Imaging Gene Expression: Methods and Protocols

Part I: Imaging Gene Expression and RNA Dynamics in Cells and Organisms

1. High-Throughput Fluorescence-Based Screen to Identify Factors Involved in Nuclear Receptor Recruitment to Response Elements

Tina B. Miranda, Ty C. Voss, and Gordon L. Hager

2. Live-Cell Imaging Combined with Immunofluorescence, RNA, or DNA FISH to Study the Nuclear Dynamics and Expression of the X-Inactivation Center

Tim Pollex, Tristan Piolot, and Edith Heard

3. Single Molecule Resolution Fluorescent In Situ Hybridization (smFISH) in the Yeast S. cerevisiae

Samir Rahman and Daniel Zenklusen

4. Measuring Transcription Dynamics in Living Cells Using Fluctuation Analysis

Matthew L. Ferguson and Daniel R. Larson

5. Tracking Nuclear Poly(A) RNA Movement Within and Among Speckle Nuclear Bodies and the Surrounding Nucleoplasm

Joan C. Ritland Politz and Thoru Pederson

6. Nuclear Trafficking and Export of Single, Native mRNPs in Chironomus tentans Salivary Gland Cells

Tim P. Kaminski, Jan-Hendrik Spille, Claudio Nietzel, Jan Peter Siebrasse, and Ulrich Kubitscheck

7. Single mRNP Tracking in Living Mammalian Cells

Alon Kalo, Pinhas Kafri, and Yaron Shav-Tal

8. Imaging Nascent RNA Dynamics in Dictyostelium

Jonathan R. Chubb, Michelle Stevense, Danielle Cannon, Tetsuya Muramoto, and Adam Corrigan

Part II: Imaging the Genome and Chromatin Dynamics

9. Monitoring Dynamic Binding of Chromatin Proteins In Vivo by Single Molecule Tracking

Davide Mazza, Sourav Ganguly, and James G. McNally

10. Single Particle Tracking for Studying the Dynamic Properties of Genomic Regions in Live Cells

Irena Bronshtein Berger, Eldad Kepten, and Yuval Garini

11. Microscopic Analysis of Chromatin Localization and Dynamics in C. elegans

Christian Lanct?t and Peter Meister

12. Measuring the Dynamics of Chromatin Proteins During Differentiation

Arigela Harikumar and Eran Meshorer

13. Electron Spectroscopic Tomography of Specific Chromatin Domains

Liron Even-Faitelson, Eden Fussner, Ren Li, Mike Strauss, and David P. Bazett-Jones

14. BAC Manipulations for Making BAC Transgene Arrays

Nimish Khanna, Qian Bian, Matt Plutz, and Andrew S. Belmont

Part III: Imaging Nuclear Processes and Sub-Nuclear Structures

15. Spatio-Temporal Visualization of DNA Replication Dynamics

Marius Reinhart, Corella S. Casas-Delucchi, and M. Cristina Cardoso

16. The Dynamics of DNA Damage Repair and Transcription

Niraj M. Shanbhag and Roger A. Greenberg

17. Fluorescence Microscopy-Based High-Throughput Screening for Factors Involved in Gene Silencing

Sebastian Bultmann and Heinrich Leonhardt

18. Actin as a Model for the Study of Nucleocytoplasmic Shuttling and Nuclear Dynamics

Kari-Pekka Skarp and Maria K. Vartiainen

19. Isochronal Visualization of Transcription and Proteasomal Proteolysis in Cell Culture or in the Model Organism, Caenorhabditis elegan

Anna von Mikecz and Andrea Scharf

20. Considering Discrete Protein Pools When Measuring the Dynamics of Nuclear Membrane Proteins

Nikolaj Zuleger, David A. Kelly, and Eric C. Schirmer

21. Correlative Microscopy of Individual Cells: Sequential Application of Microscopic Systems with Increasing Resolution to Study the Nuclear Landscape

Barbara H?bner, Thomas Cremer, and J?rgen Neumann

22. Time-Lapse, Photo-Activation, and Photo-Bleac