Description
As imaging technologies and approaches have evolved, the scope of certain imaging techniques has moved far beyond the production of purely illustrative images or appealing time-lapse movies to providing the scientist with a rich range of ways to measure and quantify the biological process and outcome of gene expression. In Imaging Gene Expression: Methods and Protocols, expert authors offer up-to-date approaches and protocols that scientists in the field have developed, which would benefit the broader scientific community. Divided in three convenient parts, this detailed book covers the output of a gene, namely the RNA molecules that are transcribed from the gene and the way by which these molecules can be tracked or quantified in fixed or living cells, protocols that focus on the gene, DNA, or chromatin, as well as a variety of ways by which nuclear processes intertwined with gene expression can be followed and quantified in living cells as well as approaches for studying several sub-nuclear structures found in eukaryotic cells. Written in the highly successful Methods in Molecular Biology series format, chapters include introductions to their respective subjects, lists of materials and reagents, step-by-step, readily reproducible laboratory protocols, and tips on troubleshooting and avoiding known pitfalls. Authoritative and up-to-date, Imaging Gene Expression: Methods and Protocols will serve researchers working toward imaging in the context of complete organisms. 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 Lanctt 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 Hbner, Thomas Cremer, and Jrgen Neumann 22. Time-Lapse, Photo-Activation, and Photo-Bleaching Imaging of Nucleolar Assembly after Mitosis Danile Hernandez-Verdun, Emilie Louvet, and Eleonora Muro 23. Nucleation of Nuclear Bodies Miroslav Dundr
