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Daiß JL, Griesenbeck J, Tschochner H, Engel C. Synthesis of the ribosomal RNA precursor in human cells: mechanisms, factors and regulation. Biol Chem 2023; 404:1003-1023. [PMID: 37454246 DOI: 10.1515/hsz-2023-0214] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2023] [Accepted: 07/04/2023] [Indexed: 07/18/2023]
Abstract
The ribosomal RNA precursor (pre-rRNA) comprises three of the four ribosomal RNAs and is synthesized by RNA polymerase (Pol) I. Here, we describe the mechanisms of Pol I transcription in human cells with a focus on recent insights gained from structure-function analyses. The comparison of Pol I-specific structural and functional features with those of other Pols and with the excessively studied yeast system distinguishes organism-specific from general traits. We explain the organization of the genomic rDNA loci in human cells, describe the Pol I transcription cycle regarding structural changes in the enzyme and the roles of human Pol I subunits, and depict human rDNA transcription factors and their function on a mechanistic level. We disentangle information gained by direct investigation from what had apparently been deduced from studies of the yeast enzymes. Finally, we provide information about how Pol I mutations may contribute to developmental diseases, and why Pol I is a target for new cancer treatment strategies, since increased rRNA synthesis was correlated with rapidly expanding cell populations.
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Affiliation(s)
- Julia L Daiß
- Regensburg Center for Biochemistry, University of Regensburg, D-93053 Regensburg, Germany
| | - Joachim Griesenbeck
- Regensburg Center for Biochemistry, University of Regensburg, D-93053 Regensburg, Germany
| | - Herbert Tschochner
- Regensburg Center for Biochemistry, University of Regensburg, D-93053 Regensburg, Germany
| | - Christoph Engel
- Regensburg Center for Biochemistry, University of Regensburg, D-93053 Regensburg, Germany
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2
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Tiwari K, Gangopadhyay A, Singh G, Singh VK, Singh SK. Ab initio modelling of an essential mammalian protein: Transcription Termination Factor 1 (TTF1). J Biomol Struct Dyn 2022:1-10. [PMID: 35947129 DOI: 10.1080/07391102.2022.2109754] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/15/2022]
Abstract
Transcription Termination Factor 1 (TTF1) is an essential mammalian protein that regulates transcription, replication fork arrest, DNA damage repair, chromatin remodelling etc. TTF1 interacts with numerous cellular proteins to regulate various cellular phenomena which play a crucial role in maintaining normal cellular physiology, and dysregulation of this protein has been reported to induce oncogenic transformation of the cells. However, despite its key role in many cellular processes, the complete structure of human TTF1 has not been elucidated to date, neither experimentally nor computationally. Therefore, understanding the structure of human TTF1 is crucial for studying its functions and interactions with other cellular factors. The aim of this study was to construct the complete structure of human TTF1 protein, using molecular modelling approaches. Owing to the lack of suitable homologues in the Protein Data Bank (PDB), the complete structure of human TTF1 was constructed by ab initio modelling. The structural stability was determined with molecular dynamics (MD) simulations in explicit solvent, and trajectory analyses. The frequently occurring conformation of human TTF1 was selected by trajectory clustering, and the central residues of this conformation were determined by centrality analyses of the Residue Interaction Network (RIN) of TTF1. Two residue clusters, one in the oligomerization domain and other in the C-terminal domain, were found to be central to the structural stability of human TTF1. To the best of our knowledge, this study is the first to report the complete structure of this essential mammalian protein, and the results obtained herein will provide structural insights for future research including that in cancer biology and related studies.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Kumud Tiwari
- School of Biotechnology, Institute of Science, Banaras Hindu University, Varanasi, India
| | - Aditi Gangopadhyay
- Department of Chemical Technology, University of Calcutta, Kolkata, India
| | | | - Vinay Kumar Singh
- School of Biotechnology, Institute of Science, Banaras Hindu University, Varanasi, India.,Center for Bioinformatics, School of Biotechnology, Institute of Science, Banaras Hindu University, Varanasi, India
| | - Samarendra Kumar Singh
- School of Biotechnology, Institute of Science, Banaras Hindu University, Varanasi, India
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3
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Genome Organization in and around the Nucleolus. Cells 2019; 8:cells8060579. [PMID: 31212844 PMCID: PMC6628108 DOI: 10.3390/cells8060579] [Citation(s) in RCA: 71] [Impact Index Per Article: 14.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2019] [Revised: 06/09/2019] [Accepted: 06/11/2019] [Indexed: 12/17/2022] Open
Abstract
The nucleolus is the largest substructure in the nucleus, where ribosome biogenesis takes place, and forms around the nucleolar organizer regions (NORs) that comprise ribosomal RNA (rRNA) genes. Each cell contains hundreds of rRNA genes, which are organized in three distinct chromatin and transcriptional states—silent, inactive and active. Increasing evidence indicates that the role of the nucleolus and rRNA genes goes beyond the control of ribosome biogenesis. Recent results highlighted the nucleolus as a compartment for the location and regulation of repressive genomic domains and, together with the nuclear lamina, represents the hub for the organization of the inactive heterochromatin. In this review, we aim to describe the crosstalk between the nucleolus and the rest of the genome and how distinct rRNA gene chromatin states affect nucleolus structure and are implicated in genome stability, genome architecture, and cell fate decision.
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4
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Park SH, Yu KL, Jung YM, Lee SD, Kim MJ, You JC. Investigation of functional roles of transcription termination factor-1 (TTF-I) in HIV-1 replication. BMB Rep 2018; 51:338-343. [PMID: 29555014 PMCID: PMC6089867 DOI: 10.5483/bmbrep.2018.51.7.032] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2018] [Indexed: 11/25/2022] Open
Abstract
Transcription termination factor-1 (TTF-I) is an RNA polymerase 1-mediated transcription terminator and consisting of a C-terminal DNA-binding domain, central domain, and N-terminal regulatory domain. This protein binds to a so-called ‘Sal box’ composed of an 11-base pair motif. The interaction of TTF-I with the ‘Sal box’ is important for many cellular events, including efficient termination of RNA polymerase-1 activity involved in pre-rRNA synthesis and formation of a chromatin loop. To further understand the role of TTF-I in human immunodeficiency virus (HIV)-I virus production, we generated various TTF-I mutant forms. Through a series of studies of the over-expression of TTF-I and its derivatives along with co-transfection with either proviral DNA or HIV-I long terminal repeat (LTR)-driven reporter vectors, we determined that wild-type TTF-I downregulates HIV-I LTR activity and virus production, while the TTF-I Myb-like domain alone upregulated virus production, suggesting that wild-type TTF-I inhibits virus production and trans-activation of the LTR sequence; the Myb-like domain of TTF-I increased virus production and trans-activated LTR activity.
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Affiliation(s)
- Seong-Hyun Park
- National Research Laboratory for Molecular Virology, Department of Pathology, School of Medicine, The Catholic University of Korea, Seoul 06591, Korea
| | - Kyung-Lee Yu
- National Research Laboratory for Molecular Virology, Department of Pathology, School of Medicine, The Catholic University of Korea, Seoul 06591, Korea
| | - Yu-Mi Jung
- National Research Laboratory for Molecular Virology, Department of Pathology, School of Medicine, The Catholic University of Korea, Seoul 06591, Korea
| | - Seong-Deok Lee
- National Research Laboratory for Molecular Virology, Department of Pathology, School of Medicine, The Catholic University of Korea, Seoul 06591, Korea
| | | | - Ji-Chang You
- National Research Laboratory for Molecular Virology, Department of Pathology, School of Medicine, The Catholic University of Korea, Seoul 06591, Korea; Avixgen Inc., Seoul 06649, Korea
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5
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Abstract
Cellular DNA is packaged into chromatin, which is the substrate of all DNA-dependent processes in eukaryotes. The regulation of chromatin requires specialized enzyme activities to allow the access of sequence-specific binding proteins and RNA polymerases. In order to dissect chromatin-dependent features of transcription regulation in detail, in vitro systems to generate defined chromatin templates for transcription are required. I present a protocol that allows the assembly of nucleosomes on ribosomal RNA (rRNA) minigenes by salt gradient dialysis and subsequent sucrose gradient centrifugation. This procedure yields high nucleosome occupancy and high dynamic response in subsequent transcriptional analysis. It provides an invaluable tool to study rRNA gene transcription, as transcription on free DNA is clearly different from the more in vivo-like transcription on reconstituted chromatin templates.
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Nardocci G, Simonet NG, Navarro C, Längst G, Alvarez M. Differential enrichment of TTF-I and Tip5 in the T-like promoter structures of the rDNA contribute to the epigenetic response of Cyprinus carpio during environmental adaptation. Biochem Cell Biol 2016; 94:315-21. [PMID: 27458840 DOI: 10.1139/bcb-2016-0015] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
To ensure homeostasis, ectothermic organisms adapt to environmental variations through molecular mechanisms. We previously reported that during the seasonal acclimatization of the common carp Cyprinus carpio, molecular and cellular functions are reprogrammed, resulting in distinctive traits. Importantly, the carp undergoes a drastic rearrangement of nucleolar components during adaptation. This ultrastructural feature reflects a fine modulation of rRNA gene transcription. Specifically, we identified the involvement of the transcription termination factor I (TTF-I) and Tip-5 (member of nucleolar remodeling complex, NoRC) in the control of rRNA transcription. Our results suggest that differential Tip5 enrichment is essential for silencing carp ribosomal genes and that the T0 element is key for regulating the ribosomal gene during the acclimatization process. Interestingly, the expression and content of Tip5 were significantly higher in winter than in summer. Since carp ribosomal gene expression is lower in the winter than in summer, and considering that expression concomitantly occurs with nucleolar ultrastructural changes of the acclimatization process, these results indicate that Tip5 importantly contributes to silencing the ribosomal genes. In conclusion, the current study provides novel evidence on the contributions of TTF-I and NoRC in the environmental reprogramming of ribosomal genes during the seasonal adaptation process in carp.
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Affiliation(s)
- Gino Nardocci
- a Laboratorio de Biología Celular y Molecular, Departamento de Ciencias Biológicas, Facultad de Ciencias Biológicas, Universidad Andrés Bello, Quillota 980, Viña del Mar, Chile
| | - Nicolas G Simonet
- a Laboratorio de Biología Celular y Molecular, Departamento de Ciencias Biológicas, Facultad de Ciencias Biológicas, Universidad Andrés Bello, Quillota 980, Viña del Mar, Chile
| | - Cristina Navarro
- b Laboratorio de Biotecnología Molecular, Departamento de Ciencias Biológicas, Facultad de Ciencias Biológicas, Universidad Andrés Bello, Avenida Republica 217, Santiago, Chile
| | - Gernot Längst
- c Institute for Biochemistry III, Biochemie-Zentrum Regensburg, University of Regensburg, Regensburg, Germany
| | - Marco Alvarez
- a Laboratorio de Biología Celular y Molecular, Departamento de Ciencias Biológicas, Facultad de Ciencias Biológicas, Universidad Andrés Bello, Quillota 980, Viña del Mar, Chile.,d Interdisciplinary Center for Aquaculture Research (INCAR), Victor Lamas 1290, PO Box 160-C, Concepción, Chile
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7
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Komatsu H, Iguchi T, Ueda M, Nambara S, Saito T, Hirata H, Sakimura S, Takano Y, Uchi R, Shinden Y, Eguchi H, Masuda T, Sugimachi K, Eguchi H, Doki Y, Mori M, Mimori K. Clinical and biological significance of transcription termination factor, RNA polymerase I in human liver hepatocellular carcinoma. Oncol Rep 2016; 35:2073-80. [PMID: 26821084 DOI: 10.3892/or.2016.4593] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2015] [Accepted: 12/04/2015] [Indexed: 11/06/2022] Open
Abstract
Recent studies have indicated that increased ribosomal activity contributes to cancer progression. Transcription termination factor, RNA polymerase I (TTF1) acts as a transcription factor for RNA polymerase I. However, the role which TTF1 plays in cancer progression still remains unknown. The present study aimed to determine whether TTF1 plays a critical role in the progression of human liver hepatocellular carcinoma (HCC). In the present study, quantitative real-time reverse transcription polymerase chain reaction was conducted to evaluate TTF1 mRNA expression in 60 HCC tissue samples in order to determine the clinicopathological significance of TTF1. To investigate whether the expression levels of TTF1 were associated known gene signatures which represented ribosomal activity, we applied gene set enrichment analysis (GSEA) to HCC cases in The Cancer Genome Atlas (TCGA) a. We also performed in vitro proliferation assays using TTF1‑overexpressing HCC cells. TTF1 expression was significantly higher in HCC tumor tissues than in adjacent liver tissues (P<0.001). The overall survival (OS) of patients with high TTF1 expression levels was significantly shorter than that of patients with low TTF1 expression (P=0.027). Multivariate analysis indicated that TTF1 expression was an independent prognostic factor for OS (P=0.020). GSEA revealed significant associations between TTF1 expression and gene sets involved in ribosomal function. In vitro, cell proliferation and rRNA transcription were significantly promoted by overexpression of TTF1 in the HCC cell lines HuH-7 and HepG2. From these results, it was suggested that TTF1 participate in poor prognoses and play a role in tumor cell growth in HCC, possibly by upregulating ribosomal activity. In conclusion, we first propose that TTF1 may be a novel biomarker and therapeutic target in HCC. Increased expression of TTF1 was significantly associated with poor prognosis in two independent sets of HCC cases. Furthermore, in vitro experiments provided an explanation for clinical data showing that overexpression of TTF1 contributed to the proliferation of cancer cells.
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Affiliation(s)
- Hisateru Komatsu
- Department of Surgery, Kyushu University, Beppu Hospital, Beppu, Oita, Japan
| | - Tomohiro Iguchi
- Department of Surgery, Kyushu University, Beppu Hospital, Beppu, Oita, Japan
| | - Masami Ueda
- Department of Surgery, Kyushu University, Beppu Hospital, Beppu, Oita, Japan
| | - Sho Nambara
- Department of Surgery, Kyushu University, Beppu Hospital, Beppu, Oita, Japan
| | - Tomoko Saito
- Department of Surgery, Kyushu University, Beppu Hospital, Beppu, Oita, Japan
| | - Hidenari Hirata
- Department of Surgery, Kyushu University, Beppu Hospital, Beppu, Oita, Japan
| | - Shotaro Sakimura
- Department of Surgery, Kyushu University, Beppu Hospital, Beppu, Oita, Japan
| | - Yuki Takano
- Department of Surgery, Kyushu University, Beppu Hospital, Beppu, Oita, Japan
| | - Ryutaro Uchi
- Department of Surgery, Kyushu University, Beppu Hospital, Beppu, Oita, Japan
| | - Yoshiaki Shinden
- Department of Surgery, Kyushu University, Beppu Hospital, Beppu, Oita, Japan
| | - Hidetoshi Eguchi
- Department of Surgery, Kyushu University, Beppu Hospital, Beppu, Oita, Japan
| | - Takaaki Masuda
- Department of Surgery, Kyushu University, Beppu Hospital, Beppu, Oita, Japan
| | - Keishi Sugimachi
- Department of Surgery, Kyushu University, Beppu Hospital, Beppu, Oita, Japan
| | - Hidetoshi Eguchi
- Department of Gastroenterological Surgery, Graduate School of Medicine, Suita, Osaka, Japan
| | - Yuichiro Doki
- Department of Gastroenterological Surgery, Graduate School of Medicine, Suita, Osaka, Japan
| | - Masaki Mori
- Department of Gastroenterological Surgery, Graduate School of Medicine, Suita, Osaka, Japan
| | - Koshi Mimori
- Department of Surgery, Kyushu University, Beppu Hospital, Beppu, Oita, Japan
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8
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Savić N, Bär D, Leone S, Frommel SC, Weber FA, Vollenweider E, Ferrari E, Ziegler U, Kaech A, Shakhova O, Cinelli P, Santoro R. lncRNA maturation to initiate heterochromatin formation in the nucleolus is required for exit from pluripotency in ESCs. Cell Stem Cell 2015; 15:720-34. [PMID: 25479748 DOI: 10.1016/j.stem.2014.10.005] [Citation(s) in RCA: 101] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2014] [Revised: 08/08/2014] [Accepted: 10/16/2014] [Indexed: 11/29/2022]
Abstract
The open chromatin of embryonic stem cells (ESCs) condenses into repressive heterochromatin as cells exit the pluripotent state. How the 3D genome organization is orchestrated and implicated in pluripotency and lineage specification is not understood. Here, we find that maturation of the long noncoding RNA (lncRNA) pRNA is required for establishment of heterochromatin at ribosomal RNA genes, the genetic component of nucleoli, and this process is inactivated in pluripotent ESCs. By using mature pRNA to tether heterochromatin at nucleoli of ESCs, we find that localized heterochromatin condensation of ribosomal RNA genes initiates establishment of highly condensed chromatin structures outside of the nucleolus. Moreover, we reveal that formation of such highly condensed, transcriptionally repressed heterochromatin promotes transcriptional activation of differentiation genes and loss of pluripotency. Our findings unravel the nucleolus as an active regulator of chromatin plasticity and pluripotency and challenge current views on heterochromatin regulation and function in ESCs.
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Affiliation(s)
- Nataša Savić
- Institute of Veterinary Biochemistry and Molecular Biology, University of Zurich, 8057 Zurich, Switzerland; Molecular Life Science Program, Life Science Zurich Graduate School, University of Zurich, 8057 Zurich, Switzerland
| | - Dominik Bär
- Institute of Veterinary Biochemistry and Molecular Biology, University of Zurich, 8057 Zurich, Switzerland
| | - Sergio Leone
- Institute of Veterinary Biochemistry and Molecular Biology, University of Zurich, 8057 Zurich, Switzerland; Molecular Life Science Program, Life Science Zurich Graduate School, University of Zurich, 8057 Zurich, Switzerland
| | - Sandra C Frommel
- Institute of Veterinary Biochemistry and Molecular Biology, University of Zurich, 8057 Zurich, Switzerland; Molecular Life Science Program, Life Science Zurich Graduate School, University of Zurich, 8057 Zurich, Switzerland
| | - Fabienne A Weber
- Molecular Life Science Program, Life Science Zurich Graduate School, University of Zurich, 8057 Zurich, Switzerland; Institute of Laboratory Animal Science, University of Zurich, 8057 Zurich, Switzerland
| | - Eva Vollenweider
- Institute of Veterinary Biochemistry and Molecular Biology, University of Zurich, 8057 Zurich, Switzerland; Molecular Life Science Program, Life Science Zurich Graduate School, University of Zurich, 8057 Zurich, Switzerland
| | - Elena Ferrari
- Institute of Veterinary Biochemistry and Molecular Biology, University of Zurich, 8057 Zurich, Switzerland
| | - Urs Ziegler
- Center for Microscopy and Image Analysis, University of Zurich, 8057 Zurich, Switzerland
| | - Andres Kaech
- Center for Microscopy and Image Analysis, University of Zurich, 8057 Zurich, Switzerland
| | - Olga Shakhova
- Department of Oncology, University Hospital Zurich, 8952 Schlieren, Switzerland
| | - Paolo Cinelli
- Institute of Laboratory Animal Science, University of Zurich, 8057 Zurich, Switzerland; Center for Applied Biotechnology and Molecular Medicine, University of Zurich, 8057 Zurich, Switzerland; Division of Trauma Surgery, Center for Clinical Research, University Hospital Zurich, 8091 Zurich, Switzerland
| | - Raffaella Santoro
- Institute of Veterinary Biochemistry and Molecular Biology, University of Zurich, 8057 Zurich, Switzerland; Center for Applied Biotechnology and Molecular Medicine, University of Zurich, 8057 Zurich, Switzerland.
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9
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Ueda M, Iguchi T, Nambara S, Saito T, Komatsu H, Sakimura S, Hirata H, Uchi R, Takano Y, Shinden Y, Eguchi H, Masuda T, Sugimachi K, Yamamoto H, Doki Y, Mori M, Mimori K. Overexpression of Transcription Termination Factor 1 is Associated with a Poor Prognosis in Patients with Colorectal Cancer. Ann Surg Oncol 2015; 22 Suppl 3:S1490-8. [PMID: 26036188 DOI: 10.1245/s10434-015-4652-7] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2015] [Indexed: 01/10/2023]
Abstract
BACKGROUND RNA polymerase 1 transcription termination factor (TTF1) mediates the transcription of ribosomal RNA (rRNA). In the current study, we investigated the clinical and biological significance of the TTF1 gene in colorectal cancer (CRC). METHODS The expression of TTF1 messenger RNA (mRNA) in tumor and normal tissues from 136 patients with CRC was examined by quantitative real-time reverse transcription polymerase chain reaction (qRT-PCR). We also performed in vitro cell proliferation and migration assays in TTF1-expressing CRC cells. The biological role of TTF1 in CRC was further elucidated using gene set enrichment analysis (GSEA) with CRC samples. RESULTS TTF1 expression was significantly higher in tumor tissues than in corresponding normal tissues (p = 0.016). In clinicopathological analysis, the high-TTF1 expression group showed a higher incidence of liver metastasis and lymphatic invasion than the low-TTF1 expression group (p < 0.05), and tended to have more frequent venous invasion than the low-TTF1 expression group. Furthermore, the high-TTF1 expression group had a significantly poorer prognosis than the low-TTF1 expression group (p = 0.011). Moreover, overexpression of TTF1 enhanced the proliferation and migration capacity of CRC cells in vitro. GSEA revealed that TTF1 was significantly associated with the RAS and MYC pathways, and this observation was confirmed in samples from 136 patients with CRC. CONCLUSION TTF1 was involved in cancer progression via the RAS and MYC pathways in CRC, suggesting that TTF1 may be a prognostic indicator and therapeutic target in CRC.
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Affiliation(s)
- Masami Ueda
- Department of Surgery, Kyushu University Beppu Hospital, Beppu, Japan. .,Department of Gastroenterological Surgery, Graduate School of Medicine, Osaka University, Suita, Japan.
| | - Tomohiro Iguchi
- Department of Surgery, Kyushu University Beppu Hospital, Beppu, Japan
| | - Sho Nambara
- Department of Surgery, Kyushu University Beppu Hospital, Beppu, Japan
| | - Tomoko Saito
- Department of Surgery, Kyushu University Beppu Hospital, Beppu, Japan
| | - Hisateru Komatsu
- Department of Surgery, Kyushu University Beppu Hospital, Beppu, Japan.,Department of Gastroenterological Surgery, Graduate School of Medicine, Osaka University, Suita, Japan
| | - Shotaro Sakimura
- Department of Surgery, Kyushu University Beppu Hospital, Beppu, Japan
| | - Hidenari Hirata
- Department of Surgery, Kyushu University Beppu Hospital, Beppu, Japan
| | - Ryutaro Uchi
- Department of Surgery, Kyushu University Beppu Hospital, Beppu, Japan
| | - Yuki Takano
- Department of Surgery, Kyushu University Beppu Hospital, Beppu, Japan
| | - Yoshiaki Shinden
- Department of Surgery, Kyushu University Beppu Hospital, Beppu, Japan
| | - Hidetoshi Eguchi
- Department of Surgery, Kyushu University Beppu Hospital, Beppu, Japan
| | - Takaaki Masuda
- Department of Surgery, Kyushu University Beppu Hospital, Beppu, Japan
| | - Keishi Sugimachi
- Department of Surgery, Kyushu University Beppu Hospital, Beppu, Japan
| | - Hirofumi Yamamoto
- Department of Gastroenterological Surgery, Graduate School of Medicine, Osaka University, Suita, Japan
| | - Yuichiro Doki
- Department of Gastroenterological Surgery, Graduate School of Medicine, Osaka University, Suita, Japan
| | - Masaki Mori
- Department of Gastroenterological Surgery, Graduate School of Medicine, Osaka University, Suita, Japan
| | - Koshi Mimori
- Department of Surgery, Kyushu University Beppu Hospital, Beppu, Japan.
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10
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Jaiswal R, Singh SK, Bastia D, Escalante CR. Crystallization and preliminary X-ray characterization of the eukaryotic replication terminator Reb1-Ter DNA complex. Acta Crystallogr F Struct Biol Commun 2015; 71:414-8. [PMID: 25849502 PMCID: PMC4388176 DOI: 10.1107/s2053230x15004112] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2014] [Accepted: 02/26/2015] [Indexed: 11/10/2022] Open
Abstract
The Reb1 protein from Schizosaccharomyces pombe is a member of a family of proteins that control programmed replication termination and/or transcription termination in eukaryotic cells. These events occur at naturally occurring replication fork barriers (RFBs), where Reb1 binds to termination (Ter) DNA sites and coordinates the polar arrest of replication forks and transcription approaching in opposite directions. The Reb1 DNA-binding and replication-termination domain was expressed in Escherichia coli, purified and crystallized in complex with a 26-mer DNA Ter site. Batch crystallization under oil was required to produce crystals of good quality for data collection. Crystals grew in space group P2₁, with unit-cell parameters a = 68.9, b = 162.9, c = 71.1 Å, β = 94.7°. The crystals diffracted to a resolution of 3.0 Å. The crystals were mosaic and required two or three cycles of annealing. This study is the first to yield structural information about this important family of proteins and will provide insights into the mechanism of replication and transcription termination.
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Affiliation(s)
- Rahul Jaiswal
- Department of Physiology and Biophysics, Virginia Commonwealth University, 1220 East Broad Street, Richmond, VA 23298, USA
- Nanyang Technological University, SBS, 60 Nanyang Drive, Singapore-637551
| | - Samarendra K. Singh
- Department of Biochemistry and Molecular Biology, Medical University of South Carolina, Charleston, SC 29425, USA
- National Institutes of Health, Bethesda, MD 20892, USA
| | - Deepak Bastia
- Department of Biochemistry and Molecular Biology, Medical University of South Carolina, Charleston, SC 29425, USA
| | - Carlos R. Escalante
- Department of Physiology and Biophysics, Virginia Commonwealth University, 1220 East Broad Street, Richmond, VA 23298, USA
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11
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Smith CL, Matheson TD, Trombly DJ, Sun X, Campeau E, Han X, Yates JR, Kaufman PD. A separable domain of the p150 subunit of human chromatin assembly factor-1 promotes protein and chromosome associations with nucleoli. Mol Biol Cell 2014; 25:2866-81. [PMID: 25057015 PMCID: PMC4161520 DOI: 10.1091/mbc.e14-05-1029] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Chromatin assembly factor-1 contains a separable domain unrelated to histone deposition, which provides a previously unrecognized ability to maintain nucleolar protein and chromosome associations. Chromatin assembly factor-1 (CAF-1) is a three-subunit protein complex conserved throughout eukaryotes that deposits histones during DNA synthesis. Here we present a novel role for the human p150 subunit in regulating nucleolar macromolecular interactions. Acute depletion of p150 causes redistribution of multiple nucleolar proteins and reduces nucleolar association with several repetitive element–containing loci. Of note, a point mutation in a SUMO-interacting motif (SIM) within p150 abolishes nucleolar associations, whereas PCNA or HP1 interaction sites within p150 are not required for these interactions. In addition, acute depletion of SUMO-2 or the SUMO E2 ligase Ubc9 reduces α-satellite DNA association with nucleoli. The nucleolar functions of p150 are separable from its interactions with the other subunits of the CAF-1 complex because an N-terminal fragment of p150 (p150N) that cannot interact with other CAF-1 subunits is sufficient for maintaining nucleolar chromosome and protein associations. Therefore these data define novel functions for a separable domain of the p150 protein, regulating protein and DNA interactions at the nucleolus.
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Affiliation(s)
- Corey L Smith
- Program in Gene Function and Expression, Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, MA 01605
| | - Timothy D Matheson
- Program in Gene Function and Expression, Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, MA 01605
| | - Daniel J Trombly
- Program in Gene Function and Expression, Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, MA 01605
| | - Xiaoming Sun
- Program in Gene Function and Expression, Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, MA 01605
| | - Eric Campeau
- Program in Gene Function and Expression, Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, MA 01605
| | - Xuemei Han
- Department of Chemical Physiology, Scripps Research Institute, La Jolla, CA 92037
| | - John R Yates
- Department of Chemical Physiology, Scripps Research Institute, La Jolla, CA 92037
| | - Paul D Kaufman
- Program in Gene Function and Expression, Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, MA 01605
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12
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Giannakakis A, Karapetsas A, Dangaj D, Lanitis E, Tanyi J, Coukos G, Sandaltzopoulos R. Overexpression of SMARCE1 is associated with CD8+ T-cell infiltration in early stage ovarian cancer. Int J Biochem Cell Biol 2014; 53:389-98. [PMID: 24880093 DOI: 10.1016/j.biocel.2014.05.031] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2014] [Revised: 05/08/2014] [Accepted: 05/19/2014] [Indexed: 10/25/2022]
Abstract
T-lymphocyte infiltration in ovarian tumors has been linked to a favorable prognosis, hence, exploring the mechanism of T-cell recruitment in the tumor is warranted. We employed a differential expression analysis to identify genes over-expressed in early stage ovarian cancer samples that contained CD8 infiltrating T-lymphocytes. Among other genes, we discovered that TTF1, a regulator of ribosomal RNA gene expression, and SMARCE1, a factor associated with chromatin remodeling were overexpressed in first stage CD8+ ovarian tumors. TTF1 and SMARCE1 mRNA levels showed a strong correlation with the number of intra-tumoral CD8+ cells in ovarian tumors. Interestingly, forced overexpression of SMARCE1 in SKOV3 ovarian cancer cells resulted in secretion of IL8, MIP1b and RANTES chemokines in the supernatant and triggered chemotaxis of CD8+ lymphocytes in a cell culture assay. The potency of SMARCE1-mediated chemotaxis appeared comparable to that caused by the transfection of the CXCL9 gene, coding for a chemokine known to attract T-cells. Our analysis pinpoints TTF1 and SMARCE1 as genes potentially involved in cancer immunology. Since both TTF1 and SMARCE1 are involved in chromatin remodeling, our results imply an epigenetic regulatory mechanism for T-cell recruitment that invites deciphering.
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Affiliation(s)
- Antonis Giannakakis
- Laboratory of Gene Expression, Molecular Diagnosis and Modern Therapeutics, Department of Molecular Biology and Genetics, Faculty of Health Sciences, Democritus University of Thrace, Alexandroupolis, Greece; Division of Genome and Gene Expression Data Analysis, Bioinformatics Institute A*STAR (Agency for Science, Technology and Research), Singapore 138671, Singapore
| | - Athanasios Karapetsas
- Laboratory of Gene Expression, Molecular Diagnosis and Modern Therapeutics, Department of Molecular Biology and Genetics, Faculty of Health Sciences, Democritus University of Thrace, Alexandroupolis, Greece
| | - Denarda Dangaj
- Laboratory of Gene Expression, Molecular Diagnosis and Modern Therapeutics, Department of Molecular Biology and Genetics, Faculty of Health Sciences, Democritus University of Thrace, Alexandroupolis, Greece; Department of Oncology, Ludwig Cancer Research Center, University of Lausanne, Lausanne, Switzerland
| | - Evripidis Lanitis
- Laboratory of Gene Expression, Molecular Diagnosis and Modern Therapeutics, Department of Molecular Biology and Genetics, Faculty of Health Sciences, Democritus University of Thrace, Alexandroupolis, Greece; Department of Oncology, Ludwig Cancer Research Center, University of Lausanne, Lausanne, Switzerland
| | - Janos Tanyi
- Division of Gynecologic Oncology, University of Pennsylvania, Philadelphia, USA
| | - George Coukos
- Department of Oncology, University Hospital of Lausanne (CHUV), Ludwig Cancer Research Center, University of Lausanne, Lausanne, Switzerland
| | - Raphael Sandaltzopoulos
- Laboratory of Gene Expression, Molecular Diagnosis and Modern Therapeutics, Department of Molecular Biology and Genetics, Faculty of Health Sciences, Democritus University of Thrace, Alexandroupolis, Greece.
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13
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Diermeier SD, Németh A, Rehli M, Grummt I, Längst G. Chromatin-specific regulation of mammalian rDNA transcription by clustered TTF-I binding sites. PLoS Genet 2013; 9:e1003786. [PMID: 24068958 PMCID: PMC3772059 DOI: 10.1371/journal.pgen.1003786] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2013] [Accepted: 07/26/2013] [Indexed: 12/04/2022] Open
Abstract
Enhancers and promoters often contain multiple binding sites for the same transcription factor, suggesting that homotypic clustering of binding sites may serve a role in transcription regulation. Here we show that clustering of binding sites for the transcription termination factor TTF-I downstream of the pre-rRNA coding region specifies transcription termination, increases the efficiency of transcription initiation and affects the three-dimensional structure of rRNA genes. On chromatin templates, but not on free rDNA, clustered binding sites promote cooperative binding of TTF-I, loading TTF-I to the downstream terminators before it binds to the rDNA promoter. Interaction of TTF-I with target sites upstream and downstream of the rDNA transcription unit connects these distal DNA elements by forming a chromatin loop between the rDNA promoter and the terminators. The results imply that clustered binding sites increase the binding affinity of transcription factors in chromatin, thus influencing the timing and strength of DNA-dependent processes. The sequence-specific binding of proteins to regulatory regions controls gene expression. Binding sites for transcription factors are rather short and present several million times in large genomes. However, only a small number of these binding sites are functionally important. How proteins can discriminate and select their functional regions is not clear, to date. Regulatory loci like gene promoters and enhancers commonly comprise multiple binding sites for either one factor or a combination of several DNA binding proteins, allowing efficient factor recruitment. We studied the cluster of TTF-I binding sites downstream of the rRNA gene and identified that cooperative binding to the multimeric termination sites in combination with low-affinity binding of TTF-I to individual sites upstream of the gene serves multiple regulatory functions. Packaging of the clustered sites into chromatin is a prerequisite for high-affinity binding, coordinated activation of transcription and the formation of a chromatin loop between the promoter and the terminator.
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Affiliation(s)
- Sarah D. Diermeier
- Biochemistry Centre Regensburg (BCR), University of Regensburg, Regensburg, Germany
| | - Attila Németh
- Biochemistry Centre Regensburg (BCR), University of Regensburg, Regensburg, Germany
| | - Michael Rehli
- Department of Hematology, University Hospital Regensburg, Regensburg, Germany
| | - Ingrid Grummt
- Molecular Biology of the Cell II, German Cancer Research Centre (DKFZ), Heidelberg, Germany
| | - Gernot Längst
- Biochemistry Centre Regensburg (BCR), University of Regensburg, Regensburg, Germany
- * E-mail:
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14
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Montanaro L, Treré D, Derenzini M. The emerging role of RNA polymerase I transcription machinery in human malignancy: a clinical perspective. Onco Targets Ther 2013; 6:909-16. [PMID: 23888116 PMCID: PMC3722134 DOI: 10.2147/ott.s36627] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023] Open
Abstract
Ribosome biogenesis – the complex and highly coordinated cellular process leading to the production of ribosomes – is strictly dependent on the activity of RNA polymerase I (Pol I) transcriptional machinery. Pol I activity is continually increased in proliferating cells to sustain the increased demand for ribosome production and protein synthesis, which are necessary for appropriate cell growth and division. The integrity of the process of ribosome biogenesis represents an important sensor of cellular stress: when this process is altered, a tumor suppressor response is triggered, which leads to proliferative arrest. The present review focuses on the possible implications of Pol I targeting in the treatment of human malignancies.
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Affiliation(s)
- Lorenzo Montanaro
- Department of Experimental, Diagnostic and Specialty Medicine, University of Bologna, Bologna, ItalyAlma Mater Studiorum, University of Bologna, Bologna, Italy
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15
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Goodfellow SJ, Zomerdijk JCBM. Basic mechanisms in RNA polymerase I transcription of the ribosomal RNA genes. Subcell Biochem 2013; 61:211-36. [PMID: 23150253 PMCID: PMC3855190 DOI: 10.1007/978-94-007-4525-4_10] [Citation(s) in RCA: 120] [Impact Index Per Article: 10.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
RNA Polymerase (Pol) I produces ribosomal (r)RNA, an essential component of the cellular protein synthetic machinery that drives cell growth, underlying many fundamental cellular processes. Extensive research into the mechanisms governing transcription by Pol I has revealed an intricate set of control mechanisms impinging upon rRNA production. Pol I-specific transcription factors guide Pol I to the rDNA promoter and contribute to multiple rounds of transcription initiation, promoter escape, elongation and termination. In addition, many accessory factors are now known to assist at each stage of this transcription cycle, some of which allow the integration of transcriptional activity with metabolic demands. The organisation and accessibility of rDNA chromatin also impinge upon Pol I output, and complex mechanisms ensure the appropriate maintenance of the epigenetic state of the nucleolar genome and its effective transcription by Pol I. The following review presents our current understanding of the components of the Pol I transcription machinery, their functions and regulation by associated factors, and the mechanisms operating to ensure the proper transcription of rDNA chromatin. The importance of such stringent control is demonstrated by the fact that deregulated Pol I transcription is a feature of cancer and other disorders characterised by abnormal translational capacity.
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Affiliation(s)
- Sarah J. Goodfellow
- Wellcome Trust Centre for Gene Regulation and Expression, College of Life Sciences, University of Dundee , Dundee DD1 5EH , UK
| | - Joost C. B. M. Zomerdijk
- Wellcome Trust Centre for Gene Regulation and Expression, College of Life Sciences, University of Dundee , Dundee DD1 5EH , UK
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16
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Epigenetic control of RNA polymerase I transcription in mammalian cells. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2012; 1829:393-404. [PMID: 23063748 DOI: 10.1016/j.bbagrm.2012.10.004] [Citation(s) in RCA: 103] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/10/2012] [Revised: 10/04/2012] [Accepted: 10/06/2012] [Indexed: 11/22/2022]
Abstract
rRNA synthesis is regulated by genetic and epigenetic mechanisms. Epigenetic states are metastable, changing in response to appropriate signals, thereby modulating transcription in vivo. The establishment, maintenance and reversal of epigenetic features are fundamental for the cell's ability to 'remember' past events, to adapt to environmental changes or developmental cues and to propagate this information to the progeny. As packaging into chromatin is critical for the stability and integrity of repetitive DNA, keeping a fraction of rRNA genes in a metastable heterochromatic conformation prevents aberrant exchanges between repeats, thus safeguarding nucleolar structure and rDNA stability. In this review, we will focus on the nature of the molecular signatures that characterize a given epigenetic state of rDNA in mammalian cells, including noncoding RNA, DNA methylation and histone modifications, and the mechanisms by which they are established and maintained. This article is part of a Special Issue entitled: Transcription by Odd Pols.
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17
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The chromatin remodeling complex NuRD establishes the poised state of rRNA genes characterized by bivalent histone modifications and altered nucleosome positions. Proc Natl Acad Sci U S A 2012; 109:8161-6. [PMID: 22570494 DOI: 10.1073/pnas.1201262109] [Citation(s) in RCA: 93] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
rRNA genes (rDNA) exist in two distinct epigenetic states, active promoters being unmethylated and marked by euchromatic histone modifications, whereas silent ones are methylated and exhibit heterochromatic features. Here we show that the nucleosome remodeling and deacetylation (NuRD) complex establishes a specific chromatin structure at rRNA genes that are poised for transcription activation. The promoter of poised rRNA genes is unmethylated, associated with components of the preinitiation complex, marked by bivalent histone modifications and covered by a nucleosome in the "off" position, which is refractory to transcription initiation. Repression of rDNA transcription in growth-arrested and differentiated cells correlates with elevated association of NuRD and increased levels of poised rRNA genes. Reactivation of transcription requires resetting the promoter-bound nucleosome into the "on" position by the DNA-dependent ATPase CSB (Cockayne syndrome protein B). The results uncover a unique mechanism by which ATP-dependent chromatin remodeling complexes with opposing activities establish a specific chromatin state and regulate transcription.
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18
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Brannan K, Kim H, Erickson B, Glover-Cutter K, Kim S, Fong N, Kiemele L, Hansen K, Davis R, Lykke-Andersen J, Bentley DL. mRNA decapping factors and the exonuclease Xrn2 function in widespread premature termination of RNA polymerase II transcription. Mol Cell 2012; 46:311-24. [PMID: 22483619 DOI: 10.1016/j.molcel.2012.03.006] [Citation(s) in RCA: 167] [Impact Index Per Article: 13.9] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2011] [Revised: 12/27/2011] [Accepted: 03/08/2012] [Indexed: 02/07/2023]
Abstract
We report a function of human mRNA decapping factors in control of transcription by RNA polymerase II. Decapping proteins Edc3, Dcp1a, and Dcp2 and the termination factor TTF2 coimmunoprecipitate with Xrn2, the nuclear 5'-3' exonuclease "torpedo" that facilitates transcription termination at the 3' ends of genes. Dcp1a, Xrn2, and TTF2 localize near transcription start sites (TSSs) by ChIP-seq. At genes with 5' peaks of paused pol II, knockdown of decapping or termination factors Xrn2 and TTF2 shifted polymerase away from the TSS toward upstream and downstream distal positions. This redistribution of pol II is similar in magnitude to that caused by depletion of the elongation factor Spt5. We propose that coupled decapping of nascent transcripts and premature termination by the "torpedo" mechanism is a widespread mechanism that limits bidirectional pol II elongation. Regulated cotranscriptional decapping near promoter-proximal pause sites followed by premature termination could control productive pol II elongation.
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Affiliation(s)
- Kris Brannan
- Department of Biochemistry and Molecular Genetics, University of Colorado School of Medicine, Aurora, CO 80045, USA
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19
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Lessard F, Stefanovsky V, Tremblay MG, Moss T. The cellular abundance of the essential transcription termination factor TTF-I regulates ribosome biogenesis and is determined by MDM2 ubiquitinylation. Nucleic Acids Res 2012; 40:5357-67. [PMID: 22383580 PMCID: PMC3384320 DOI: 10.1093/nar/gks198] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
Abstract
The ARF tumour suppressor stabilizes p53 by negatively regulating the E3 ubiquitin ligase MDM2 to promote cell cycle arrest and cell death. However, ARF is also able to arrest cell proliferation by inhibiting ribosome biogenesis. In greater part this is achieved by targeting the transcription termination factor I (TTF-I) for nucleolar export, leading to an inhibition of both ribosomal RNA synthesis and processing. We now show that in the absence of ARF, TTF-I is ubiquitinylated by MDM2. MDM2 interacts directly with TTF-I and regulates its cellular abundance by targeting it for degradation by the proteasome. Enhanced TTF-I levels inhibit ribosome biogenesis by suppressing ribosomal RNA synthesis and processing, strongly suggesting that exact TTF-I levels are critical for efficient ribosome biogenesis. We further show that concomitant with its ability to displace TTF-I from the nucleolus, ARF inhibits MDM2 ubiquitinylation of TTF-I by competitively binding to a site overlapping the MDM2 interaction site. Thus, both the sub-nuclear localization and the abundance of TTF-I are key regulators of ribosome biogenesis.
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Affiliation(s)
- Frédéric Lessard
- Cancer Research Centre and Department of Molecular Biology, Medical Biochemistry and Pathology of Laval University, CHUQ Research Centre, Pavillon St Patrick, 9 rue McMahon, Québec, G1R 3S3 Québec, Canada
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20
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Zhai N, Zhao ZL, Cheng MB, Di YW, Yan HX, Cao CY, Dai H, Zhang Y, Shen YF. Human PIH1 associates with histone H4 to mediate the glucose-dependent enhancement of pre-rRNA synthesis. J Mol Cell Biol 2012; 4:231-41. [PMID: 22368283 DOI: 10.1093/jmcb/mjs003] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Ribosome biogenesis is critical in the growth of eukaryotic cells, in which the synthesis of precursor ribosomal RNA is the first and rate-limiting step. Here, we show that human PIH1 domain-containing protein 1 (PIH1) interacts directly with histone H4 and recruits the Brg1-SWI/SNF complex via SNF5 to human rRNA genes. This process is likely involved in PIH1-dependent DNase I-hypersensitive chromatin remodeling at the core promoter of the rRNA genes. PIH1 mediates the occupancy of not only the Brg1 complex but also the Pol I complex at the core promoter and enhances transcription initiation of rRNA genes. Additionally, the interaction between PIH1 and H4K16 expels TIP5, a component of the silencing nucleolar remodeling complex (NoRC), from the core region, suggesting that PIH1 is involved in the derepression of NoRC-silenced rRNA genes. These data indicate that PIH1 is a positive regulator of human rRNA genes and is of great importance for the recovery of human cells from nutrient starvation and the transition to glucose-induced exponential growth in vivo.
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Affiliation(s)
- Niu Zhai
- Department of Biochemistry and Molecular Biology, National Laboratory of Medical Molecular Biology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences and Peking Union Medical College, 5 Dongdan Santiao, Beijing 100005, China
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21
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Percipalle P, Louvet E. In vivo run-on assays to monitor nascent precursor RNA transcripts. Methods Mol Biol 2012; 809:519-33. [PMID: 22113298 DOI: 10.1007/978-1-61779-376-9_34] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
Biochemical methods have provided mechanistic insights into the different transcription phases during which the RNA polymerase is assembled at gene promoter and becomes engaged in the elongation of nascent transcripts. Evidence that transcription takes place in specific regions of the nucleus has fuelled the need to develop assays that can be performed in living cells and provide information on the location of the specific foci, where transcription takes place. In this chapter, we describe a method that is based on the incorporation of a fluorine-conjugated uridine analogue, incorporation that can be monitored by immunofluorescence and light microscopy using specific fluorochrome-conjugated monoclonal antibodies. This assay allows direct monitoring of active transcription foci in living cells. When coupled to suitable software, the method outlined here also provides a semiquantitative approach to measure the number of active transcription foci that correlate with the proliferation state of the cell. Therefore, the assay we present here is a sensitive analytical tool to monitor the topology of transcription foci in the eukaryotic cell nucleus and to gain insight into transcription rates.
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22
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Schneider DA. RNA polymerase I activity is regulated at multiple steps in the transcription cycle: recent insights into factors that influence transcription elongation. Gene 2011; 493:176-84. [PMID: 21893173 DOI: 10.1016/j.gene.2011.08.006] [Citation(s) in RCA: 60] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2011] [Revised: 07/11/2011] [Accepted: 08/08/2011] [Indexed: 01/21/2023]
Abstract
Synthesis of the translation apparatus is a central activity in growing and/or proliferating cells. Because of its fundamental importance and direct connection to cell proliferation, ribosome synthesis has been a focus of ongoing research for several decades. As a consequence, much is known about the essential factors involved in this process. Many studies have shown that transcription of the ribosomal DNA by RNA polymerase I is a major target for cellular regulation of ribosome synthesis rates. The initiation of transcription by RNA polymerase I has been implicated as a regulatory target, however, recent studies suggest that the elongation step in transcription is also influenced and regulated by trans-acting factors. This review describes the factors required for rRNA synthesis and focuses on recent works that have begun to identify and characterize factors that influence transcription elongation by RNA polymerase I and its regulation.
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Affiliation(s)
- David Alan Schneider
- Department of Biochemistry and Molecular Genetics, University of Alabama at Birmingham, 720 20th Street South, Kaul Human Genetics, Room 442, Birmingham, AL 35294, USA.
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23
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Rodríguez-Sánchez L, Rodríguez-López M, García Z, Tenorio-Gómez M, Schvartzman JB, Krimer DB, Hernández P. The fission yeast rDNA-binding protein Reb1 regulates G1 phase under nutritional stress. J Cell Sci 2010; 124:25-34. [PMID: 21118960 DOI: 10.1242/jcs.070987] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Yeast Reb1 and its mammalian ortholog TTF1 are conserved Myb-type DNA-binding proteins that bind to specific sites near the 3'-end of rRNA genes (rDNA). Here, they participate in the termination of transcription driven by RNA polymerase I and block DNA replication forks approaching in the opposite direction. We found that Schizosaccharomyces pombe Reb1 also upregulates transcription of the ste9(+) gene that is required for nitrogen-starvation-induced growth arrest with a G1 DNA content and sexual differentiation. Ste9 activates the anaphase-promoting complex or cyclosome ('APC/C') in G1, targeting B-cyclin for proteasomal degradation in response to nutritional stress. Reb1 binds in vivo and in vitro to a specific DNA sequence at the promoter of ste9(+), similar to the sequence recognized in the rDNA, and this binding is required for ste9(+) transcriptional activation and G1 arrest. This suggests that Reb1 acts as a link between rDNA metabolism and cell cycle control in response to nutritional stress. In agreement with this new role for Reb1 in the regulation of the G1-S transition, reb1Δ and wee1(ts) mutations are synthetically lethal owing to the inability of these cells to lengthen G1 before entering S phase. Similarly, reb1Δ cdc10(ts) cells are unable to arrest in G1 and die at the semi-permissive temperature.
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Affiliation(s)
- Leonor Rodríguez-Sánchez
- Department of Cell Proliferation and Development, Centro de Investigaciones Biológicas, Consejo Superior de Investigaciones Científicas, Ramiro de Maeztu 9, 28040 Madrid, Spain
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24
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Felle M, Exler JH, Merkl R, Dachauer K, Brehm A, Grummt I, Längst G. DNA sequence encoded repression of rRNA gene transcription in chromatin. Nucleic Acids Res 2010; 38:5304-14. [PMID: 20421213 PMCID: PMC2938192 DOI: 10.1093/nar/gkq263] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
Abstract
Eukaryotic genomes are packaged into nucleosomes that occlude DNA from interacting with most DNA-binding proteins. Nucleosome positioning and chromatin organization is critical for gene regulation. We have investigated the mechanism by which nucleosomes are positioned at the promoters of active and silent rRNA genes (rDNA). The reconstitution of nucleosomes on rDNA results in sequence-dependent nucleosome positioning at the rDNA promoter that mimics the chromatin structure of silent rRNA genes in vivo, suggesting that active mechanisms are required to reorganize chromatin structure upon gene activation. Nucleosomes are excluded from positions observed at active rRNA genes, resulting in transcriptional repression on chromatin. We suggest that the repressed state is the default chromatin organization of the rDNA and gene activation requires ATP-dependent chromatin remodelling activities that move the promoter-bound nucleosome about 22-bp upstream. We suggest that nucleosome remodelling precedes promoter-dependent transcriptional activation as specific inhibition of ATP-dependent chromatin remodelling suppresses the initiation of RNA Polymerase I transcription in vitro. Once initiated, RNA Polymerase I is capable of elongating through reconstituted chromatin without apparent displacement of the nucleosomes. The results reveal the functional cooperation of DNA sequence and chromatin remodelling complexes in nucleosome positioning and in establishing the epigenetic active or silent state of rRNA genes.
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Affiliation(s)
- Max Felle
- Institut für Biochemie III, Universität Regensburg, Universitätsstr. 31, 93053 Regensburg, Germany
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25
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González V, Guo K, Hurley L, Sun D. Identification and characterization of nucleolin as a c-myc G-quadruplex-binding protein. J Biol Chem 2009; 284:23622-35. [PMID: 19581307 PMCID: PMC2749137 DOI: 10.1074/jbc.m109.018028] [Citation(s) in RCA: 233] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2009] [Revised: 07/02/2009] [Indexed: 11/06/2022] Open
Abstract
myc is a proto-oncogene that plays an important role in the promotion of cellular growth and proliferation. Understanding the regulation of c-myc is important in cancer biology, as it is overexpressed in a wide variety of human cancers, including most gynecological, breast, and colon cancers. We previously demonstrated that a guanine-rich region upstream of the P1 promoter of c-myc that controls 85-90% of the transcriptional activation of this gene can form an intramolecular G-quadruplex (G4) that functions as a transcriptional repressor element. In this study, we used an affinity column to purify proteins that selectively bind to the human c-myc G-quadruplex. We found that nucleolin, a multifunctional phosphoprotein, binds in vitro to the c-myc G-quadruplex structure with high affinity and selectivity when compared with other known quadruplex structures. In addition, we demonstrate that upon binding, nucleolin facilitates the formation and increases the stability of the c-myc G-quadruplex structure. Furthermore, we provide evidence that nucleolin overexpression reduces the activity of a c-myc promoter in plasmid presumably by inducing and stabilizing the formation of the c-myc G-quadruplex. Finally, we show that nucleolin binds to the c-myc promoter in HeLa cells, which indicates that this interaction occurs in vivo. In summary, nucleolin may induce c-myc G4 formation in vivo.
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Affiliation(s)
| | - Kexiao Guo
- Department of Biochemistry and Molecular Biophysics, University of Arizona, Tucson, Arizona 85721
| | - Laurence Hurley
- From the College of Pharmacy and
- BIO5 Institute, Tucson, Arizona 85721, and
- Arizona Cancer Center, Tucson, Arizona 85724
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26
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Affiliation(s)
- Brian McStay
- Biomedical Research Center, Ninewells Hospital, University of Dundee, Dundee DD1 9SY, United Kingdom;
| | - Ingrid Grummt
- Molecular Biology of the Cell II, German Cancer Research Center, DKFZ-ZMBH Alliance, D-69120 Heidelberg, Germany;
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27
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Mechanistic insights into replication termination as revealed by investigations of the Reb1-Ter3 complex of Schizosaccharomyces pombe. Mol Cell Biol 2008; 28:6844-57. [PMID: 18794373 DOI: 10.1128/mcb.01235-08] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Relatively little is known about the interaction of eukaryotic replication terminator proteins with the cognate termini and the replication termination mechanism. Here, we report a biochemical analysis of the interaction of the Reb1 terminator protein of Schizosaccharomyces pombe, which binds to the Ter3 site present in the nontranscribed spacers of ribosomal DNA, located in chromosome III. We show that Reb1 is a dimeric protein and that the N-terminal dimerization domain of the protein is dispensable for replication termination. Unlike its mammalian counterpart Ttf1, Reb1 did not need an accessory protein to bind to Ter3. The two myb/SANT domains and an adjacent, N-terminal 154-amino-acid-long segment (called the myb-associated domain) were both necessary and sufficient for optimal DNA binding in vitro and fork arrest in vivo. The protein and its binding site Ter3 were unable to arrest forks initiated in vivo from ars of Saccharomyces cerevisiae in the cell milieu of the latter despite the facts that the protein retained the proper affinity of binding, was located in vivo at the Ter site, and apparently was not displaced by the "sweepase" Rrm3. These observations suggest that replication fork arrest is not an intrinsic property of the Reb1-Ter3 complex.
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28
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Abstract
Transcription of the major ribosomal RNAs by Pol I (RNA polymerase I) is a key determinant of ribosome biogenesis, driving cell growth and proliferation in eukaryotes. Hundreds of copies of rRNA genes are present in each cell, and there is evidence that the cellular control of Pol I transcription involves adjustments to the number of rRNA genes actively engaged in transcription, as well as to the rate of transcription from each active gene. Chromatin structure is inextricably linked to rRNA gene activity, and the present review highlights recent advances in this area.
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Affiliation(s)
- Joanna L. Birch
- Wellcome Trust Centre for Gene Regulation and Expression, College of Life Sciences, University of Dundee, Dundee DD1 5EH, U.K
| | - Joost C.B.M. Zomerdijk
- Wellcome Trust Centre for Gene Regulation and Expression, College of Life Sciences, University of Dundee, Dundee DD1 5EH, U.K
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29
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Németh A, Guibert S, Tiwari VK, Ohlsson R, Längst G. Epigenetic regulation of TTF-I-mediated promoter-terminator interactions of rRNA genes. EMBO J 2008; 27:1255-65. [PMID: 18354495 DOI: 10.1038/emboj.2008.57] [Citation(s) in RCA: 83] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2007] [Accepted: 02/28/2008] [Indexed: 11/09/2022] Open
Abstract
Ribosomal RNA synthesis is the eukaryotic cell's main transcriptional activity, but little is known about the chromatin domain organization and epigenetics of actively transcribed rRNA genes. Here, we show epigenetic and spatial organization of mouse rRNA genes at the molecular level. TTF-I-binding sites subdivide the rRNA transcription unit into functional chromatin domains and sharply delimit transcription factor occupancy. H2A.Z-containing nucleosomes occupy the spacer promoter next to a newly characterized TTF-I-binding site. The spacer and the promoter proximal TTF-I-binding sites demarcate the enhancer. DNA from both the enhancer and the coding region is hypomethylated in actively transcribed repeats. 3C analysis revealed an interaction between promoter and terminator regions, which brings the beginning and end of active rRNA genes into close contact. Reporter assays show that TTF-I mediates this interaction, thereby linking topology and epigenetic regulation of the rRNA genes.
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Affiliation(s)
- Attila Németh
- Department of Biochemistry III, University of Regensburg, Regensburg, Germany
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30
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Louvet E, Percipalle P. Transcriptional control of gene expression by actin and myosin. INTERNATIONAL REVIEW OF CELL AND MOLECULAR BIOLOGY 2008; 272:107-47. [PMID: 19121817 DOI: 10.1016/s1937-6448(08)01603-1] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
Abstract
Recent years have witnessed a new turn in the field of gene expression regulation. Actin and an ever-growing family of actin-associated proteins have been accepted as members of the nuclear crew, regulating eukaryotic gene transcription. In complex with heterogeneous nuclear ribonucleoproteins and certain myosin species, actin has been shown to be an important regulator in RNA polymerase II transcription. Furthermore, actin-based molecular motors are believed to facilitate RNA polymerase I transcription and possibly downstream events during rRNA biogenesis. Probably these findings represent the tip of the iceberg of a rapidly expanding area within the functional architecture of the cell nucleus. Further studies will contribute to clarify how actin mediates nuclear functions with a glance to cytoplasmic signalling. These discoveries have the potential to define novel regulatory networks required to control gene expression at multiple levels.
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Affiliation(s)
- Emilie Louvet
- Department of Cell and Molecular Biology, Medical Nobel Institute, Karolinska Institutet, S-171 77 Stockholm, Sweden
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31
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Sirri V, Urcuqui-Inchima S, Roussel P, Hernandez-Verdun D. Nucleolus: the fascinating nuclear body. Histochem Cell Biol 2007; 129:13-31. [PMID: 18046571 PMCID: PMC2137947 DOI: 10.1007/s00418-007-0359-6] [Citation(s) in RCA: 295] [Impact Index Per Article: 17.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/06/2007] [Indexed: 11/30/2022]
Abstract
Nucleoli are the prominent contrasted structures of the cell nucleus. In the nucleolus, ribosomal RNAs are synthesized, processed and assembled with ribosomal proteins. RNA polymerase I synthesizes the ribosomal RNAs and this activity is cell cycle regulated. The nucleolus reveals the functional organization of the nucleus in which the compartmentation of the different steps of ribosome biogenesis is observed whereas the nucleolar machineries are in permanent exchange with the nucleoplasm and other nuclear bodies. After mitosis, nucleolar assembly is a time and space regulated process controlled by the cell cycle. In addition, by generating a large volume in the nucleus with apparently no RNA polymerase II activity, the nucleolus creates a domain of retention/sequestration of molecules normally active outside the nucleolus. Viruses interact with the nucleolus and recruit nucleolar proteins to facilitate virus replication. The nucleolus is also a sensor of stress due to the redistribution of the ribosomal proteins in the nucleoplasm by nucleolus disruption. The nucleolus plays several crucial functions in the nucleus: in addition to its function as ribosome factory of the cells it is a multifunctional nuclear domain, and nucleolar activity is linked with several pathologies. Perspectives on the evolution of this research area are proposed.
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Affiliation(s)
- Valentina Sirri
- Nuclei and Cell Cycle, CNRS, Université Paris VI, Université Paris VII, Institut Jacques Monod, 2 place Jussieu, 75251 Paris Cedex 05, France
| | - Silvio Urcuqui-Inchima
- Nuclei and Cell Cycle, CNRS, Université Paris VI, Université Paris VII, Institut Jacques Monod, 2 place Jussieu, 75251 Paris Cedex 05, France
- Grupo de Inmunovirología, Biogénesis, Universidad de Antioquia, Calle 62 No. 52-59, Medellin, Colombia
| | - Pascal Roussel
- Nuclei and Cell Cycle, CNRS, Université Paris VI, Université Paris VII, Institut Jacques Monod, 2 place Jussieu, 75251 Paris Cedex 05, France
| | - Danièle Hernandez-Verdun
- Nuclei and Cell Cycle, CNRS, Université Paris VI, Université Paris VII, Institut Jacques Monod, 2 place Jussieu, 75251 Paris Cedex 05, France
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Grummt I. Different epigenetic layers engage in complex crosstalk to define the epigenetic state of mammalian rRNA genes. Hum Mol Genet 2007; 16 Spec No 1:R21-7. [PMID: 17613545 DOI: 10.1093/hmg/ddm020] [Citation(s) in RCA: 57] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
Eukaryotic cells contain several hundred ribosomal RNA (rRNA) genes (rDNA), a fraction of them being silenced by epigenetic mechanisms. The presence of two epigenetically distinct states of rRNA genes provides a unique opportunity to decipher the molecular mechanisms that establish the euchromatic, i.e. transcriptionally active, and the heterochromatic, i.e. transcriptionally silent, state of rDNA. This article summarizes our knowledge of the epigenetic mechanisms that control rDNA transcription and emphasizes how DNA methyltransferases and histone-modifying enzymes work in concert with chromatin-remodeling complexes and RNA-guided mechanisms to establish a specific chromatin structure that defines the transcriptional state of rRNA genes. These studies exemplify the mutual dependence and complex crosstalk among different epigenetic players in the alteration of the chromatin structure during the process of gene activation or silencing.
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Affiliation(s)
- Ingrid Grummt
- Division of Molecular Biology of the Cell II, German Cancer Research Center, Heidelberg, Germany
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Yuan X, Feng W, Imhof A, Grummt I, Zhou Y. Activation of RNA polymerase I transcription by cockayne syndrome group B protein and histone methyltransferase G9a. Mol Cell 2007; 27:585-95. [PMID: 17707230 DOI: 10.1016/j.molcel.2007.06.021] [Citation(s) in RCA: 134] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2007] [Revised: 05/11/2007] [Accepted: 06/12/2007] [Indexed: 12/16/2022]
Abstract
Cockayne syndrome group B (CSB) protein plays a role in both transcription-coupled DNA repair and transcriptional regulation of all three classes of nuclear RNA polymerases. Here we show that a complex consisting of CSB, RNA polymerase I (Pol I), and histone methyltransferase G9a is present at active rRNA genes. G9a methylates histone H3 on lysine 9 (H3K9me2) in the pre-rRNA coding region and facilitates the association of heterochromatin protein 1gamma (HP1gamma) with rDNA. Both H3K9 methylation and HP1gamma association require ongoing transcription. Knockdown of CSB prevents the association of Pol I with rDNA, impairs the interaction of G9a with Pol I, and inhibits pre-rRNA synthesis. Likewise, knockdown of G9a leads to decreased levels of H3K9me2 in the transcribed region and downregulation of pre-rRNA synthesis. The results reveal the mechanism underlying CSB-mediated activation of rDNA transcription and link G9a-dependent H3K9 methylation to Pol I transcription elongation through chromatin.
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Affiliation(s)
- Xuejun Yuan
- Division of Molecular Biology of the Cell II, German Cancer Research Center, D-69120 Heidelberg, Germany
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34
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Conconi A. The yeast rDNA locus: a model system to study DNA repair in chromatin. DNA Repair (Amst) 2007; 4:897-908. [PMID: 15996904 DOI: 10.1016/j.dnarep.2005.04.008] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/18/2005] [Indexed: 11/23/2022]
Abstract
Most of the studies on the effect of chromatin structure and chromatin remodeling on DNA repair are based on in vitro reconstituted assays. In such experiments individual nucleosomes are either released by nuclease digestion of native chromatin fibers or are assembled from purified histones. Though reconstituted assays are valid approaches to follow NER in chromatin they are of somehow limited physiological relevance since single core particles do not exist in vivo [K. van Holde, J. Zlatanova, The nucleosome core particle: does it have structural and physiological relevance? Bioessays 21 (1999) 776-778]. This is particularly true for studies involving core histones tails, as in their natural chromatin context histones tails participate in interactions that are not necessarily present in vitro [J.C. Hansen, C. Tse, A.P. Wolffe, Structure and function of the core histone N-termini: more than meets the eye, Biochemistry 37 (1998) 17637-17641; J.J. Hayes, J.C. Hansen, Nucleosomes and chromatin fiber, Curr. Opin. Genet. Dev. 11 (2001) 124-129]. Indeed it was found that human DNA ligase I has the capability to ligate a nick on the surface of a 215bp nucleosome but not a nick in a nucleosome lacking linker DNA, possibly because of forced interactions between histone tails and core DNA present in the latter complex [D.R. Chafin, J.M. Vitolo, L.A. Henricksen, B.A. Bambara, J.J. Hayes, Human DNA ligase I efficiently seals nicks in nucleosomes, EMBO J. 19 (2000) 5492-5501]. In addition, chromatin remodeling could also occur in the higher ordered folding of chromatin and involve multiple arrays of nucleosomes [P.J. Horn, C.L. Peterson, Chromatin higher order folding: wrapping up transcription, Science 297 (2002) 1824-1827]. By studying the chromatin structure of ribosomal genes in yeast, our knowledge of the fate of nucleosomes during transcription and DNA replication has improved considerably [R. Lucchini, J.M. Sogo, The dynamic structure of ribosomal RNA gene chromatin, in: M.R. Paule (Ed.), Transcription of Ribosomal RNA Genes by Eukaryotic RNA Polymerase I, Springer-Verlag/R.G. Landes Company, 1998, pp. 254-276]. How nuclear processes such as DNA repair take place in chromatin is still largely unknown, and in this review I discuss how the yeast rDNA locus may be exploited to investigate DNA repair and chromatin modification in vivo.
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Affiliation(s)
- Antonio Conconi
- Department de Microbiologie et Infectiologie, Faculte de Medecine, Universite de Sherbrooke, 3001, 12(e) Avenue Nord, Sherbrooke, Que., Canada J1H 5N4
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Preuss S, Pikaard CS. rRNA gene silencing and nucleolar dominance: insights into a chromosome-scale epigenetic on/off switch. ACTA ACUST UNITED AC 2007; 1769:383-92. [PMID: 17439825 PMCID: PMC2000449 DOI: 10.1016/j.bbaexp.2007.02.005] [Citation(s) in RCA: 97] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2007] [Revised: 02/25/2007] [Accepted: 02/27/2007] [Indexed: 01/25/2023]
Abstract
Ribosomal RNA (rRNA) gene transcription accounts for most of the RNA in prokaryotic and eukaryotic cells. In eukaryotes, there are hundreds (to thousands) of rRNA genes tandemly repeated head-to-tail within nucleolus organizer regions (NORs) that span millions of basepairs. These nucleolar rRNA genes are transcribed by RNA Polymerase I (Pol I) and their expression is regulated according to the physiological need for ribosomes. Regulation occurs at several levels, one of which is an epigenetic on/off switch that controls the number of active rRNA genes. Additional mechanisms then fine-tune transcription initiation and elongation rates to dictate the total amount of rRNA produced per gene. In this review, we focus on the DNA and histone modifications that comprise the epigenetic on/off switch. In both plants and animals, this system is important for controlling the dosage of active rRNA genes. The dosage control system is also responsible for the chromatin-mediated silencing of one parental set of rRNA genes in genetic hybrids, a large-scale epigenetic phenomenon known as nucleolar dominance.
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Affiliation(s)
| | - Craig S. Pikaard
- *Author to whom correspondence should be addressed: , phone: 314-935-7569, FAX: 314-935-4432
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36
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Mongelard F, Bouvet P. Nucleolin: a multiFACeTed protein. Trends Cell Biol 2007; 17:80-6. [PMID: 17157503 DOI: 10.1016/j.tcb.2006.11.010] [Citation(s) in RCA: 247] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2006] [Accepted: 11/30/2006] [Indexed: 11/28/2022]
Abstract
Nucleolin is an abundant, ubiquitously expressed protein that is found in various cell compartments, especially in the nucleolus, of which it is a major component. This multifunctional protein has been described as being a part of many pathways, from interactions with viruses at the cellular membrane to essential processing of the ribosomal RNA in the nucleolus. However, most of the molecular details of these different functions are not understood. Here, we focus on the role of nucleolin in transcription, especially some recent findings describing the protein as a histone chaperone [with functional similarity to the facilitates chromatin transcription (FACT) complex] and a chromatin co-remodeler. These new properties could help reconcile discrepancies in the literature regarding the role of nucleolin in transcription.
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Affiliation(s)
- Fabien Mongelard
- Laboratoire Joliot-Curie, Ecole Normale Supérieure de Lyon, 46 Allée d'Italie, 69007 Lyon, France
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37
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Abstract
Mammalian cells contain approximately 400 copies of the ribosomal RNA genes organized as tandem, head-to-tail repeats spread among 6-8 chromosomes. Only a subset of the genes is transcribed at any given time. Experimental evidence suggests that, in a specific cell type, only a fraction of the genes exists in a conformation that can be transcribed. An increasing body of study indicates that eukaryotic ribosomal RNA genes exist in either a heterochromatic nucleosomal state or in open euchromatic states in which they can be, or are, transcribed. This review will attempt to summarize our current understanding of the structure and organization of ribosomal chromatin.
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Affiliation(s)
- Sui Huang
- Department of Cell and Molecular Biology, The Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA.
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38
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Li J, Längst G, Grummt I. NoRC-dependent nucleosome positioning silences rRNA genes. EMBO J 2006; 25:5735-41. [PMID: 17139253 PMCID: PMC1698900 DOI: 10.1038/sj.emboj.7601454] [Citation(s) in RCA: 95] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2006] [Accepted: 10/25/2006] [Indexed: 12/29/2022] Open
Abstract
Previous studies have established that the Snf2h-containing chromatin remodeling complex NoRC mediates epigenetic silencing of a subset of rRNA genes (rDNA) by recruiting enzymatic activities that modify histones and methylate DNA. Here we have analyzed nucleosome positions at the murine rDNA promoter and show that active and silent rDNA copies are characterized not only by specific epigenetic marks but also by differently positioned nucleosomes. At active genes the promoter-bound nucleosome covers nucleotides from -157 to -2, whereas at silent genes the nucleosome is positioned 25 nucleotides further downstream. We provide evidence that NoRC is the molecular machine that shifts the promoter-bound nucleosome downstream of the transcription start site into a translational position that is unfavorable for transcription complex formation.
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Affiliation(s)
- Junwei Li
- German Cancer Research Center, Division of Molecular Biology of the Cell II, Heidelberg, Germany
| | - Gernot Längst
- Institut für Biochemie, Genetik und Mikrobiologie, Regensburg, Germany
| | - Ingrid Grummt
- German Cancer Research Center, Division of Molecular Biology of the Cell II, Heidelberg, Germany
- Molecular Biology of the Cell II, German Cancer Research Center, Im Neuenheimer Feld 280, 69120 Heidelberg, Germany. Tel.: +49 6221 423423; Fax: +49 6221 423404; E-mail:
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39
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Johnson SM, Tan FJ, McCullough HL, Riordan DP, Fire AZ. Flexibility and constraint in the nucleosome core landscape of Caenorhabditis elegans chromatin. Genome Res 2006; 16:1505-16. [PMID: 17038564 PMCID: PMC1665634 DOI: 10.1101/gr.5560806] [Citation(s) in RCA: 145] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
Nucleosome positions within the chromatin landscape are known to serve as a major determinant of DNA accessibility to transcription factors and other interacting components. To delineate nucleosomal patterns in a model genetic organism, Caenorhabditis elegans, we have carried out a genome-wide analysis in which DNA fragments corresponding to nucleosome cores were liberated using an enzyme (micrococcal nuclease) with a strong preference for cleavage in non-nucleosomal regions. Sequence analysis of 284,091 putative nucleosome cores obtained in this manner from a mixed-stage population of C. elegans reveals a combined picture of flexibility and constraint in nucleosome positioning. As has previously been observed in studies of individual loci in diverse biological systems, we observe areas in the genome where nucleosomes can adopt a wide variety of positions in a given region, areas with little or no nucleosome coverage, and areas where nucleosomes reproducibly adopt a specific positional pattern. In addition to illuminating numerous aspects of chromatin structure for C. elegans, this analysis provides a reference from which to begin an investigation of relationships between the nucleosomal pattern, chromosomal architecture, and lineage-based gene activity on a genome-wide scale.
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Affiliation(s)
- Steven M. Johnson
- Department of Pathology, Stanford University School of Medicine, Stanford, California 94305-5324, USA
| | - Frederick J. Tan
- Department of Biology, Johns Hopkins University, Baltimore, Maryland, 21218, USA
| | - Heather L. McCullough
- Department of Genetics, Stanford University School of Medicine, Stanford, California 94305-5324, USA
| | - Daniel P. Riordan
- Department of Genetics, Stanford University School of Medicine, Stanford, California 94305-5324, USA
| | - Andrew Z. Fire
- Department of Pathology, Stanford University School of Medicine, Stanford, California 94305-5324, USA
- Department of Genetics, Stanford University School of Medicine, Stanford, California 94305-5324, USA
- Corresponding author.E-mail ; fax (650) 724-9070
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40
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Gray SJ, Liu G, Altman AL, Small LE, Fanning E. Discrete functional elements required for initiation activity of the Chinese hamster dihydrofolate reductase origin beta at ectopic chromosomal sites. Exp Cell Res 2006; 313:109-20. [PMID: 17078947 PMCID: PMC1810229 DOI: 10.1016/j.yexcr.2006.09.020] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2006] [Revised: 09/20/2006] [Accepted: 09/21/2006] [Indexed: 01/06/2023]
Abstract
The Chinese hamster dihydrofolate reductase (DHFR) DNA replication initiation region, the 5.8 kb ori-beta, can function as a DNA replicator at random ectopic chromosomal sites in hamster cells. We report a detailed genetic analysis of the DiNucleotide Repeat (DNR) element, one of several sequence elements necessary for ectopic ori-beta activity. Deletions within ori-beta identified a 132 bp core region within the DNR element, consisting mainly of dinucleotide repeats, and a downstream region that are required for ori-beta initiation activity at non-specific ectopic sites in hamster cells. Replacement of the DNR element with Xenopus or mouse transcriptional elements from rDNA genes restored full levels of initiation activity, but replacement with a nucleosome positioning element or a viral intron sequence did not. The requirement for the DNR element and three other ori-beta sequence elements was conserved when ori-beta activity was tested at either random sites or at a single specific ectopic chromosomal site in human cells. These results confirm the importance of specific cis-acting elements in directing the initiation of DNA replication in mammalian cells, and provide new evidence that transcriptional elements can functionally substitute for one of these elements in ori-beta.
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Affiliation(s)
- Steven J. Gray
- Department of Biological Sciences and the Vanderbilt-Ingram Cancer Center, Vanderbilt University, Nashville, Tennessee 37235
| | - Guoqi Liu
- Department of Biological Sciences and the Vanderbilt-Ingram Cancer Center, Vanderbilt University, Nashville, Tennessee 37235
| | - Amy L. Altman
- Department of Biological Sciences and the Vanderbilt-Ingram Cancer Center, Vanderbilt University, Nashville, Tennessee 37235
| | - Lawrence E. Small
- Department of Biological Sciences and the Vanderbilt-Ingram Cancer Center, Vanderbilt University, Nashville, Tennessee 37235
| | - Ellen Fanning
- Department of Biological Sciences and the Vanderbilt-Ingram Cancer Center, Vanderbilt University, Nashville, Tennessee 37235
- * To whom correspondence should be addressed: Department of Biological Sciences, Vanderbilt University, VU Station B 351634 Nashville, TN 37235-1634 Tel: (615) 343-5677 Fax: (615) 343-6707
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Affiliation(s)
- Brian McStay
- Biomedical Research Centre, University of Dundee, Ninewells Hospital, Dundee DD1 9SY, United Kingdom.
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42
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Angelov D, Bondarenko VA, Almagro S, Menoni H, Mongélard F, Hans F, Mietton F, Studitsky VM, Hamiche A, Dimitrov S, Bouvet P. Nucleolin is a histone chaperone with FACT-like activity and assists remodeling of nucleosomes. EMBO J 2006; 25:1669-79. [PMID: 16601700 PMCID: PMC1440837 DOI: 10.1038/sj.emboj.7601046] [Citation(s) in RCA: 189] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2005] [Accepted: 02/21/2006] [Indexed: 11/09/2022] Open
Abstract
Remodeling machines play an essential role in the control of gene expression, but how their activity is regulated is not known. Here we report that the nuclear protein nucleolin possesses a histone chaperone activity and that this factor greatly enhances the activity of the chromatin remodeling machineries SWI/SNF and ACF. Interestingly, nucleolin is able to induce the remodeling by SWI/SNF of macroH2A, but not of H2ABbd nucleosomes, which are otherwise resistant to remodeling. This new histone chaperone promotes the destabilization of the histone octamer, helping the dissociation of a H2A-H2B dimer, and stimulates the SWI/SNF-mediated transfer of H2A-H2B dimers. Furthermore, nucleolin facilitates transcription through the nucleosome, which is reminiscent of the activity of the FACT complex. This work defines new functions for histone chaperones in chromatin remodeling and regulation of transcription and explains how nucleolin could act on transcription.
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Affiliation(s)
- Dimitar Angelov
- Ecole Normale Supérieure de Lyon, CNRS-UMR 5161/INRA 1237/IFR128 Biosciences, Lyon-Gerland, France
- Laboratoire Joliot-Curie, Lyon, France
| | - Vladimir A Bondarenko
- Department of Pharmacology, University of Medicine and Dentistry of New Jersey, Piscataway, NJ, USA
| | - Sébastien Almagro
- Ecole Normale Supérieure de Lyon, CNRS-UMR 5161/INRA 1237/IFR128 Biosciences, Lyon-Gerland, France
- Laboratoire Joliot-Curie, Lyon, France
| | - Hervé Menoni
- Ecole Normale Supérieure de Lyon, CNRS-UMR 5161/INRA 1237/IFR128 Biosciences, Lyon-Gerland, France
- Laboratoire Joliot-Curie, Lyon, France
| | - Fabien Mongélard
- Ecole Normale Supérieure de Lyon, CNRS-UMR 5161/INRA 1237/IFR128 Biosciences, Lyon-Gerland, France
- Laboratoire Joliot-Curie, Lyon, France
| | - Fabienne Hans
- Institut Albert Bonniot, INSERM U309, La Tronche Cedex, France
| | - Flore Mietton
- Institut Albert Bonniot, INSERM U309, La Tronche Cedex, France
| | - Vasily M Studitsky
- Department of Pharmacology, University of Medicine and Dentistry of New Jersey, Piscataway, NJ, USA
| | - Ali Hamiche
- Institut André Lwoff, CNRS UPR 9079, Villejuif, France
| | - Stefan Dimitrov
- Laboratoire Joliot-Curie, Lyon, France
- Institut Albert Bonniot, INSERM U309, La Tronche Cedex, France
| | - Philippe Bouvet
- Ecole Normale Supérieure de Lyon, CNRS-UMR 5161/INRA 1237/IFR128 Biosciences, Lyon-Gerland, France
- Laboratoire Joliot-Curie, Lyon, France
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43
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Percipalle P, Fomproix N, Cavellán E, Voit R, Reimer G, Krüger T, Thyberg J, Scheer U, Grummt I, Farrants AKO. The chromatin remodelling complex WSTF-SNF2h interacts with nuclear myosin 1 and has a role in RNA polymerase I transcription. EMBO Rep 2006; 7:525-30. [PMID: 16514417 PMCID: PMC1479564 DOI: 10.1038/sj.embor.7400657] [Citation(s) in RCA: 140] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2005] [Revised: 01/30/2006] [Accepted: 02/06/2006] [Indexed: 12/27/2022] Open
Abstract
Nuclear actin and myosin 1 (NM1) are key regulators of gene transcription. Here, we show by biochemical fractionation of nuclear extracts, protein-protein interaction studies and chromatin immunoprecipitation assays that NM1 is part of a multiprotein complex that contains WICH, a chromatin remodelling complex containing WSTF (Williams syndrome transcription factor) and SNF2h. NM1, WSTF and SNF2h were found to be associated with RNA polymerase I (Pol I) and ribosomal RNA genes (rDNA). RNA interference-mediated knockdown of NM1 and WSTF reduced pre-rRNA synthesis in vivo, and antibodies to WSTF inhibited Pol I transcription on pre-assembled chromatin templates but not on naked DNA. The results indicate that NM1 cooperates with WICH to facilitate transcription on chromatin.
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Affiliation(s)
- Piergiorgio Percipalle
- Department of Cell and Molecular Biology, Medical Nobel Institute, Karolinska Institute, Box 285, Stockholm 171 77, Sweden.
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Abstract
The mitochondrial ribomotor model has been proposed to explain how the balance between rRNA and mRNA in mammalian mitochondria is regulated. In this model, the interaction of the mitochondrial transcription termination factor (mTERF) with some unknown component(s), causes a loop to form in the mtDNA chain that brings the initiation and termination regions together at its base. By bringing these sites into closer proximity, the mtRNA polymerase molecules can be directly transferred from the termination site to the IH1 initiation site of the H-strand once transcription terminates. This process occurs when mTERF is phosphorylated. When unphosphorylated, transcription is initiated from the IH2 site and the polymerase reads through the mTERF-dependent termination site, resulting in the transcription of almost the entire H-strand.
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45
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Mais C, Wright JE, Prieto JL, Raggett SL, McStay B. UBF-binding site arrays form pseudo-NORs and sequester the RNA polymerase I transcription machinery. Genes Dev 2005; 19:50-64. [PMID: 15598984 PMCID: PMC540225 DOI: 10.1101/gad.310705] [Citation(s) in RCA: 140] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2004] [Accepted: 10/19/2004] [Indexed: 11/25/2022]
Abstract
Human ribosomal genes (rDNA) are located in nucleolar organizer regions (NORs) on the short arms of acrocentric chromosomes. Metaphase NORs that were transcriptionally active in the previous cell cycle appear as prominent chromosomal features termed secondary constrictions that are achromatic in chromosome banding and positive in silver staining. The architectural RNA polymerase I (pol I) transcription factor UBF binds extensively across rDNA throughout the cell cycle. To determine if UBF binding underpins NOR structure, we integrated large arrays of heterologous UBF-binding sequences at ectopic sites on human chromosomes. These arrays efficiently recruit UBF even to sites outside the nucleolus and, during metaphase, form novel silver stainable secondary constrictions, termed pseudo-NORs, morphologically similar to NORs. We demonstrate for the first time that in addition to UBF the other components of the pol I machinery are found associated with sequences across the entire human rDNA repeat. Remarkably, a significant fraction of these same pol I factors are sequestered by pseudo-NORs independent of both transcription and nucleoli. Because of the heterologous nature of the sequence employed, we infer that sequestration is mediated primarily by protein-protein interactions with UBF. These results suggest that extensive binding of UBF is responsible for formation and maintenance of the secondary constriction at active NORs. Furthermore, we propose that UBF mediates recruitment of the pol I machinery to nucleoli independently of promoter elements.
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Affiliation(s)
- Christine Mais
- Biomedical Research Centre, Ninewells Hospital and Medical School, University of Dundee, Dundee, DD1 9SY Scotland, United Kingdom
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Németh A, Strohner R, Grummt I, Längst G. The chromatin remodeling complex NoRC and TTF-I cooperate in the regulation of the mammalian rRNA genes in vivo. Nucleic Acids Res 2004; 32:4091-9. [PMID: 15292447 PMCID: PMC514363 DOI: 10.1093/nar/gkh732] [Citation(s) in RCA: 55] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
The transcription termination factor (TTF)-I is a multifunctional nucleolar protein that terminates ribosomal gene transcription, mediates replication fork arrest and regulates RNA polymerase I transcription on chromatin. TTF-I plays a dual role in rDNA regulation, being involved in both activation and silencing of rDNA transcription. The N-terminal part of TTF-I contains a negative regulatory domain (NRD) that inhibits DNA binding. Here we show that interactions between the NRD and the C-terminal part of TTF-I mask the DNA-binding domain of TTF-I. However, interaction with TIP5, a subunit of the nucleolar chromatin remodeling complex, NoRC, recovers DNA-binding activity. We have mapped the protein domains that mediate the interaction between TTF-I and TIP5. The association of TIP5 with the NRD facilitates DNA binding of TTF-I and leads to the recruitment of NoRC to the rDNA promoter. Thus, TTF-I and NoRC act in concert to silence rDNA transcription.
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Affiliation(s)
- Attila Németh
- Adolf Butenandt Institut, Molekularbiologie, Ludwig-Maximilians-Universität München, Schillerstrasse 44, D-80336 München, Germany
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Korber P, Hörz W. In vitro assembly of the characteristic chromatin organization at the yeast PHO5 promoter by a replication-independent extract system. J Biol Chem 2004; 279:35113-20. [PMID: 15192097 DOI: 10.1074/jbc.m405446200] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
An extensive set of analyses of the yeast PHO5 gene, mostly performed in vivo, has made this gene a model for the role of chromatin structure in gene regulation. In the repressed state, the PHO5 promoter shows a characteristic chromatin organization with four positioned nucleosomes and a short hypersensitive site. So far the basis for this nucleosome positioning has remained unresolved. We have therefore decided to complement the in vivo studies by an in vitro approach. As a first step, we have asked whether the characteristic PHO5 promoter chromatin structure depends on the cellular context including replication or higher order nuclear chromatin organization or whether it can be reconstituted in vitro in a cell-free system. To this end we have established an in vitro chromatin assembly system based on yeast extracts. It is capable of generating extensive regular nucleosomal arrays with physiological spacing. Assembly requires supplementation with exogenous histones and is dependent on energy leading to chromatin with dynamic properties due to ATP-dependent activities of the extract. Using the PHO5 promoter sequence as template in this replication independent system, we obtain a nucleosomal pattern over the PHO5 promoter region that is very similar to the in vivo pattern of the repressed state. This shows that the chromatin structure at the PHO5 promoter represents a self-organizing system in cell-free yeast extracts and provides a promising substrate for in vitro studies with a direct in vivo correlate.
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Affiliation(s)
- Philipp Korber
- Adolf-Butenandt-Institut, University of Munich, Schillerstrasse 44, 80336 Munich, Germany
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Abstract
Although the mechanisms of cell cycle control are well established, the factors controlling cell growth and target size are still poorly understood. Much evidence suggests that ribosome biogenesis, and in particular the synthesis of the rRNAs, plays a central role not only in permitting growth, but also in regulating it. In the past few years we have begun to penetrate the network linking rRNA gene transcription to growth.
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Affiliation(s)
- Tom Moss
- Cancer Research Centre and Department of Medical Biology, Laval University, Hôtel-Dieu de Québec, 9 rue McMahon, G1R 2J6 Québec, Canada.
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Affiliation(s)
- Lucio Comai
- Department of Molecular Microbiology and Immunology, Keck School of Medicine, University of Southern California, Los Angeles, CA 90033, USA
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Strohner R, Németh A, Nightingale KP, Grummt I, Becker PB, Längst G. Recruitment of the nucleolar remodeling complex NoRC establishes ribosomal DNA silencing in chromatin. Mol Cell Biol 2004; 24:1791-8. [PMID: 14749393 PMCID: PMC344174 DOI: 10.1128/mcb.24.4.1791-1798.2004] [Citation(s) in RCA: 66] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The rRNA gene cluster consists of multiple transcription units. Half of these are active, while the other half are transcriptionally inactive. Previously, in vivo studies have demonstrated that silencing of ribosomal DNA (rDNA) is mediated by the chromatin remodeling NoRC (nucleolar remodeling complex). To explore the mechanisms underlying NoRC-directed silencing of rDNA transcription, we investigated the effect of recombinant NoRC on RNA polymerase I transcription on reconstituted chromatin templates. We show that NoRC interacts with the transcription terminator factor (TTF-I), and this interaction is required both for the binding of TTF-I to its promoter-proximal target site and for the recruitment of NoRC to the promoter. After association with the rDNA promoter, NoRC alters the position of the promoter-bound nucleosome, thereby repressing RNA polymerase I transcription. This NoRC-directed rDNA repression requires the N terminus of histone H4. Repression is effective before preinitiation complex formation and as such is unable to exert an effect upon activated rDNA genes. Furthermore, the early steps of rDNA repression do not depend on DNA and histone modifications. These results reveal an important role for TTF-I in recruiting NoRC to rDNA and an active role for NoRC in the establishment of rDNA silencing.
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MESH Headings
- Acetylation
- Adenosine Triphosphatases/genetics
- Adenosine Triphosphatases/metabolism
- Animals
- Cell Line
- Chromatin/genetics
- Chromatin/metabolism
- Chromatin Assembly and Disassembly
- Chromosomal Proteins, Non-Histone/genetics
- Chromosomal Proteins, Non-Histone/metabolism
- DNA Methylation
- DNA, Ribosomal/chemistry
- DNA, Ribosomal/genetics
- DNA, Ribosomal/metabolism
- DNA, Superhelical/chemistry
- DNA, Superhelical/genetics
- DNA, Superhelical/metabolism
- DNA-Binding Proteins/metabolism
- Gene Silencing
- Histones/chemistry
- Histones/metabolism
- Kinetics
- Macromolecular Substances
- Promoter Regions, Genetic/genetics
- Protein Binding
- RNA Polymerase I/metabolism
- Repressor Proteins/genetics
- Repressor Proteins/metabolism
- Templates, Genetic
- Transcription Factors
- Transcription, Genetic/genetics
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Affiliation(s)
- Ralf Strohner
- Adolf-Butenandt-Institut, Molekularbiologie, Ludwig Maximilians Universität, 80336 Munich. German
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