The Nuclear Envelope: Methods and Protocols

ISBN-13: 9781493980680 / Angielski / Miękka / 2018 / 523 str.

Sue Shackleton; Philippe Collas; Eric C. Schirmer

Spis treści

Part I Nuclear Envelope Isolation

1. Isolation, Proteomic Analysis and Microscopy Confirmation of the Liver Nuclear Envelope Proteome
   Nadia Korfali, Laurence Florens, and Eric C. Schirmer
   
   
2. Exploring the Protein Composition of the Plant Nuclear Envelope
   Xiao Zhou, Kentaro Tamura, Katja Graumann, and Iris Meier
   
   
3. High Efficiency Isolation of Nuclear Envelope Protein Complexes from Trypanosomes
   Samson Obado, Mark C. Field, Brian T. Chait, and Michael P. Rout

 

Part II Nuclear Envelope Protein Interactions, Localization, and Dynamics

4.    Super Resolution Microscopy of the Nuclear Envelope and Associated Proteins
Wei Xie, Henning F. Horn, and Graham D. Wright

1. Analyses of the Dynamic Properties of Nuclear Lamins by Fluorescence Recovery after Photobleaching (FRAP) and Fluorescence Correlation Spectroscopy (FCS)
   Shimi Takeshi, Chan-Gi Pack, and Robert D. Goldman
   
   
2. Probing Protein Distribution Along the Nuclear Envelope In Vivo by Using Single-Point FRAP
   Krishna C. Mudumbi and Weidong Yang
   
   
The Use of 2-Photon FLIM/FRET to Study Protein Interactions during Nuclear Envelope Fusion In Vivo and In Vitro
Richard D. Byrne, Banafshé Larijani, and Dominic L. Poccia


3. Identifying Protein-Protein Associations at the Nuclear Envelope with BioID
   Dae In Kim, Samuel C. Jensen, and Kyle J. Roux
   
   
4. In Situ Detection of Interactions between Nuclear Envelope Proteins and Partners
   Alice Barateau and Brigitte Buendia
   
Methods for Single-Cell Pulse-Chase Analysis of Nuclear Components
Marek Drozdz and David J. Vaux


5. Analysis of Nuclear Lamina Proteins in Myoblast Differentiation by Functional Complementation
   Olga Tapia and Larry Gerace
   
   
6. Analysis of Meiotic Telomere Behavior in the Mouse
   Jana Link, Ricardo Benavente, and Manfred Alsheimer

 

Part III Nuclear Envelope Interactions with the Cytoskeleton

1. Identification and Validation of Putative Nesprin Variants
   Flavia Autore, Catherine M. Shanahan, and Qiuping Zhang
   
   
2. Detection of Diverse and High Molecular Weight Nesprin-1 and Nesprin-2 Isoforms Using Western Blotting
   James Carthew and Iakowos Karakesisoglou
   
   
3. The Use of Polyacrylamide Hydrogels to Study the Effects of Matrix Stiffness on Nuclear Envelope Properties
   Rose-Marie Minaisah, Susan Cox, and Derek T. Warren
   
   
4. Cell Microharpooning to Study Nucleo-Cytoskeletal Coupling
   Gregory Fedorchak and Jan Lammerding
   
   
5. Wound Healing Assays to Study Mechanisms of Nuclear Movement in Fibroblasts and Myoblasts
   Wakam Chang, Susumu Antoku, and Gregg G. Gundersen
   
   
6. Methods for Assessing Nuclear Rotation and Nuclear Positioning in Developing Skeletal Muscle Cells
   Meredith H. Wilson, Matthew G. Bray, and Erika L. F. Holzbaur
   
   
7. Imaging Approaches to Investigate Myonuclear Positioning in Drosophila
   Mafalda Azavedo, Victoria K. Schulman, Eric Folker, Mridula Balakrishnana,  and Mary Baylies

 

Part IV Nuclear Envelope-Chromatin Interactions

Mapping Nuclear Lamin-Genome Interactions by Chromatin Immunoprecipitation of Nuclear Lamins
Anja R. Oldenburg and Philippe Collas


1. Lamin ChIP from Chromatin Prepared by Micrococcal Nuclease Digestion Isabelle Dubant-Goulet
   
   
2. DamID Analysis of Nuclear Organization in Caenorhabditis elegans
   Georgina Gómez-Saldivar, Peter Meister, and Peter Askjaer
   
   
The Application of DamID to Identify Peripheral Gene Sequences in Differentiated and Primary Cells
Michael I. Robson and Eric C. Schirmer


3. Visualizing the Spatial Relationship of the Genome with the Nuclear Envelope Using Fluorescence in situ Hybridization
   Craig S. Clements, Ural Bikkul, Mai Hassan Ahmed, Helen A. Foster, Lauren S. Godwin, and Joanna M. Bridger
   
   
4. Visualization of Genomic Loci in Living Cells with a Fluorescent CRISPR/Cas9 System
   Tobias Anton, Heinrich Leonhardt, and Yolanda Markaki
   
   
5. Methods to Monitor DNA Repair Defects and Genomic Instability in the Context of a Disrupted Nuclear Lamina
   Suzanna Gonzalo and Ray Kreienkamp

 

Part V Nucleo-Cytoplasmic Transport

1. High Resolution Scanning Electron Microscopy and Immuno-Gold Labeling of the Nuclear Lamina and Nuclear Pore Complex
   Martin W. Goldberg
   
   
2. An In Vitro Assay to Study Targeting of Membrane Proteins to the Inner Nuclear Membrane
   Rosemarie Ungricht, Sumit Pawar, and Ulrike Kutay
   
   
3. Nuclear Protein Transport in Digitonin Permeabilized Cells
   Steven A. Adam
   
   
4. Analysis of CRM1-Dependent Nuclear Export in Permeabilized Cells
   Ralph H. Kehlenbach and Sarah A. Port
   
   
5. SPEED Microscopy and Its Application in Nucleocytoplasmic Transport
   Jiong Ma, Joseph M. Kelich, and Weidong Yang

Blurb

This volume provides a wide range of protocols used in studying the nuclear envelope, with special attention to the experimental adjustments that may be required to successfully investigate this complex organelle in cells from various organisms. The Nuclear Envelope: Methods and Protocols is divided into five sections: Part I – Nuclear Envelope Isolation; Part II – Nuclear Envelope Protein Interactions, Localization, and Dynamics; Part III – Nuclear Envelope Interactions with the Cytoskeleton; Part IV – Nuclear Envelope-Chromatin Interactions; and Part V – Nucleo-Cytoplasmic Transport. Many of the modifications discussed in this book have only been circulated within laboratories that have conducted research in this field for many years. Written in the highly successful Methods in Molecular Biology series format, chapters include introductions to their respective topics, lists of the necessary materials and reagents, step-by-step, readily reproducible laboratory protocols, and tips on troubleshooting and avoiding known pitfalls.

Cutting edge and thorough, The Nuclear Envelope: Methods and Protocols is a timely resource for researchers who have joined this dynamic and rapidly growing field.