Part I. Isolation of Nuclei

1. Cell Type-Specific Affinity Purification of Nuclei for Chromatin Profiling in Whole Animals

Florian A. Steiner and Steven Henikoff

2. Lysis Gradient Centrifugation - A Flexible Method for the Isolation of Nuclei from Primary Cells

Karl Katholnig, Marko Poglitsch, Markus Hengstschläger, and Thomas Weichhart

3. Isolation of Nuclei in Media Containing an Inert Polymer to Mimic the Crowded Cytoplasm

Ronald Hancock and Yasmina Hadj-Sahraoui

Part II. Nucleoli

4. A New Rapid Method for Isolating Nucleoli

Zhou Fang Li, Yun Wah Lam

5. Sequential Recovery of Macromolecular Components of the Nucleolus

Baoyan Bai and Marikki Laiho

Part III. Genes and Chromatin

6. Au Nanoinjectors for Electrotriggered Gene Delivery into the Cell Nucleus

Mijeong Kang and Bongsoo Kim

7. Improving Chromatin Immunoprecipitation (ChIP) by Suppression of Method-Induced DNA-Damage Signaling

Sascha Beneke

8. Purification of Specific Chromatin Loci for Proteomic Analysis

Stephanie D. Byrum, Sean D. Taverna, and Alan J. Tackett

9. Chromatin Structure Analysis of Single Gene Molecules by Psoralen Crosslinking and Electron Microscopy

Chris Brown, Julian Eskin, Stephan Hamperl, Joachim Griesenbeck, Melissa Jurica, Hinrich Boeger

10. Purification of Proteins on Newly Synthesized DNA Using iPOND

Huzefa Dungrawala and David Cortez

11. Applying the Ribopuromycylation Method to Detect Nuclear Translation

Alexandre David and Jonathan W. Yewdell

Part IV. The Intranuclear Milieu

12. Targeted Nano Analysis of Water and Ions in the Nucleus Using Cryo-Correlative Microscopy

Frédérique Nolin, Dominique Ploton, Laurence Wortham, Pavel Tchelidze, Hélène Bobichon, Vincent Banchet, Nathalie Lalun, Christine Terryn, and Jean Michel

13. A Redox-Sensitive Yellow Fluorescent Protein Sensor for Monitoring Nuclear Glutathione Redox Dynamics

Agata Banach-Latapy, Michèle Dardalhon, and Meng-Er Huang

Part V. Imaging Nuclear Structures

14. Determination of the Dissociation Constant of the NFkB p50/p65 Heterodimer in Living Cells Using Fluorescence Cross-Correlation Spectroscopy

Manisha Tiwari and Masataka Kinjo

15. Imaging and Quantification of Amyloid Fibrillation in the Cell Nucleus

Florian Arnhold, Andrea Scharf, and Anna von Mikecz

16. Analysis of Nuclear Organization with TANGO, Software for High-Throughput Quantitative Analysis of 3D Fluorescence Microscopy Images

Jean Ollion, Julien Cochennec. François Loll, Christophe Escudé, and Thomas Boudier

17. Quantitative Analysis of Chromosome Localization in the Nucleus

Sandeep Chakraborty, Ishita Mehta, Mugdha Kulashreshtha, and B. J. Rao