collapse
Affiliation(s)
- Giulia Venturi
- Department of Experimental, Diagnostic and Specialty Medicine, Alma Mater Studiorum-University of Bologna, Via Massarenti 9, 40138 Bologna, Italy;
- Center for Applied Biomedical Research, Alma Mater Studiorum-University of Bologna, Via Massarenti 9, 40138 Bologna, Italy
| | - Lorenzo Montanaro
- Department of Experimental, Diagnostic and Specialty Medicine, Alma Mater Studiorum-University of Bologna, Via Massarenti 9, 40138 Bologna, Italy;
- Center for Applied Biomedical Research, Alma Mater Studiorum-University of Bologna, Via Massarenti 9, 40138 Bologna, Italy
- Azienda Ospedaliero-Universitaria di Bologna, Via Albertoni 15, 40138 Bologna, Italy
| |
Collapse
|
49
|
Fan X, Liu L, Shi Y, Guo F, Wang H, Zhao X, Zhong D, Li G. Integrated analysis of RNA-binding proteins in human colorectal cancer. World J Surg Oncol 2020; 18:222. [PMID: 32828126 PMCID: PMC7443297 DOI: 10.1186/s12957-020-01995-5] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2020] [Accepted: 08/09/2020] [Indexed: 12/15/2022] Open
Abstract
Background Although RNA-binding proteins play an essential role in a variety of different tumours, there are still limited efforts made to systematically analyse the role of RNA-binding proteins (RBPs) in the survival of colorectal cancer (CRC) patients. Methods Analysis of CRC transcriptome data collected from the TCGA database was conducted, and RBPs were extracted from CRC. R software was applied to analyse the differentially expressed genes (DEGs) of RBPs. To identify related pathways and perform functional annotation of RBP DEGs, Gene Ontology (GO) function and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analyses were carried out using the database for annotation, visualization and integrated discovery. Protein-protein interactions (PPIs) of these DEGs were analysed based on the Search Tool for the Retrieval of Interacting Genes (STRING) database and visualized by Cytoscape software. Based on the Cox regression analysis of the prognostic value of RBPs (from the PPI network) with survival time, the RBPs related to survival were identified, and a prognostic model was constructed. To verify the model, the data stored in the TCGA database were designated as the training set, while the chip data obtained from the GEO database were treated as the test set. Then, both survival analysis and ROC curve verification were conducted. Finally, the risk curves and nomograms of the two groups were generated to predict the survival period. Results Among RBP DEGs, 314 genes were upregulated while 155 were downregulated, of which twelve RBPs (NOP14, MRPS23, MAK16, TDRD6, POP1, TDRD5, TDRD7, PPARGC1A, LIN28B, CELF4, LRRFIP2, MSI2) with prognostic value were obtained. Conclusions The twelve identified genes may be promising predictors of CRC and play an essential role in the pathogenesis of CRC. However, further investigation of the underlying mechanism is needed.
Collapse
Affiliation(s)
- Xuehui Fan
- Department of Neurology, The First Affiliated Hospital of Harbin Medical University, 23 You Zheng Street, Harbin, 150001, Heilongjiang Province, People's Republic of China
| | - Lili Liu
- Department of Neurology, The First Affiliated Hospital of Harbin Medical University, 23 You Zheng Street, Harbin, 150001, Heilongjiang Province, People's Republic of China
| | - Yue Shi
- Department of Neurology, The First Affiliated Hospital of Harbin Medical University, 23 You Zheng Street, Harbin, 150001, Heilongjiang Province, People's Republic of China
| | - Fanghan Guo
- Department of Neurology, The First Affiliated Hospital of Harbin Medical University, 23 You Zheng Street, Harbin, 150001, Heilongjiang Province, People's Republic of China
| | - Haining Wang
- Department of Neurology, The First Affiliated Hospital of Harbin Medical University, 23 You Zheng Street, Harbin, 150001, Heilongjiang Province, People's Republic of China
| | - Xiuli Zhao
- Department of Neurology, The First Affiliated Hospital of Harbin Medical University, 23 You Zheng Street, Harbin, 150001, Heilongjiang Province, People's Republic of China
| | - Di Zhong
- Department of Neurology, The First Affiliated Hospital of Harbin Medical University, 23 You Zheng Street, Harbin, 150001, Heilongjiang Province, People's Republic of China
| | - Guozhong Li
- Department of Neurology, The First Affiliated Hospital of Harbin Medical University, 23 You Zheng Street, Harbin, 150001, Heilongjiang Province, People's Republic of China.
| |
Collapse
|
50
|
Perederina A, Li D, Lee H, Bator C, Berezin I, Hafenstein SL, Krasilnikov AS. Cryo-EM structure of catalytic ribonucleoprotein complex RNase MRP. Nat Commun 2020; 11:3474. [PMID: 32651392 PMCID: PMC7351766 DOI: 10.1038/s41467-020-17308-z] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2020] [Accepted: 06/24/2020] [Indexed: 11/09/2022] Open
Abstract
RNase MRP is an essential eukaryotic ribonucleoprotein complex involved in the maturation of rRNA and the regulation of the cell cycle. RNase MRP is related to the ribozyme-based RNase P, but it has evolved to have distinct cellular roles. We report a cryo-EM structure of the S. cerevisiae RNase MRP holoenzyme solved to 3.0 Å. We describe the structure of this 450 kDa complex, interactions between its components, and the organization of its catalytic RNA. We show that some of the RNase MRP proteins shared with RNase P undergo an unexpected RNA-driven remodeling that allows them to bind to divergent RNAs. Further, we reveal how this RNA-driven protein remodeling, acting together with the introduction of new auxiliary elements, results in the functional diversification of RNase MRP and its progenitor, RNase P, and demonstrate structural underpinnings of the acquisition of new functions by catalytic RNPs.
Collapse
Affiliation(s)
- Anna Perederina
- Department of Biochemistry and Molecular Biology, Pennsylvania State University, University Park, 16802, PA, USA
| | - Di Li
- Department of Biochemistry and Molecular Biology, Pennsylvania State University, University Park, 16802, PA, USA
| | - Hyunwook Lee
- Department of Biochemistry and Molecular Biology, Pennsylvania State University, University Park, 16802, PA, USA
| | - Carol Bator
- Department of Biochemistry and Molecular Biology, Pennsylvania State University, University Park, 16802, PA, USA
| | - Igor Berezin
- Department of Biochemistry and Molecular Biology, Pennsylvania State University, University Park, 16802, PA, USA
| | - Susan L Hafenstein
- Department of Biochemistry and Molecular Biology, Pennsylvania State University, University Park, 16802, PA, USA.,Department of Medicine, Pennsylvania State University, Hershey, 17033, PA, USA
| | - Andrey S Krasilnikov
- Department of Biochemistry and Molecular Biology, Pennsylvania State University, University Park, 16802, PA, USA. .,Center for RNA Biology, Pennsylvania State University, University Park, 16802, PA, USA.
| |
Collapse
|