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McCool MA, Bryant CJ, Huang H, Ogawa LM, Farley-Barnes KI, Sondalle SB, Abriola L, Surovtseva YV, Baserga SJ. Human nucleolar protein 7 (NOL7) is required for early pre-rRNA accumulation and pre-18S rRNA processing. RNA Biol 2023; 20:257-271. [PMID: 37246770 PMCID: PMC10228412 DOI: 10.1080/15476286.2023.2217392] [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] [Accepted: 05/19/2023] [Indexed: 05/30/2023] Open
Abstract
The main components of the essential cellular process of eukaryotic ribosome biogenesis are highly conserved from yeast to humans. Among these, the U3 Associated Proteins (UTPs) are a small subunit processome subcomplex that coordinate the first two steps of ribosome biogenesis in transcription and pre-18S processing. While we have identified the human counterparts of most of the yeast Utps, the homologs of yeast Utp9 and Bud21 (Utp16) have remained elusive. In this study, we find that NOL7 is the likely ortholog of Bud21. Previously described as a tumour suppressor through regulation of antiangiogenic transcripts, we now show that NOL7 is required for early pre-rRNA accumulation and pre-18S rRNA processing in human cells. These roles lead to decreased protein synthesis and induction of the nucleolar stress response upon NOL7 depletion. Beyond Bud21's nonessential role in yeast, we establish human NOL7 as an essential UTP that is necessary to maintain both early pre-rRNA levels and processing.
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Affiliation(s)
- Mason A. McCool
- Department of Molecular Biophysics & Biochemistry, Yale University School of Medicine, New Haven, CT, USA
| | - Carson J. Bryant
- Department of Molecular Biophysics & Biochemistry, Yale University School of Medicine, New Haven, CT, USA
| | - Hannah Huang
- Department of Molecular Biophysics & Biochemistry, Yale University School of Medicine, New Haven, CT, USA
| | - Lisa M. Ogawa
- Department of Molecular Biophysics & Biochemistry, Yale University School of Medicine, New Haven, CT, USA
| | - Katherine I. Farley-Barnes
- Department of Molecular Biophysics & Biochemistry, Yale University School of Medicine, New Haven, CT, USA
| | - Samuel B. Sondalle
- Department of Genetics, Yale University School of Medicine, New Haven, CT, USA
| | - Laura Abriola
- Yale Center for Molecular Discovery, Yale University, West Haven, CT, USA
| | | | - Susan J. Baserga
- Department of Molecular Biophysics & Biochemistry, Yale University School of Medicine, New Haven, CT, USA
- Department of Genetics, Yale University School of Medicine, New Haven, CT, USA
- Department of Therapeutic Radiology, Yale University School of Medicine, New Haven, CT, USA
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2
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Falcon KT, Watt KEN, Dash S, Zhao R, Sakai D, Moore EL, Fitriasari S, Childers M, Sardiu ME, Swanson S, Tsuchiya D, Unruh J, Bugarinovic G, Li L, Shiang R, Achilleos A, Dixon J, Dixon MJ, Trainor PA. Dynamic regulation and requirement for ribosomal RNA transcription during mammalian development. Proc Natl Acad Sci U S A 2022; 119:e2116974119. [PMID: 35881792 PMCID: PMC9351356 DOI: 10.1073/pnas.2116974119] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2021] [Accepted: 05/11/2022] [Indexed: 01/28/2023] Open
Abstract
Ribosomal RNA (rRNA) transcription by RNA polymerase I (Pol I) is a critical rate-limiting step in ribosome biogenesis, which is essential for cell survival. Despite its global function, disruptions in ribosome biogenesis cause tissue-specific birth defects called ribosomopathies, which frequently affect craniofacial development. Here, we describe a cellular and molecular mechanism underlying the susceptibility of craniofacial development to disruptions in Pol I transcription. We show that Pol I subunits are highly expressed in the neuroepithelium and neural crest cells (NCCs), which generate most of the craniofacial skeleton. High expression of Pol I subunits sustains elevated rRNA transcription in NCC progenitors, which supports their high tissue-specific levels of protein translation, but also makes NCCs particularly sensitive to rRNA synthesis defects. Consistent with this model, NCC-specific deletion of Pol I subunits Polr1a, Polr1c, and associated factor Tcof1 in mice cell-autonomously diminishes rRNA synthesis, which leads to p53 protein accumulation, resulting in NCC apoptosis and craniofacial anomalies. Furthermore, compound mutations in Pol I subunits and associated factors specifically exacerbate the craniofacial anomalies characteristic of the ribosomopathies Treacher Collins syndrome and Acrofacial Dysostosis-Cincinnati type. Mechanistically, we demonstrate that diminished rRNA synthesis causes an imbalance between rRNA and ribosomal proteins. This leads to increased binding of ribosomal proteins Rpl5 and Rpl11 to Mdm2 and concomitantly diminished binding between Mdm2 and p53. Altogether, our results demonstrate a dynamic spatiotemporal requirement for rRNA transcription during mammalian cranial NCC development and corresponding tissue-specific threshold sensitivities to disruptions in rRNA transcription in the pathogenesis of congenital craniofacial disorders.
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Affiliation(s)
- Karla T. Falcon
- Stowers Institute for Medical Research, Kansas City, MO 64110
| | | | - Soma Dash
- Stowers Institute for Medical Research, Kansas City, MO 64110
| | - Ruonan Zhao
- Stowers Institute for Medical Research, Kansas City, MO 64110
- Department of Anatomy and Cell Biology, University of Kansas Medical Center, Kansas City, KS 66160
| | - Daisuke Sakai
- Stowers Institute for Medical Research, Kansas City, MO 64110
- Department of Biology, Kanazawa Medical University, Uchinada, Ishikawa 920-0293, Japan
| | - Emma L. Moore
- Stowers Institute for Medical Research, Kansas City, MO 64110
| | | | | | - Mihaela E. Sardiu
- Stowers Institute for Medical Research, Kansas City, MO 64110
- Department of Biostatistics and Data Science, University of Kansas Medical Center, Kansas City, KS 66160
| | - Selene Swanson
- Stowers Institute for Medical Research, Kansas City, MO 64110
| | - Dai Tsuchiya
- Stowers Institute for Medical Research, Kansas City, MO 64110
| | - Jay Unruh
- Stowers Institute for Medical Research, Kansas City, MO 64110
| | - George Bugarinovic
- Stowers Institute for Medical Research, Kansas City, MO 64110
- Department of Orthopedic Surgery, Stanford University, Stanford, CA 94305
| | - Lin Li
- Department of Human and Molecular Genetics, Virginia Commonwealth University, Richmond, VA 23284
| | - Rita Shiang
- Department of Human and Molecular Genetics, Virginia Commonwealth University, Richmond, VA 23284
| | - Annita Achilleos
- Stowers Institute for Medical Research, Kansas City, MO 64110
- Department of Basic and Clinical Sciences, University of Nicosia Medical School, Nicosia 2408, Cyprus
| | - Jill Dixon
- Faculty of Biology, Medicine, and Health, University of Manchester, Manchester M13 9PL, United Kingdom
| | - Michael J. Dixon
- Faculty of Biology, Medicine, and Health, University of Manchester, Manchester M13 9PL, United Kingdom
| | - Paul A. Trainor
- Stowers Institute for Medical Research, Kansas City, MO 64110
- Department of Anatomy and Cell Biology, University of Kansas Medical Center, Kansas City, KS 66160
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3
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TAUPELET F, DONNIO LM, MAGNANI C, MARI PO, GIGLIA-MARI G. A stable XPG protein is required for proper ribosome biogenesis: Insights on the phenotype of combinate Xeroderma Pigmentosum/Cockayne Syndrome patients. PLoS One 2022; 17:e0271246. [PMID: 35802638 PMCID: PMC9269744 DOI: 10.1371/journal.pone.0271246] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2022] [Accepted: 06/24/2022] [Indexed: 11/18/2022] Open
Abstract
Nucleotide Excision Repair is one of the five DNA repair systems. More than 30 proteins are involved in this process, including the seven XP proteins. When mutated, the genes coding for these proteins are provoking the rare disease Xeroderma Pigmentosum, which causes cutaneous defects and a high prevalence of skin cancers in patients. The CSA and CSB proteins are also involved in Nucleotide Excision Repair, and their mutation leads to Cockayne Syndrome, another rare disease, causing dwarfism, neurodegeneration, and ultimately early death, but without high skin cancer incidence. Some mutations of ERCC5, the gene coding for XPG, may give rise to a combined Xeroderma Pigmentosum and Cockayne Syndrome. A defect in Nucleotide Excision Repair alone cannot explain all these phenotypes. XPG has been located in the nucleolus, where ribosome biogenesis happens. This energy-consuming process starts with the transcription of the ribosomal DNA in a long ribosomal RNA, the pre-rRNA 47S, by RNA Polymerase 1. 47S pre-rRNA undergoes several cleavages and modifications to form three mature products: the ribosomal RNAs 18S, 5.8S and 28S. In the cytoplasm, these three products will enter the ribosomes’ composition, the producers of protein in our cells. Our work aimed to observe ribosome biogenesis in presence of an unstable XPG protein. By working on Xeroderma Pigmentosum/Cockayne Syndrome cell lines, meaning in the absence of XPG, we uncovered that the binding of UBF, as well as the number of unresolved R-loops, is increased along the ribosomal DNA gene body and flanking regions. Furthermore, ribosomal RNA maturation is impaired, with increased use of alternative pathways of maturation as well as an increase of immature precursors. These defective processes may explain the neurodegeneration observed when the XPG protein is heavily truncated, as ribosomal homeostasis and R-loops resolution are critical for proper neuronal development.
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Affiliation(s)
- Florent TAUPELET
- Institut NeuroMyoGène–Physiopathologie et Génétique du Neurone et du Muscle, CNRS UMR 5261, INSERM U1315, Faculté de Médecine et de Pharmacie Rockefeller, Université Claude Bernard Lyon 1, Lyon, France
| | - Lise-Marie DONNIO
- Institut NeuroMyoGène–Physiopathologie et Génétique du Neurone et du Muscle, CNRS UMR 5261, INSERM U1315, Faculté de Médecine et de Pharmacie Rockefeller, Université Claude Bernard Lyon 1, Lyon, France
| | - Charlène MAGNANI
- Institut NeuroMyoGène–Physiopathologie et Génétique du Neurone et du Muscle, CNRS UMR 5261, INSERM U1315, Faculté de Médecine et de Pharmacie Rockefeller, Université Claude Bernard Lyon 1, Lyon, France
| | - Pierre-Olivier MARI
- Institut NeuroMyoGène–Physiopathologie et Génétique du Neurone et du Muscle, CNRS UMR 5261, INSERM U1315, Faculté de Médecine et de Pharmacie Rockefeller, Université Claude Bernard Lyon 1, Lyon, France
| | - Giuseppina GIGLIA-MARI
- Institut NeuroMyoGène–Physiopathologie et Génétique du Neurone et du Muscle, CNRS UMR 5261, INSERM U1315, Faculté de Médecine et de Pharmacie Rockefeller, Université Claude Bernard Lyon 1, Lyon, France
- * E-mail:
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4
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The Role of Glycogen Synthase Kinase-3 in the Regulation of Ribosome Biogenesis in Rat Soleus Muscle under Disuse Conditions. Int J Mol Sci 2022; 23:ijms23052751. [PMID: 35269893 PMCID: PMC8911371 DOI: 10.3390/ijms23052751] [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: 12/29/2021] [Revised: 02/16/2022] [Accepted: 02/28/2022] [Indexed: 02/04/2023] Open
Abstract
It is well-established that prolonged exposure to real or simulated microgravity/disuse conditions results in a significant reduction in the rate of muscle protein synthesis (PS) and loss of muscle mass. Muscle protein synthesis is largely dependent upon translational capacity (ribosome content), the regulation of which is poorly explored under conditions of mechanical unloading. Glycogen synthase kinase-3 (GSK-3) (a negative regulator of PS) is known to be activated in rat soleus muscle under unloading conditions. We hypothesized that inhibition of GSK-3 activity under disuse conditions (hindlimb suspension, HS) would reduce disuse-induced downregulation of ribosome biogenesis in rat soleus muscle. Wistar rats were randomly divided into four groups: (1) vivarium control (C), (2) vivarium control + daily injections (4 mg/kg) of AR-A014418 (GSK-3 inhibitor) for 7 days, (3) 7-day HS, (4) 7-day HS + daily injections (4 mg/kg) of AR-A014418. GSK-3beta and glycogen synthase 1 (GS-1) phosphorylation levels were measured by Western-blotting. The key markers of ribosome biogenesis were assessed via agarose gel-electrophoresis and RT-PCR. The rate of muscle PS was assessed by puromycin-based SUnSET method. As expected, 7-day HS resulted in a significant decrease in the inhibitory Ser9 GSK-3beta phosphorylation and an increase in GS-1 (Ser641) phosphorylation compared to the C group. Treatment of rats with GSK-3 inhibitor prevented HS-induced increase in GS1 (Ser641) phosphorylation, which was indicative of GSK-3 inhibition. Administration of GSK-3 inhibitor partly attenuated disuse-induced downregulation of c-Myc expression as well as decreases in the levels of 45S pre-rRNA and 18S + 28S rRNAs. These AR-A014418-induced alterations in the markers of ribosome biogenesis were paralleled with partial prevention of a decrease in the rate of muscle PS. Thus, inhibition of GSK-3 during 7-day HS is able to partially attenuate the reductions in translational capacity and the rate of PS in rat soleus muscle.
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5
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Tseng TL, Wang YT, Tsao CY, Ke YT, Lee YC, Hsu HJ, Poss KD, Chen CH. The RNA helicase Ddx52 functions as a growth switch in juvenile zebrafish. Development 2021; 148:271093. [PMID: 34323273 DOI: 10.1242/dev.199578] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2021] [Accepted: 06/30/2021] [Indexed: 12/18/2022]
Abstract
Vertebrate animals usually display robust growth trajectories during juvenile stages, and reversible suspension of this growth momentum by a single genetic determinant has not been reported. Here, we report a single genetic factor that is essential for juvenile growth in zebrafish. Using a forward genetic screen, we recovered a temperature-sensitive allele, pan (after Peter Pan), that suspends whole-organism growth at juvenile stages. Remarkably, even after growth is halted for a full 8-week period, pan mutants are able to resume a robust growth trajectory after release from the restrictive temperature, eventually growing into fertile adults without apparent adverse phenotypes. Positional cloning and complementation assays revealed that pan encodes a probable ATP-dependent RNA helicase (DEAD-Box Helicase 52; ddx52) that maintains the level of 47S precursor ribosomal RNA. Furthermore, genetic silencing of ddx52 and pharmacological inhibition of bulk RNA transcription similarly suspend the growth of flies, zebrafish and mice. Our findings reveal evidence that safe, reversible pauses of juvenile growth can be mediated by targeting the activity of a single gene, and that its pausing mechanism has high evolutionary conservation.
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Affiliation(s)
- Tzu-Lun Tseng
- Institute of Cellular and Organismic Biology, Academia Sinica, Taipei 11529, Taiwan
| | - Ying-Ting Wang
- Institute of Cellular and Organismic Biology, Academia Sinica, Taipei 11529, Taiwan
| | - Chang-Yu Tsao
- Institute of Cellular and Organismic Biology, Academia Sinica, Taipei 11529, Taiwan
| | - Yi-Teng Ke
- Institute of Cellular and Organismic Biology, Academia Sinica, Taipei 11529, Taiwan
| | - Yi-Ching Lee
- Institute of Cellular and Organismic Biology, Academia Sinica, Taipei 11529, Taiwan
| | - Hwei-Jan Hsu
- Institute of Cellular and Organismic Biology, Academia Sinica, Taipei 11529, Taiwan
| | - Kenneth D Poss
- Department of Cell Biology, Regeneration Next, Duke University Medical Center, Durham, NC 27710, USA
| | - Chen-Hui Chen
- Institute of Cellular and Organismic Biology, Academia Sinica, Taipei 11529, Taiwan
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6
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Kim HG, Huot JR, Pin F, Guo B, Bonetto A, Nader GA. Reduced rDNA transcription diminishes skeletal muscle ribosomal capacity and protein synthesis in cancer cachexia. FASEB J 2021; 35:e21335. [PMID: 33527503 PMCID: PMC7863588 DOI: 10.1096/fj.202002257r] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2020] [Revised: 12/07/2020] [Accepted: 12/16/2020] [Indexed: 12/18/2022]
Abstract
Muscle wasting in cancer is associated with deficits in protein synthesis, yet, the mechanisms underlying this anabolic impairment remain poorly understood. The capacity for protein synthesis is mainly determined by the abundance of muscle ribosomes, which is in turn regulated by transcription of the ribosomal (r)RNA genes (rDNA). In this study, we investigated whether muscle loss in a preclinical model of ovarian cancer is associated with a reduction in ribosomal capacity and was a consequence of impaired rDNA transcription. Tumor bearing resulted in a significant loss in gastrocnemius muscle weight and protein synthesis capacity, and was consistent with a significant reduction in rDNA transcription and ribosomal capacity. Despite the induction of the ribophagy receptor NUFIP1 mRNA and the loss of NUFIP1 protein, in vitro studies revealed that while inhibition of autophagy rescued NUFIP1, it did not prevent the loss of rRNA. Electrophoretic analysis of rRNA fragmentation from both in vivo and in vitro models showed no evidence of endonucleolytic cleavage, suggesting that rRNA degradation may not play a major role in modulating muscle ribosome abundance. Our results indicate that in this model of ovarian cancer-induced cachexia, the ability of skeletal muscle to synthesize protein is compromised by a reduction in rDNA transcription and consequently a lower ribosomal capacity. Thus, impaired ribosomal production appears to play a key role in the anabolic deficits associated with muscle wasting in cancer cachexia.
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Affiliation(s)
- Hyo-Gun Kim
- Department of Kinesiology, The Pennsylvania State University, University Park, PA, USA
| | - Joshua R Huot
- Department of Surgery, Indiana University School of Medicine, Indianapolis, IN, USA
| | - Fabrizio Pin
- Department of Anatomy and Cell Biology & Physiology, Indiana University School of Medicine, Indianapolis, IN, USA
| | - Bin Guo
- Department of Kinesiology, The Pennsylvania State University, University Park, PA, USA
| | - Andrea Bonetto
- Department of Surgery, Indiana University School of Medicine, Indianapolis, IN, USA.,Department of Anatomy and Cell Biology & Physiology, Indiana University School of Medicine, Indianapolis, IN, USA.,Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, PA, USA
| | - Gustavo A Nader
- Department of Kinesiology, The Pennsylvania State University, University Park, PA, USA.,Penn State Cancer Institute, The Pennsylvania State University, University Park, PA, USA.,Indiana Center for Musculoskeletal Health, Indiana University School of Medicine, Indianapolis, IN, USA
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7
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Figueiredo VC, D'Souza RF, Van Pelt DW, Lawrence MM, Zeng N, Markworth JF, Poppitt SD, Miller BF, Mitchell CJ, McCarthy JJ, Dupont‐Versteegden EE, Cameron‐Smith D. Ribosome biogenesis and degradation regulate translational capacity during muscle disuse and reloading. J Cachexia Sarcopenia Muscle 2021; 12:130-143. [PMID: 33231914 PMCID: PMC7890271 DOI: 10.1002/jcsm.12636] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/26/2020] [Revised: 09/02/2020] [Accepted: 09/16/2020] [Indexed: 12/17/2022] Open
Abstract
BACKGROUND Translational capacity (i.e. ribosomal mass) is a key determinant of protein synthesis and has been associated with skeletal muscle hypertrophy. The role of translational capacity in muscle atrophy and regrowth from disuse is largely unknown. Therefore, we investigated the effect of muscle disuse and reloading on translational capacity in middle-aged men (Study 1) and in rats (Study 2). METHODS In Study 1, 28 male participants (age 50.03 ± 3.54 years) underwent 2 weeks of knee immobilization followed by 2 weeks of ambulatory recovery and a further 2 weeks of resistance training. Muscle biopsies were obtained for measurement of total RNA and pre-ribosomal (r)RNA expression, and vastus lateralis cross-sectional area (CSA) was determined via peripheral quantitative computed tomography. In Study 2, male rats underwent hindlimb suspension (HS) for either 24 h (HS 24 h, n = 4) or 7 days (HS 7d, n = 5), HS for 7 days followed by 7 days of reloading (Rel, n = 5) or remained as ambulatory weight bearing (WB, n = 5) controls. Rats received deuterium oxide throughout the study to determine RNA synthesis and degradation, and mTORC1 signalling pathway was assessed. RESULTS Two weeks of immobilization reduced total RNA concentration (20%) and CSA (4%) in men (both P ≤ 0.05). Ambulatory recovery restored total RNA concentration to baseline levels and partially restored muscle CSA. Total RNA concentration and 47S pre-rRNA expression increased above basal levels after resistance training (P ≤ 0.05). In rats, RNA synthesis was 30% lower while degradation was ~400% higher in HS 7d in soleus and plantaris muscles compared with WB (P ≤ 0.05). mTORC1 signalling was lower in HS compared with WB as was 47S pre-rRNA (P ≤ 0.05). With reloading, the aforementioned parameters were restored to WB levels while RNA degradation was suppressed (P ≤ 0.05). CONCLUSIONS Changes in RNA concentration following muscle disuse and reloading were associated with changes in ribosome biogenesis and degradation, indicating that both processes are important determinants of translational capacity. The pre-clinical data help explain the reduced translational capacity after muscle immobilization in humans and demonstrate that ribosome biogenesis and degradation might be valuable therapeutic targets to maintain muscle mass during disuse.
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Affiliation(s)
- Vandré C. Figueiredo
- Liggins InstituteThe University of AucklandAucklandNew Zealand
- Department of Physical Therapy, College of Health SciencesUniversity of KentuckyKYUSA
- Center of Muscle BiologyUniversity of KentuckyKYUSA
| | | | - Douglas W. Van Pelt
- Department of Physical Therapy, College of Health SciencesUniversity of KentuckyKYUSA
- Center of Muscle BiologyUniversity of KentuckyKYUSA
| | - Marcus M. Lawrence
- Aging and Metabolism Research ProgramOklahoma Medical Research Foundation (OMRF)Oklahoma CityOKUSA
| | - Nina Zeng
- Liggins InstituteThe University of AucklandAucklandNew Zealand
| | | | - Sally D. Poppitt
- School of Biological SciencesThe University of AucklandAucklandNew Zealand
| | - Benjamin F. Miller
- Aging and Metabolism Research ProgramOklahoma Medical Research Foundation (OMRF)Oklahoma CityOKUSA
| | - Cameron J. Mitchell
- Liggins InstituteThe University of AucklandAucklandNew Zealand
- School of KinesiologyUniversity of British ColumbiaVancouverCanada
| | - John J. McCarthy
- Center of Muscle BiologyUniversity of KentuckyKYUSA
- College of MedicineUniversity of KentuckyKYUSA
| | - Esther E. Dupont‐Versteegden
- Department of Physical Therapy, College of Health SciencesUniversity of KentuckyKYUSA
- Center of Muscle BiologyUniversity of KentuckyKYUSA
| | - David Cameron‐Smith
- Liggins InstituteThe University of AucklandAucklandNew Zealand
- Human Potential Translational Research Programme, Yong Loo Lin School of MedicineNational University of SingaporeSingapore
- Singapore Institute for Clinical SciencesAgency for Science, Technology and ResearchSingapore
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8
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Sorino C, Catena V, Bruno T, De Nicola F, Scalera S, Bossi G, Fabretti F, Mano M, De Smaele E, Fanciulli M, Iezzi S. Che-1/AATF binds to RNA polymerase I machinery and sustains ribosomal RNA gene transcription. Nucleic Acids Res 2020; 48:5891-5906. [PMID: 32421830 PMCID: PMC7293028 DOI: 10.1093/nar/gkaa344] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2019] [Revised: 04/21/2020] [Accepted: 04/24/2020] [Indexed: 02/06/2023] Open
Abstract
Originally identified as an RNA polymerase II interactor, Che-1/AATF (Che-1) has now been recognized as a multifunctional protein involved in cell-cycle regulation and cancer progression, as well as apoptosis inhibition and response to stress. This protein displays a peculiar nucleolar localization and it has recently been implicated in pre-rRNA processing and ribosome biogenesis. Here, we report the identification of a novel function of Che-1 in the regulation of ribosomal RNA (rRNA) synthesis, in both cancer and normal cells. We demonstrate that Che-1 interacts with RNA polymerase I and nucleolar upstream binding factor (UBF) and promotes RNA polymerase I-dependent transcription. Furthermore, this protein binds to the rRNA gene (rDNA) promoter and modulates its epigenetic state by contrasting the recruitment of HDAC1. Che-1 downregulation affects RNA polymerase I and UBF recruitment on rDNA and leads to reducing rDNA promoter activity and 47S pre-rRNA production. Interestingly, Che-1 depletion induces abnormal nucleolar morphology associated with re-distribution of nucleolar proteins. Finally, we show that upon DNA damage Che-1 re-localizes from rDNA to TP53 gene promoter to induce cell-cycle arrest. This previously uncharacterized function of Che-1 confirms the important role of this protein in the regulation of ribosome biogenesis, cellular proliferation and response to stress.
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Affiliation(s)
- Cristina Sorino
- SAFU Laboratory, Department of Research, Advanced Diagnostics and Technological Innovation, Translational Research Area, IRCCS Regina Elena National Cancer Institute, 00144 Rome, Italy.,Department of Experimental Medicine, Sapienza-University of Rome, 00161 Rome, Italy
| | - Valeria Catena
- SAFU Laboratory, Department of Research, Advanced Diagnostics and Technological Innovation, Translational Research Area, IRCCS Regina Elena National Cancer Institute, 00144 Rome, Italy
| | - Tiziana Bruno
- SAFU Laboratory, Department of Research, Advanced Diagnostics and Technological Innovation, Translational Research Area, IRCCS Regina Elena National Cancer Institute, 00144 Rome, Italy
| | - Francesca De Nicola
- SAFU Laboratory, Department of Research, Advanced Diagnostics and Technological Innovation, Translational Research Area, IRCCS Regina Elena National Cancer Institute, 00144 Rome, Italy
| | - Stefano Scalera
- SAFU Laboratory, Department of Research, Advanced Diagnostics and Technological Innovation, Translational Research Area, IRCCS Regina Elena National Cancer Institute, 00144 Rome, Italy
| | - Gianluca Bossi
- Oncogenomic and Epigenetic Unit, Department of Research, Advanced Diagnostics and Technological Innovation, Translational Research Area, IRCCS Regina Elena National Cancer Institute, 00144 Rome, Italy
| | - Francesca Fabretti
- Department II of Internal Medicine and Center for Molecular Medicine Cologne, University of Cologne, Faculty of Medicine and University Hospital of Cologne, 50937 Cologne, Germany.,CECAD, University of Cologne, Faculty of Medicine and University Hospital of Cologne, 50931 Cologne, Germany
| | - Miguel Mano
- Center for Neuroscience and Cell Biology (CNC), University of Coimbra, Coimbra 3060 197, Portugal
| | - Enrico De Smaele
- Department of Experimental Medicine, Sapienza-University of Rome, 00161 Rome, Italy
| | - Maurizio Fanciulli
- SAFU Laboratory, Department of Research, Advanced Diagnostics and Technological Innovation, Translational Research Area, IRCCS Regina Elena National Cancer Institute, 00144 Rome, Italy
| | - Simona Iezzi
- SAFU Laboratory, Department of Research, Advanced Diagnostics and Technological Innovation, Translational Research Area, IRCCS Regina Elena National Cancer Institute, 00144 Rome, Italy
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9
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Tiana M, Acosta-Iborra B, Hernández R, Galiana C, Fernández-Moreno MÁ, Jimenez B, Del Peso L. Metabolic labeling of RNA uncovers the contribution of transcription and decay rates on hypoxia-induced changes in RNA levels. RNA (NEW YORK, N.Y.) 2020; 26:1006-1022. [PMID: 32295863 PMCID: PMC7373995 DOI: 10.1261/rna.072611.119] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/05/2019] [Accepted: 04/12/2020] [Indexed: 05/08/2023]
Abstract
Cells adapt to environmental changes, including fluctuations in oxygen levels, through the induction of specific gene expression programs. However, most transcriptomic studies do not distinguish the relative contribution of transcription, RNA processing, and RNA degradation processes to cellular homeostasis. Here we used metabolic labeling followed by massive parallel sequencing of newly transcribed and preexisting RNA fractions to simultaneously analyze RNA synthesis and decay in primary endothelial cells exposed to low oxygen tension. We found that changes in transcription rates induced by hypoxia are the major determinant of changes in RNA levels. However, degradation rates also had a significant contribution, accounting for 24% of the observed variability in total mRNA. In addition, our results indicated that hypoxia led to a reduction of the overall mRNA stability from a median half-life in normoxia of 8.7 h, to 5.7 h in hypoxia. Analysis of RNA content per cell confirmed a decrease of both mRNA and total RNA in hypoxic samples and that this effect is dependent on the EGLN/HIF/TSC2 axis. This effect could potentially contribute to fundamental global responses such as inhibition of translation in hypoxia. In summary, our study provides a quantitative analysis of the contribution of RNA synthesis and stability to the transcriptional response to hypoxia and uncovers an unexpected effect on the latter.
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Affiliation(s)
- Maria Tiana
- Departamento de Bioquímica, Universidad Autónoma de Madrid (UAM) and Instituto de Investigaciones Biomédicas "Alberto Sols" (CSIC-UAM), 28029 Madrid, Spain
- IdiPaz, Instituto de Investigación Sanitaria del Hospital Universitario La Paz, 28029 Madrid, Spain
- CIBER de Enfermedades Respiratorias (CIBERES), Instituto de Salud Carlos III, 28029 Madrid, Spain
| | - Bárbara Acosta-Iborra
- Departamento de Bioquímica, Universidad Autónoma de Madrid (UAM) and Instituto de Investigaciones Biomédicas "Alberto Sols" (CSIC-UAM), 28029 Madrid, Spain
| | - Rosana Hernández
- Departamento de Bioquímica, Universidad Autónoma de Madrid (UAM) and Instituto de Investigaciones Biomédicas "Alberto Sols" (CSIC-UAM), 28029 Madrid, Spain
| | - Clara Galiana
- Departamento de Bioquímica, Universidad Autónoma de Madrid (UAM) and Instituto de Investigaciones Biomédicas "Alberto Sols" (CSIC-UAM), 28029 Madrid, Spain
| | - Miguel Ángel Fernández-Moreno
- Departamento de Bioquímica, Universidad Autónoma de Madrid (UAM) and Instituto de Investigaciones Biomédicas "Alberto Sols" (CSIC-UAM), 28029 Madrid, Spain
- Centro de Investigación Biomédica en Red en Enfermedades Raras (CIBERER). Facultad de Medicina, Universidad Autónoma de Madrid, Madrid 28029, Spain
- Instituto de Investigación Sanitaria Hospital 12 de Octubre (imas12), Madrid 28041, Spain
| | - Benilde Jimenez
- Departamento de Bioquímica, Universidad Autónoma de Madrid (UAM) and Instituto de Investigaciones Biomédicas "Alberto Sols" (CSIC-UAM), 28029 Madrid, Spain
- IdiPaz, Instituto de Investigación Sanitaria del Hospital Universitario La Paz, 28029 Madrid, Spain
- CIBER de Enfermedades Respiratorias (CIBERES), Instituto de Salud Carlos III, 28029 Madrid, Spain
| | - Luis Del Peso
- Departamento de Bioquímica, Universidad Autónoma de Madrid (UAM) and Instituto de Investigaciones Biomédicas "Alberto Sols" (CSIC-UAM), 28029 Madrid, Spain
- IdiPaz, Instituto de Investigación Sanitaria del Hospital Universitario La Paz, 28029 Madrid, Spain
- CIBER de Enfermedades Respiratorias (CIBERES), Instituto de Salud Carlos III, 28029 Madrid, Spain
- Unidad Asociada de Biomedicina CSIC-UCLM, 02006, Albacete, Spain
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10
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Hsieh CL, Xia J, Lin H. MIWI prevents aneuploidy during meiosis by cleaving excess satellite RNA. EMBO J 2020; 39:e103614. [PMID: 32677148 DOI: 10.15252/embj.2019103614] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2019] [Revised: 06/10/2020] [Accepted: 06/16/2020] [Indexed: 01/01/2023] Open
Abstract
MIWI, a murine member of PIWI proteins mostly expressed during male meiosis, is crucial for piRNA biogenesis, post-transcriptional regulation, and spermiogenesis. However, its meiotic function remains unknown. Here, we report that MIWI deficiency alters meiotic kinetochore assembly, significantly increases chromosome misalignment at the meiosis metaphase I plate, and causes chromosome mis-segregation. Consequently, Miwi-deficient mice show elevated aneuploidy in metaphase II and spermatid death. Furthermore, in Miwi-null and Miwi slicer-deficient mutants, major and minor satellite RNAs from centromeric and pericentromeric satellite repeats accumulate in excess. Over-expression of satellite repeats in wild-type spermatocytes also causes elevated chromosome misalignment, whereas reduction of both strands of major or minor satellite RNAs results in lower frequencies of chromosome misalignment. We show that MIWI, guided by piRNA, cleaves major satellite RNAs, generating RNA fragments that may form substrates for subsequent Dicer cleavage. Furthermore, Dicer cleaves all satellite RNAs in conjunction with MIWI. These findings reveal a novel mechanism in which MIWI- and Dicer-mediated cleavage of the satellite RNAs prevents the over-expression of satellite RNAs, thus ensuring proper kinetochore assembly and faithful chromosome segregation during meiosis.
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Affiliation(s)
- Chia-Ling Hsieh
- Yale Stem Cell Center and Department of Cell Biology, Yale University School of Medicine, New Haven, CT, USA
| | - Jing Xia
- Yale Stem Cell Center and Department of Cell Biology, Yale University School of Medicine, New Haven, CT, USA
| | - Haifan Lin
- Yale Stem Cell Center and Department of Cell Biology, Yale University School of Medicine, New Haven, CT, USA
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11
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Kirby TJ. Mechanosensitive pathways controlling translation regulatory processes in skeletal muscle and implications for adaptation. J Appl Physiol (1985) 2019; 127:608-618. [PMID: 31295035 DOI: 10.1152/japplphysiol.01031.2018] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
The ability of myofibers to sense and respond appropriately to mechanical signals is one of the primary determinants of the skeletal muscle phenotype. In response to a change in mechanical load, muscle cells alter their protein metabolism, primarily through the regulation of protein synthesis rate. Protein synthesis rates are determined by both translation efficiency and translational capacity within the muscle. Translational capacity is strongly determined by the ribosome content of the muscle; thus the regulation of ribosomal biogenesis by mechanical inputs has been an area of recent interest. Despite the clear association between mechanical signals and changes in protein metabolism, the molecular pathways that link these events are still not fully elucidated. This review focuses on recent studies looking at how mechanosignaling impacts translational events. The role of impaired mechanotransduction in aging is discussed, as is the connection between age-dependent signaling defects and compromised ribosomal biogenesis during mechanical overload. Finally, emerging evidence suggests that the nucleus can act as a mechanosensitive element and that this mode of mechanotransduction may have an important role in skeletal muscle physiology and adaptation.
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Affiliation(s)
- Tyler J Kirby
- Nancy E. and Peter C. Meinig School of Biomedical Engineering, Cornell University, Ithaca, New York.,Weill Institute for Cell and Molecular Biology, Cornell University, Ithaca, New York
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12
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Du L, Yang F, Fang H, Sun H, Chen Y, Xu Y, Li H, Zheng L, Zhou BBS. AICAr suppresses cell proliferation by inducing NTP and dNTP pool imbalances in acute lymphoblastic leukemia cells. FASEB J 2019; 33:4525-4537. [PMID: 30702927 DOI: 10.1096/fj.201801559rr] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
It has been shown that 5-amino-4-imidazolecarboxamide riboside (AICAr) can inhibit cell proliferation and induce apoptosis in childhood acute lymphoblastic leukemia (ALL) cells. Although AICAr could regulate cellular energy metabolism by activating AMPK, the cytotoxic mechanisms of AICAr are still unclear. Here, we knocked out TP53 or PRKAA1 gene (encoding AMPKα1) in NALM-6 and Reh cells by using the clustered regularly interspaced short palindromic repeats/Cas9 system and found that AICAr-induced proliferation inhibition was independent of AMPK activation but dependent on p53. Liquid chromatography-mass spectrometry analysis of nucleotide metabolites indicated that AICAr caused an increase in adenosine triphosphate, deoxyadenosine triphosphate, and deoxyguanosine triphosphate levels by up-regulating purine biosynthesis, while AICAr led to a decrease in cytidine triphosphate, uridine triphosphate, deoxycytidine triphosphate, and deoxythymidine triphosphate levels because of reduced phosphoribosyl pyrophosphate production, which consequently impaired the pyrimidine biosynthesis. Ribonucleoside triphosphate (NTP) pool imbalances suppressed the rRNA transcription efficiency. Furthermore, deoxy-ribonucleoside triphosphate (dNTP) pool imbalances induced DNA replication stress and DNA double-strand breaks, followed by cell cycle arrest and apoptosis in ALL cells. Exogenous uridine could rebalance the NTP and dNTP pools by supplementing pyrimidine and then attenuate AICAr-induced cytotoxicity. Our data indicate that RNA transcription inhibition and DNA replication stress induced by NTP and dNTP pool imbalances might play a key role in AICAr-mediated cytotoxic effects on ALL cells, suggesting a potential clinical application of AICAr in future ALL therapy.-Du, L., Yang, F., Fang, H., Sun, H., Chen, Y., Xu, Y., Li, H., Zheng, L., Zhou, B.-B. S. AICAr suppresses cell proliferation by inducing NTP and dNTP pool imbalances in acute lymphoblastic leukemia cells.
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Affiliation(s)
- Lijuan Du
- Key Laboratory of Pediatric Hematology and Oncology, Ministry of Health, Shanghai Jiao Tong University School of Medicine, Shanghai, China.,Pediatric Translational Medicine Institute, Shanghai Children's Medical Center, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Fan Yang
- Key Laboratory of Pediatric Hematology and Oncology, Ministry of Health, Shanghai Jiao Tong University School of Medicine, Shanghai, China.,Pediatric Translational Medicine Institute, Shanghai Children's Medical Center, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Houshun Fang
- Key Laboratory of Pediatric Hematology and Oncology, Ministry of Health, Shanghai Jiao Tong University School of Medicine, Shanghai, China.,Pediatric Translational Medicine Institute, Shanghai Children's Medical Center, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Huiying Sun
- Key Laboratory of Pediatric Hematology and Oncology, Ministry of Health, Shanghai Jiao Tong University School of Medicine, Shanghai, China.,Pediatric Translational Medicine Institute, Shanghai Children's Medical Center, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Yao Chen
- Key Laboratory of Pediatric Hematology and Oncology, Ministry of Health, Shanghai Jiao Tong University School of Medicine, Shanghai, China.,Pediatric Translational Medicine Institute, Shanghai Children's Medical Center, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Yan Xu
- Key Laboratory of Pediatric Hematology and Oncology, Ministry of Health, Shanghai Jiao Tong University School of Medicine, Shanghai, China.,Pediatric Translational Medicine Institute, Shanghai Children's Medical Center, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Hui Li
- Key Laboratory of Pediatric Hematology and Oncology, Ministry of Health, Shanghai Jiao Tong University School of Medicine, Shanghai, China.,Pediatric Translational Medicine Institute, Shanghai Children's Medical Center, Shanghai Jiao Tong University School of Medicine, Shanghai, China.,Department of Pharmacology and Chemical Biology, School of Basic Medicine, Shanghai Jiao Tong University School of Medicine, Shanghai, China.,Collaborative Innovation Center for Translational Medicine, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Liang Zheng
- Key Laboratory of Pediatric Hematology and Oncology, Ministry of Health, Shanghai Jiao Tong University School of Medicine, Shanghai, China.,Pediatric Translational Medicine Institute, Shanghai Children's Medical Center, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Bin-Bing S Zhou
- Key Laboratory of Pediatric Hematology and Oncology, Ministry of Health, Shanghai Jiao Tong University School of Medicine, Shanghai, China.,Pediatric Translational Medicine Institute, Shanghai Children's Medical Center, Shanghai Jiao Tong University School of Medicine, Shanghai, China.,Department of Pharmacology and Chemical Biology, School of Basic Medicine, Shanghai Jiao Tong University School of Medicine, Shanghai, China.,Collaborative Innovation Center for Translational Medicine, Shanghai Jiao Tong University School of Medicine, Shanghai, China
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13
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Gaviraghi M, Vivori C, Pareja Sanchez Y, Invernizzi F, Cattaneo A, Santoliquido BM, Frenquelli M, Segalla S, Bachi A, Doglioni C, Pelechano V, Cittaro D, Tonon G. Tumor suppressor PNRC1 blocks rRNA maturation by recruiting the decapping complex to the nucleolus. EMBO J 2018; 37:embj.201899179. [PMID: 30373810 DOI: 10.15252/embj.201899179] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2018] [Revised: 09/14/2018] [Accepted: 09/19/2018] [Indexed: 12/20/2022] Open
Abstract
Focal deletions occur frequently in the cancer genome. However, the putative tumor-suppressive genes residing within these regions have been difficult to pinpoint. To robustly identify these genes, we implemented a computational approach based on non-negative matrix factorization, NMF, and interrogated the TCGA dataset. This analysis revealed a metagene signature including a small subset of genes showing pervasive hemizygous deletions, reduced expression in cancer patient samples, and nucleolar function. Amid the genes belonging to this signature, we have identified PNRC1, a nuclear receptor coactivator. We found that PNRC1 interacts with the cytoplasmic DCP1α/DCP2 decapping machinery and hauls it inside the nucleolus. PNRC1-dependent nucleolar translocation of the decapping complex is associated with a decrease in the 5'-capped U3 and U8 snoRNA fractions, hampering ribosomal RNA maturation. As a result, PNRC1 ablates the enhanced proliferation triggered by established oncogenes such as RAS and MYC These observations uncover a previously undescribed mechanism of tumor suppression, whereby the cytoplasmic decapping machinery is hauled within nucleoli, tightly regulating ribosomal RNA maturation.
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Affiliation(s)
- Marco Gaviraghi
- Functional Genomics of Cancer Unit, Division of Experimental Oncology, Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS) San Raffaele Scientific Institute, Milan, Italy
| | - Claudia Vivori
- Functional Genomics of Cancer Unit, Division of Experimental Oncology, Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS) San Raffaele Scientific Institute, Milan, Italy
| | - Yerma Pareja Sanchez
- Science for Life Laboratory, Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Solna, Sweden
| | - Francesca Invernizzi
- Pathology Unit, Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS) San Raffaele Scientific Institute, Milan, Italy
| | - Angela Cattaneo
- Functional Proteomics Program, Istituto FIRC di Oncologia Molecolare (IFOM), Milan, Italy
| | - Benedetta Maria Santoliquido
- Functional Genomics of Cancer Unit, Division of Experimental Oncology, Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS) San Raffaele Scientific Institute, Milan, Italy
| | - Michela Frenquelli
- Functional Genomics of Cancer Unit, Division of Experimental Oncology, Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS) San Raffaele Scientific Institute, Milan, Italy
| | - Simona Segalla
- Functional Genomics of Cancer Unit, Division of Experimental Oncology, Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS) San Raffaele Scientific Institute, Milan, Italy
| | - Angela Bachi
- Functional Proteomics Program, Istituto FIRC di Oncologia Molecolare (IFOM), Milan, Italy
| | - Claudio Doglioni
- Pathology Unit, Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS) San Raffaele Scientific Institute, Milan, Italy
| | - Vicent Pelechano
- Science for Life Laboratory, Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Solna, Sweden
| | - Davide Cittaro
- Center for Translational Genomics and Bioinformatics, Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS) San Raffaele Scientific Institute, Milan, Italy
| | - Giovanni Tonon
- Functional Genomics of Cancer Unit, Division of Experimental Oncology, Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS) San Raffaele Scientific Institute, Milan, Italy .,Center for Translational Genomics and Bioinformatics, Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS) San Raffaele Scientific Institute, Milan, Italy
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14
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Mechanistic insights in transcription-coupled nucleotide excision repair of ribosomal DNA. Proc Natl Acad Sci U S A 2018; 115:E6770-E6779. [PMID: 29967171 DOI: 10.1073/pnas.1716581115] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Nucleotide excision repair (NER) guarantees genome integrity against UV light-induced DNA damage. After UV irradiation, cells have to cope with a general transcriptional block. To ensure UV lesions repair specifically on transcribed genes, NER is coupled with transcription in an extremely organized pathway known as transcription-coupled repair. In highly metabolic cells, more than 60% of total cellular transcription results from RNA polymerase I activity. Repair of the mammalian transcribed ribosomal DNA has been scarcely studied. UV lesions severely block RNA polymerase I activity and the full transcription-coupled repair machinery corrects damage on actively transcribed ribosomal DNAs. After UV irradiation, RNA polymerase I is more bound to the ribosomal DNA and both are displaced to the nucleolar periphery. Importantly, the reentry of RNA polymerase I and the ribosomal DNA is dependent on the presence of UV lesions on DNA and independent of transcription restart.
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15
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Miller BF, Hamilton KL, Majeed ZR, Abshire SM, Confides AL, Hayek AM, Hunt ER, Shipman P, Peelor FF, Butterfield TA, Dupont‐Versteegden EE. Enhanced skeletal muscle regrowth and remodelling in massaged and contralateral non-massaged hindlimb. J Physiol 2018; 596:83-103. [PMID: 29090454 PMCID: PMC5746529 DOI: 10.1113/jp275089] [Citation(s) in RCA: 49] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2017] [Accepted: 10/16/2017] [Indexed: 12/21/2022] Open
Abstract
KEY POINTS Muscle fibre cross sectional area is enhanced with massage in the form of cyclic compressive loading during regrowth after atrophy. Massage enhances protein synthesis of the myofibrillar and cytosolic, but not the mitochondrial fraction, in muscle during regrowth. Focal adhesion kinase activation and satellite cell number are elevated in muscles undergoing massage during regrowth. Muscle fibre cross sectional area and protein synthesis of the myofibrillar fraction, but not DNA synthesis, are elevated in muscle of the contralateral non-massaged limb. Massage in the form of cyclic compressive loading is a potential anabolic intervention during muscle regrowth after atrophy. ABSTRACT Massage, in the form of cyclic compressive loading (CCL), is associated with multiple health benefits, but its potential anabolic effect on atrophied muscle has not been investigated. We hypothesized that the mechanical activity associated with CCL induces an anabolic effect in skeletal muscle undergoing regrowth after a period of atrophy. Fischer-Brown Norway rats at 10 months of age were hindlimb unloaded for a period of 2 weeks. The rats were then allowed reambulation with CCL applied at a 4.5 N load at 0.5 Hz frequency for 30 min every other day for four bouts during a regrowth period of 8 days. Muscle fibre cross sectional area was enhanced by 18% with massage during regrowth compared to reloading alone, and this was accompanied by elevated myofibrillar and cytosolic protein as well as DNA synthesis. Focal adhesion kinase phosphorylation indicated that CCL increased mechanical stimulation, while a higher number of Pax7+ cells likely explains the elevated DNA synthesis. Surprisingly, the contralateral non-massaged limb exhibited a comparable 17% higher muscle fibre size compared to reloading alone, and myofibrillar protein synthesis, but not DNA synthesis, was also elevated. We conclude that massage in the form of CCL induces an anabolic response in muscles regrowing after an atrophy-inducing event. We suggest that massage can be used as an intervention to aid in the regrowth of muscle lost during immobilization.
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Affiliation(s)
- Benjamin F. Miller
- Health and Exercise ScienceColorado State UniversityFort CollinsCO80523‐1582USA
| | - Karyn L. Hamilton
- Health and Exercise ScienceColorado State UniversityFort CollinsCO80523‐1582USA
| | - Zana R. Majeed
- Department of Rehabilitation Sciences, College of Health SciencesUniversity of KentuckyLexingtonKY40536‐0200USA
| | - Sarah M. Abshire
- Department of Rehabilitation Sciences, College of Health SciencesUniversity of KentuckyLexingtonKY40536‐0200USA
- Center for Muscle BiologyUniversity of KentuckyLexingtonKY40536‐0200USA
| | - Amy L. Confides
- Department of Rehabilitation Sciences, College of Health SciencesUniversity of KentuckyLexingtonKY40536‐0200USA
- Center for Muscle BiologyUniversity of KentuckyLexingtonKY40536‐0200USA
| | - Amanda M. Hayek
- Department of Rehabilitation Sciences, College of Health SciencesUniversity of KentuckyLexingtonKY40536‐0200USA
| | - Emily R. Hunt
- Department of Rehabilitation Sciences, College of Health SciencesUniversity of KentuckyLexingtonKY40536‐0200USA
| | - Patrick Shipman
- Department of MathematicsColorado State UniversityFort CollinsCO80523‐1582USA
| | - Frederick F. Peelor
- Health and Exercise ScienceColorado State UniversityFort CollinsCO80523‐1582USA
| | - Timothy A. Butterfield
- Department of Rehabilitation Sciences, College of Health SciencesUniversity of KentuckyLexingtonKY40536‐0200USA
- Center for Muscle BiologyUniversity of KentuckyLexingtonKY40536‐0200USA
| | - Esther E. Dupont‐Versteegden
- Department of Rehabilitation Sciences, College of Health SciencesUniversity of KentuckyLexingtonKY40536‐0200USA
- Center for Muscle BiologyUniversity of KentuckyLexingtonKY40536‐0200USA
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16
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Phosphatidylinositol 3-Kinase/Akt Mediates Integrin Signaling To Control RNA Polymerase I Transcriptional Activity. Mol Cell Biol 2016; 36:1555-68. [PMID: 26976639 DOI: 10.1128/mcb.00004-16] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2016] [Accepted: 03/04/2016] [Indexed: 12/11/2022] Open
Abstract
RNA polymerase I-mediated rRNA production is a key determinant of cell growth. Despite extensive studies, the signaling pathways that control RNA polymerase I-mediated rRNA production are not well understood. Here we provide original evidence showing that RNA polymerase I transcriptional activity is tightly controlled by integrin signaling. Furthermore, we show that a signaling axis consisting of focal adhesion kinase (FAK), Src, phosphatidylinositol 3-kinase (PI3K), Akt, and mTOR mediates the effect of integrin signaling on rRNA transcription. Additionally, we show that in kindlin-2 knockout mouse embryonic fibroblasts, overactivation of Ras, Akt, and Src can successfully rescue the defective RNA polymerase I activity induced by the loss of kindlin-2. Finally, through experiments with inhibitors of FAK, Src, and PI3K and rescue experiments in MEFs, we found that the FAK/Src/PI3K/Akt signaling pathway to control rRNA transcription is linear. Collectively, these studies reveal, for the first time, a pivotal role of integrin signaling in regulation of RNA polymerase I transcriptional activity and shed light on the downstream signaling axis that participates in regulation of this key aspect of cell growth.
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17
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Nonnekens J, Perez-Fernandez J, Theil AF, Gadal O, Bonnart C, Giglia-Mari G. Mutations in TFIIH causing trichothiodystrophy are responsible for defects in ribosomal RNA production and processing. Hum Mol Genet 2013; 22:2881-93. [DOI: 10.1093/hmg/ddt143] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
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18
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Tan BCM, Yang CC, Hsieh CL, Chou YH, Zhong CZ, Yung BYM, Liu H. Epigeneitc silencing of ribosomal RNA genes by Mybbp1a. J Biomed Sci 2012; 19:57. [PMID: 22686419 PMCID: PMC3407492 DOI: 10.1186/1423-0127-19-57] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2011] [Accepted: 06/11/2012] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Transcription of the ribosomal RNA gene repeats by Pol I occurs in the nucleolus and is a fundamental step in ribosome biogenesis and protein translation. Due to tight coordination between ribosome biogenesis and cell proliferation, transcription of rRNA and stable maintenance of rDNA clusters are thought to be under intricate control by intercalated mechanisms, particularly at the epigenetic level. METHODS AND RESULTS Here we identify the nucleolar protein Myb-binding protein 1a (Mybbp1a) as a novel negative regulator of rRNA expression. Suppression of rDNA transcription by Mybbp1a was linked to promoter regulation as illustrated by its binding to the chromatin around the hypermethylated, inactive rDNA gene promoters. Our data further showed that downregulation of Mybbp1a abrogated the local DNA methylation levels and histone marks associated with gene silencing, and altered the promoter occupancy of various factors such UBF and HDACs, consequently leading to elevated rRNA expression. Mechanistically, we propose that Mybbp1a maintains rDNA repeats in a silenced state while in association with the negative epigenetic modifiers HDAC1/2. CONCLUSIONS Results from our present work reveal a previously unrecognized co-repressor role of Mybbp1a in rRNA expression. They are further consistent with the scenario that Mybbp1a is an integral constituent of the rDNA epigenetic regulation that underlies the balanced state of rDNA clusters.
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Affiliation(s)
- Bertrand Chin-Ming Tan
- Graduate Institute of Biomedical Sciences and Department of Biomedical Sciences, College of Medicine, Chang Gung University, Kwei-San, Tao-Yuan 333, Taiwan
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19
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Abstract
In this report, we employed a lentiviral RNA interference screen to discover nucleolar DEAD/DEAH-box helicases involved in RNA polymerase I (Pol I)-mediated transcriptional activity. Our screen identified DHX33 as an important modulator of 47S rRNA transcription. We show that DHX33 is a cell cycle-regulated nucleolar protein that associates with ribosomal DNA (rDNA) loci, where it interacts with the RNA Pol I transcription factor upstream binding factor (UBF). DHX33 knockdown decreased the association of Pol I with rDNA and caused a dramatic decrease in levels of rRNA synthesis. Wild-type DHX33 overexpression, but not a DNA binding-defective mutant, enhanced 47S rRNA synthesis by promoting the association of RNA polymerase I with rDNA loci. In addition, an NTPase-defective DHX33 mutant (K94R) acted as a dominant negative mutant, inhibiting endogenous rRNA synthesis. Moreover, DHX33 deficiency in primary human fibroblasts triggered a nucleolar p53 stress response, resulting in an attenuation of proliferation. Thus, we show the mechanistic importance of DHX33 in rRNA transcription and proliferation.
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20
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Nucleolar stress is an early response to myocardial damage involving nucleolar proteins nucleostemin and nucleophosmin. Proc Natl Acad Sci U S A 2011; 108:6145-50. [PMID: 21444791 DOI: 10.1073/pnas.1017935108] [Citation(s) in RCA: 58] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Nucleolar stress, characterized by loss of nucleolar integrity, has not been described in the cardiac context. In addition to ribosome biogenesis, nucleoli are critical for control of cell proliferation and stress responses. Our group previously demonstrated induction of the nucleolar protein nucleostemin (NS) in response to cardiac pathological insult. NS interacts with nucleophosmin (NPM), a marker of nucleolar stress with cytoprotective properties. The dynamic behavior of NS and NPM reveal that nucleolar disruption is an early event associated with stress response in cardiac cells. Rapid translocation of NS and NPM to the nucleoplasm and suppression of new preribosomal RNA synthesis occurs in both neonatal rat cardiomyocytes (NRCM) and cardiac progenitor cells (CPC) upon exposure to doxorubicin or actinomycin D. Silencing of NS significantly increases cell death resulting from doxorubicin treatment in CPC, whereas NPM knockdown alone induces cell death. Overexpression of either NS or NPM significantly decreases caspase 8 activity in cultured cardiomyocytes challenged with doxorubicin. The presence of altered nucleolar structures resulting from myocardial infarction in mice supports the model of nucleolar stress as a general response to pathological injury. Collectively, these findings serve as the initial description of myocardial nucleolar stress and establish the postulate that nucleoli acts as sensors of stress, regulating the cellular response to pathological insults.
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21
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Nucleophosmin serves as a rate-limiting nuclear export chaperone for the Mammalian ribosome. Mol Cell Biol 2008; 28:7050-65. [PMID: 18809582 DOI: 10.1128/mcb.01548-07] [Citation(s) in RCA: 161] [Impact Index Per Article: 10.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Nucleophosmin (NPM) (B23) is an essential protein in mouse development and cell growth; however, it has been assigned numerous roles in very diverse cellular processes. Here, we present a unified mechanism for NPM's role in cell growth; NPM directs the nuclear export of both 40S and 60S ribosomal subunits. NPM interacts with rRNA and large and small ribosomal subunit proteins and also colocalizes with large and small ribosomal subunit proteins in the nucleolus, nucleus, and cytoplasm. The transduction of NPM shuttling-defective mutants or the loss of Npm1 inhibited the nuclear export of both the 40S and 60S ribosomal subunits, reduced the available pool of cytoplasmic polysomes, and diminished overall protein synthesis without affecting rRNA processing or ribosome assembly. While the inhibition of NPM shuttling can block cellular proliferation, the dramatic effects on ribosome export occur prior to cell cycle inhibition. Modest increases in NPM expression amplified the export of newly synthesized rRNAs, resulting in increased rates of protein synthesis and indicating that NPM is rate limiting in this pathway. These results support the idea that NPM-regulated ribosome export is a fundamental process in cell growth.
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22
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A non-tumor suppressor role for basal p19ARF in maintaining nucleolar structure and function. Mol Cell Biol 2007; 28:1068-80. [PMID: 18070929 DOI: 10.1128/mcb.00484-07] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
The nucleolus is the center of ribosome synthesis, with the nucleophosmin (NPM) and p19(ARF) proteins antagonizing one another to either promote or inhibit growth. However, basal NPM and ARF proteins form nucleolar complexes whose functions remain unknown. Nucleoli from Arf(-/)(-) cells displayed increased nucleolar area, suggesting that basal ARF might regulate key nucleolar functions. Concordantly, ribosome biogenesis and protein synthesis were dramatically elevated in the absence of Arf, causing these cells to exhibit tremendous gains in protein amounts and increases in cell volume. The transcription of ribosomal DNA (rDNA), the processing of nascent rRNA molecules, and the nuclear export of ribosomes were all increased in the absence of ARF. Similar results were obtained using targeted lentiviral RNA interference of ARF in wild-type MEFs. Postmitotic osteoclasts from Arf-null mice exhibited hyperactivity in vitro and in vivo, demonstrating a physiological function for basal ARF. Moreover, the knockdown of NPM blocked the increases in Arf(-/-) ribosome output and osteoclast activity, demonstrating that these gains require NPM. Thus, basal ARF proteins act as a monitor of steady-state ribosome biogenesis and growth independent of their ability to prevent unwarranted hyperproliferation.
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23
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Abstract
Ribosomal RNA transcription was one of the first model systems for molecular characterization of a transcription regulatory mechanism and certainly one of the best studied in the widest range of organisms. In multicellular organisms, however, the issue of cell-type-specific regulation of rRNA transcription has not been well addressed. Here I propose that a systematic study of cell-type-specific regulation of rRNA transcription may reveal new regulatory mechanisms that have not been previously realized. Specifically, issues concerning the cell-type-specific requirement for rRNA production, the universality of Pol I transcription complex and the division of rDNA into regulatory subdomains are discussed.
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Affiliation(s)
- Hung Tseng
- Department of Dermatology, Department of Cell and Developmental Biology, Center for Research on Reproduction and Women's Health, University of Pennsylvania, CRB Room 242B, 415 Curie Boulevard, Philadelphia, PA 19104, USA.
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24
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Abstract
All cells must make ribosomes, in which rRNA transcription is the rate-limiting step; however, some cells may require more ribosomes than others. Cell-type specific regulation of rRNA synthesis has been largely ignored in the past, because of the inability to measure rRNA transcription rate in situ. Here we map rRNA transcription activity in individual cells in mouse ocular tissues detected by a novel in situ hybridization technique, which detects the full-length transcripts (47S pre-rRNA) as well as various rRNA processing intermediates. In the adult mouse eye, the corneal and lens epithelia and some retinal neurons contain a higher level of 47S pre-rRNA and rRNA processing intermediates, which are regulated developmentally in neonates prior to eye opening. In the cornea and lens epithelia, the higher rRNA level of 47S rRNA correlates with cell proliferation, which is consistent with the notion that dividing cells require more protein synthesis. Interestingly, in some retinal neurons, the high level of 47S pre-rRNA does not correlate with mature rRNA accumulation or protein synthesis, suggesting the existence of unappreciated biochemical needs of these cells.
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Affiliation(s)
- Jiangchao Qian
- Department of Dermatology, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
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25
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Cui C, Elsam T, Tian Q, Seykora JT, Grachtchouk M, Dlugosz A, Tseng H. Gli proteins up-regulate the expression of basonuclin in Basal cell carcinoma. Cancer Res 2004; 64:5651-8. [PMID: 15313903 DOI: 10.1158/0008-5472.can-04-0801] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Tumorigenesis is frequently accompanied by enhanced rRNA transcription, but the signaling mechanisms responsible for such enhancement remain unclear. Here, we report evidence suggesting a novel link between deregulated Hedgehog signaling and the augmented rRNA transcription in cancer. Aberrant activation of the Hedgehog pathway in keratinocytes is a hallmark of basal cell carcinoma (BCC), the most common cancer in light-skinned individuals. We show that Gli proteins, downstream effectors of the Hedgehog pathway, increase expression of a novel rRNA gene (rDNA) transcription factor, basonuclin, whose expression is markedly elevated in BCCs. The promoter of the human basonuclin gene contains a Gli-binding site, which is required for Gli protein binding and transcriptional activation. We show also that the level of 47S pre-rRNA is much higher in BCCs than in normal epidermis, suggesting an accelerated rRNA transcription in the neoplastic cells. Within BCC, those cells expressing the highest level of basonuclin also exhibit the greatest increase in 47S pre-rRNA, consistent with a role for basonuclin in increasing rRNA transcription in these cells. Our data suggest that Hedgehog-Gli pathway enhances rRNA transcription in BCC by increasing basonuclin gene expression.
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Affiliation(s)
- Chunhua Cui
- Department of Dermatology, School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
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