Contents

• Dedication
• Preface
• Acknowledgments
• Contributors
• I. Ribosome Biogenesis
  • 1. A Comparative Perspective on Ribosome Biogenesis: Unity and Diversity Across the Tree of Life
    Michael Jüttner and Sébastien Ferreira-Cerca.
    Published online: July 8, 2022.
    • 1. In Search of Unity?
    • 2. Ribosome Biogenesis
    • 3. The Ribosome Assembly Process
    • 4. Facilitating Ribosome Assembly
    • 5. Processing and Modifications of Ribosomal RNA
    • 6. Learning from Organelle Ribosome Biogenesis?
    • 7. Concluding Remarks
    • Acknowledgments
    • References
• II. Genomic Organization
  • 2. Establishment and Maintenance of Open Ribosomal RNA Gene Chromatin States in Eukaryotes
    Christopher Schächner, Philipp E. Merkl, Michael Pilsl, Katrin Schwank, Kristin Hergert, Sebastian Kruse, Philipp Milkereit, Herbert Tschochner, and Joachim Griesenbeck.
    Published online: July 8, 2022.
    • 1. Introduction
    • 2. Visualization of rRNA Transcription
    • 3. Conclusions
    • Acknowledgments
    • References
  • 3. Analysis of Yeast RNAP I Transcription of Nucleosomal Templates In Vitro
    Philipp E. Merkl, Christopher Schächner, Michael Pilsl, Katrin Schwank, Kristin Hergert, Gernot Längst, Philipp Milkereit, Joachim Griesenbeck, and Herbert Tschochner.
    Published online: July 8, 2022.
    • 1. Introduction
    • 2. Materials
    • 3. Methods
    • 4. Notes
    • Acknowledgments
    • References
• III. RNA Polymerases
  • 4. Specialization of RNA Polymerase I in Comparison to Other Nuclear RNA Polymerases of Saccharomyces cerevisiae
    Philipp E. Merkl, Christopher Schächner, Michael Pilsl, Katrin Schwank, Catharina Schmid, Gernot Längst, Philipp Milkereit, Joachim Griesenbeck, and Herbert Tschochner.
    Published online: July 8, 2022.
    • 1. RNA Polymerase I Has Only One Essential Genomic Target
    • 2. RNA Polymerase I Contains Additional Subunits Resembling Transcription Factors of RNAP II
    • 3. Nuclear RNAPs Transcribe Chromatin Templates
    • Acknowledgments
    • References
  • 5. Structural Studies of Eukaryotic RNA Polymerase I Using Cryo-Electron Microscopy
    Michael Pilsl and Christoph Engel.
    Published online: July 8, 2022.
    • 1. Cryo-Electron Microscopy: The New Standard in Transcription Research
    • 2. Pol I Specific Subunits Resemble Built-in Transcription Factors
    • 3. The Pol I Transcription Cycle Visualized In Vitro
    • 4. Outlook
    • Acknowledgements
    • References
  • 6. Preparation of RNA Polymerase Complexes for Their Analysis by Single-Particle Cryo-Electron Microscopy
    Michael Pilsl, Florian B. Heiss, Gisela Pöll, Mona Höcherl, Philipp Milkereit, and Christoph Engel.
    Published online: July 8, 2022.
    • 1. Introduction
    • 2. Materials
    • 3. Methods
    • 4. Notes
    • Acknowledgments
    • References
• IV. Ribosome Assembly, Transport and RNP Complexes
  • 7. Eukaryotic Ribosome assembly and Nucleocytoplasmic Transport
    Michaela Oborská-Oplová, Ute Fischer, Martin Altvater, and Vikram Govind Panse.
    Published online: July 8, 2022.
    • 1. Introduction
    • 2. Materials, Reagents, and Yeast Media
    • 3. Pre-ribosome Isolation for Single Particle Cryo-Electron Microscopy
    • 4. Conclusions
    • 5. Notes
    • Acknowledgments
    • References
  • 8. Tethered MNase Structure Probing as Versatile Technique for Analyzing RNPs Using Tagging Cassettes for Homologous Recombination in Saccharomyces cerevisiae
    Fabian Teubl, Katrin Schwank, Uli Ohmayer, Joachim Griesenbeck, Herbert Tschochner, and Philipp Milkereit.
    Published online: July 8, 2022.
    • 1. Introduction
    • 2. Materials
    • 3. Methods
    • 4. Notes
    • Acknowledgments
    • References
• V. RNA Modification
  • 9. Chemical Modifications of Ribosomal RNA
    Sunny Sharma and Karl-Dieter Entian.
    Published online: July 8, 2022.
    • 1. Introduction
    • 2. Ribose Methylation
    • 3. Pseudouridylation
    • 4. Base Modifications
    • 5. Base Modifications of 18S rRNA
    • 6. Base Modifications of 25S rRNA
    • Acknowledgments
    • References
  • 10. In Vitro Selection of Deoxyribozymes for the Detection of RNA Modifications
    Anam Liaqat, Maksim V. Sednev, and Claudia Höbartner.
    Published online: July 8, 2022.
    • 1. Introduction
    • 2. Materials
    • 3. Methods
    • 4. Notes
    • Acknowledgments
    • References
  • 11. Mapping of the Chemical Modifications of rRNAs
    Jun Yang, Peter Watzinger, and Sunny Sharma.
    Published online: July 8, 2022.
    • 1. Introduction
    • 2. Materials
    • 3. Methods
    • 4. Notes
    • References
  • 12. Non-radioactive In Vivo Labeling of RNA with 4-Thiouracil
    Christina Braun, Robert Knüppel, Jorge Perez-Fernandez, and Sébastien Ferreira-Cerca.
    Published online: July 8, 2022.
    • 1. Introduction
    • 2. Materials
    • 3. Methods (See Notes 4 and 5)
    • 4. Notes
    • Acknowledgments
    • References
• VI. Translation
  • 13. Translation Phases in Eukaryotes
    Sandra Blanchet and Namit Ranjan.
    Published online: July 8, 2022.
    • 1. Introduction
    • 2. Initiation
    • 3. Elongation
    • 4. Termination
    • 5. Ribosome Recycling
    • Acknowledgments
    • References
  • 14. Differential Translation Activity Analysis Using Bioorthogonal Noncanonical Amino Acid Tagging (BONCAT) in Archaea
    Michael Kern and Sébastien Ferreira-Cerca.
    Published online: July 8, 2022.
    • 1. Introduction
    • 2. Materials
    • 3. Methods (Workflow Is Summarized in Fig. 1c)
    • 4. Notes
    • Acknowledgments
    • References
  • 15. Thermofluor-Based Analysis of Protein Integrity and Ligand Interactions
    Sophia Pinz, Eva Doskocil, and Wolfgang Seufert.
    Published online: July 8, 2022.
    • 1. Introduction
    • 2. Materials
    • 3. Methods
    • 4. Notes
    • Acknowledgments
    • References
  • 16. In Vitro Assembly of a Fully Reconstituted Yeast Translation System for Studies of Initiation and Elongation Phases of Protein Synthesis
    Sandra Blanchet and Namit Ranjan.
    Published online: July 8, 2022.
    • 1. Introduction
    • 2. Materials
    • 3. Methods
    • 4. Notes
    • Acknowledgments
    • References