Ribosome Biogenesis: Methods and Protocols

Dedication......
Acknowledgments...
Preface...
Table of Contents...
Contributing Authors...

Part I Ribosome Biogenesis

1. A Comparative Perspective on Ribosome Biogenesis: Unity and Diversity across the Tree of Life
Michael Jtner and S嶵astien Ferreira-Cerca

Part II Genomic Organization

2. Establishment and Maintenance of Open Ribosomal RNA Gene Chromatin States in Eukaryotes
Christopher Sch踄hner, Philipp E. Merkl, Michael Pilsl, Katrin Schwank, Kristin Hergert, Sebastian Kruse, Philipp Milkereit, Herbert Tschochner, and Joachim Griesenbeck

3. Analysis of Yeast RNAP I Transcription of Nucleosomal Templates In Vitro
Philipp E. Merkl, Christopher Sch踄hner, Michael Pilsl, Katrin Schwank, Kristin Hergert, Gernot L鄚gst, Philipp Milkereit, Joachim Griesenbeck, and Herbert Tschochner

Part III RNA Polymerases

4. Specialization of RNA Polymerase I in Comparison to Other Nuclear RNA Polymerases of Saccharomyces cerevisiae
Philipp E. Merkl, Christopher Sch踄hner, Michael Pilsl, Katrin Schwank, Catharina Schmid, Gernot L鄚gst, Philipp Milkereit, Joachim Griesenbeck, and Herbert Tschochner

5. Structural Studies of Eukaryotic RNA Polymerase I using Cryo-Electron Microscopy
Michael Pilsl and Christoph Engel

6. Preparation of RNA Polymerase Complexes for their Analysis by Single Particle Cryo-Electron Microscopy
Michael Pilsl, Florian B. Heiss, Gisela P闤l, Mona H鐼herl, Philipp Milkereit, and Christoph Engel

Part IV Ribosome Assembly, Transport and RNP Complexes

7. Eukaryotic Ribosome Assembly and Nucleo-Cytoplasmic Transport
Michaela Oborsk?Oplov? Ute Fischer, Martin Altvater, and Vikram Govind Panse

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

Part V RNA Modification

9. Chemical Modifications of Ribosomal RNA
Sunny Sharma and Karl-Dieter Entian

10. In Vitro Selection of Deoxyribozymes for the Detection of RNA Modifications
Anam Liaqat, Maksim V. Sednev, and Claudia H鐽artner

11. Mapping of the Chemical Modifications of rRNAs
Jun Yang, Peter Watzinger, and Sunny Sharma

12. Non-Radioactive In Vivo Labelling of RNA with 4-thio-uracil
Christina Braun, Robert Knpel, Jorge Perez-Fernandez, and S嶵astien Ferreira-Cerca

Part VI Translation

13. Translation Phases in Eukaryotes
Sandra Blanchet and Namit Ranjan

14. Differential Translation Activity using Bio-Orthogonal Non-Canonical Amino Acids Tagging (BONCAT) in Archaea
Michael Kern and S嶵astien Ferreira-Cerca

15. Thermofluor-Based Analysis of Protein Integrity and Ligand Interactions
Sophia Pinz, Eva Doskocil, and Wolfgang Seufert

16. In Vitro Assembly of a Fully Reconstituted Yeast Translation System for Studies of Initiation and Elongation Phases of Protein Synthesis
Sandra Blancher and Namit Ranjan