The Relationship between Human Nucleolar Organizer Regions and Nucleoli, Probed by 3D-Immunofish -- Correlative Light and Electron Microscopy of Nucleolar Transcription in Saccharomyces Cerevisiae -- High-Throughput Live-Cell Microscopy Analysis of Chromosome Domain - Nucleolus Associations in S. Cerevisiae -- Quantitative Immunofluorescence Analysis of Nucleolus-Associated Chromatin -- Visualization of The Nucleolus in Living Cells with Cell-Penetrating Fluorescent Peptides -- Purification of S. Cerevisiae RNA Polymerase I for Structural and Functional Studies -- Analysis of S. Cerevisiae RNA Polymerase I Transcription In Vitro -- Preparation of Chromatin Templates to Study RNA Polymerase I Transcription In Vitro -- Measurement of Rrna Synthesis and Processing by 4su-Tagging -- Metabolic Labeling in the Study of Mammalian Ribosomal RNA Synthesis -- Quantitative Northern Blot Analysis of Mammalian Rrna Processing -- Complete Sequence Construction of the Highly Repetitive Ribosomal RNA Gene Repeats in Eukaryotes using Whole Genome Sequence Data -- Analysis of Rdna Methylation in Arabidopsis By 2D Gel Electrophoresis -- Fluorescence-Activated Sorting of Arabidopsis Nucleoli -- Purification of RNA Polymerase I-Associated Chromatin from Yeast Cells -- Bioinformatic Analysis of Chip-Seq Data on the Repetitive Rrna Gene -- Deep Sequencing Analysis of Nucleolar Small Rnas: Isolation and Library Preparation -- Deep Sequencing Analysis of Nucleolar Small RNAs: Bioinformatics -- Quantitative Proteomic Analysis of the Human Nucleolus -- Assessing Nucleolar Localization of Proteins: Bioinformatic Analysis of Proteomics Data. .

This volume provides an up-to-date compilation of current methodological approaches utilized for the exploration of nucleolar structure and function. Chapters cover a diversity of protocols that include imaging of the nucleolus, analysis of ribosomal RNA transcription and processing, and genomics and proteomics of the nucleolus. 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. Authoritative and practical, The Nucleolus: Methods and Protocols provides scientists with a reliable practical handbook to facilitate the investigation of this nuclear compartment at the advanced level.