Table of Contents

Preface
Acknowledgments 

1. SOME PRINCIPLES

Overview of the Cell Nucleus
Box 1-1. Discovery of Cells, Nuclei, and DNA
A Sense of Scale
Box 1-2. Microscopy: Problems and Solutions
Box 1-3. Green Fluorescent Protein
Thermal Motion
Local Concentrations
Structures of Nucleic Acids
The DNA Double Helix
Box 1-4. Translation
The Length of DNA Molecules
Bending and Twisting DNA
Box 1-5. Gel Electrophoresis and Blotting
The Structure of RNA
Recognizing Specific DNA Sequences
Box 1-6. DNA:Protein Binding—"Gel-Shifts," "Footprinting," "ChlP"
DNA-Binding Proteins
Making Large Structures
Assembling Nuclei in Egg Extracts
Subcellular Localization
Tensegrity Architecture and Cellular Skeletons
Nuclear Position and Shape
Some Evolutionary Considerations
Genome Size
Box 1-7. The Amount of DNA in a Human Nucleus
Gene Number and Organization
Regulatory Networks: Redundant and Robust
Box 1-8. Protein:Protein Interactions—"Two-Hybrid," "FRET"
Box 1-9. Simulating Complex Control Circuits
Subcompartments and the Origin of Nuclei
Box 1-10. The Three Primary Lineages of the Living World
Summary
References

2. STRUCTURE

Overview of Nuclear Structure
Box 2-1. Preparing Metaphase Spreads
The Nuclear Membrane
The Nuclear Lamina
Nuclear Pores
Box 2-2. Intermediate Filaments
Box 2-3. Identifying Proteins in Large Structures by MALDI Mass Spectrometry
Importing Proteins of >60 kD
Box 2-4. Autoradiography
RNA Export
Is the Nuclear Membrane an Ion Barrier?
The Nucleolus
Packaging Chromatin During Interphase
Artifacts
Box 2-5. Isolating Nuclei
Box 2-6. Nuclear Matrices and Scaffolds
The Nucleosome
Box 2-7. Nucleoids
The Zig-zagging Nucleosomal String
Chromatin Loops
Chromatin "Clouds"
Box 2-8. Position-Effect Variegation in Drosophila
Chromosome Territories
Box 2-9. in situ Hybridization
Nucleoskeletons and Nuclear Subcompartments
Chromosomes
Box 2-10. Acute Promyelocytic Leukemia
Elements of Yeast Chromosomes
Telomeres
Chromosome Bands
Models for Chromosome Organization
Polytene Chromosomes
Summary
References

3. REPLICATION

Principles
Box 3-1. Bacterial DNA Polymerases
Tracking Versus Immobile DNA Polymerases
Replication Factories
The Mechanics of Synthesis at the Fork
Separating Parental Strands
Box 3-2. Topoisomerases and Anticancer Drugs
RNA Primers
The Asymmetric Fork
Proofreading
Replicating Chromatin
The Initiation of Synthesis
Box 3-3. The Origin of Replication of E. coli
Box 3-4. Two Methods for Mapping Origins
Simple Origins of SV40 Virus and Yeast
Complex Mammalian Origins
Role of Transcription During Initiation
Replicating Ends
Box 3-5. Telomerase in Aging and Cancer
Summar
References

4. TRANSCRIPTION

Principles
Box 4-1. Mapping Transcription Units
Tracking Versus Immobile RNA Polymerases
Box 4-2. The RNA Polymerase of E. coli
The Untwining and Supercoiling Problems
Attached Polymerases Can Work in vitro
Transcribing Chromatin
The Three Kinds of Eukaryotic RNA Polymerase
RNA Polymerase I
Box 4-3. Ribosome Synthesis
RNA Polymerase II and its Transcription Factors
Number and Activity of RNA Polymerases
Box 4-4. Transcription of Heat-Shock Loci
Box 4-5. Message/Protein Profiles—"Microarrays," "SAGE," "Two-Hybrid"
Transcription Factories
Nucleolar Factories Containing Polymerase I
Extranucleolar Factories Containing Polymerases II and III
Dynamics
Processing and Transport of Polymerase II Transcripts
Capping the 5' End
Box 4-6. Analyzing Caps
Polyadenylating the 3' End
Splicing the Middle
Box 4-7. Autoimmune Antibodies
Packaging Transcripts into Ribonucleoprotein Particles
Fidelity and Quality Control
The Organization of Processing
Transport to the Cytoplasm
Summary
References

5. REPAIR

The Need for Repair of Damage
Common Damaging Agents and Lesions
Box 5-1. Consequences of Deamination of C and 5-^MeC
Some Experimental Approaches
Box 5-2. Repair Defects and Human Disease
Types of Repair
Direct Repair
Base-Excision Repair
Nucleotide-Excision Repair
Mismatch Repair
Other Repair Mechanisms
Box 5-3. Damage Response Systems in Bacteria
Accuracy in Gap Filling
Sites of Repair
Transcription and Repair
Some Consequences of Inefficient Repair
Summary
References

6. REGULATION OF GENE EXPRESSION

Simple Regulatory Circuits in Bacteria and Yeast
Box 6-1. Positive and Negative Control in the lac Operon
Box 6-2. A Complex Circuit Involving the Lambda Repressor
Principles of Eukaryotic Gene Regulation
Most Cells in an Organism Contain the Same DNA
Box 6-3. Sequence Changes in Antibody Genes
Different Levels of Control
Box 6-4. Gene Amplification
Box 6-5. Inheritance of Methylated Sequences in DNA
Box h-6. Alternative Splicing and Polyadenation
Inheriting the Differentiated State Through Mitosis
Box 6-7. Co-suppression and RNA Interference
Differential Expression Can Require Continuous Regulation
Box 6-8. Identification of MyoD, a Myogenic Transactivator
Relative Expression Levels in Different Cells
Box 6-9. Designing a Eukaryotic Repressor
Regulation at the Level of the Nucleosome
Nucleosome Positioning and Modification
Chromatin Remodeling
Regulation at the Level of the Loop
Box 6-10. Defining DNA Motifs That Regulate Transcription
Heterochromatin
Silencing in Yeast
DNA Methylation in Vertebrates
Polycomb Proteins of Drosophila
Establishing and Inheriting Patterns of Expression
Example: Inheriting Activity of rDNA Genes
Example: Anterior-Posterior Patterning in Drosophila Eggs
Box 6-11. Maternal-Effect Genes in Drosophila
Example: Commitment of Hematopoietic Stem Cells
Summary
References

7.THE CELL CYCLE

Overview
Mitosis
Box 7-1. Synchronizing Mammalian Cells
The Centrosome Cycle
Box 7-2. Microtubules
Spindles, Centromeres and Kinetochores
Box 7-3. Different Kinds of Centromeres
Microtubule-Based Motors Drive Movement
Cytokinesis
Regulation of the Cell Cycle
Box 7-4. Glycogen Phosphorylase and Protein Kinases
Role of Trans-acting Factors
Frog Embryos: MPF and Cyclins
Yeasts: cdc Mutants, START, and ORC
Box 7-5. The Life Cycles of Two Yeasts
The G2 Checkpoint in Fission Yeast The Anaphase-Promoting Complex
Some Other Checkpoints
Growth Factors
Size Control
Deranged Cycles and Cancer
Box 7-6. The Genetic Basis of Cancer
Box 7-7. Oncogenes
Genes Controlling Proliferation
Box 7-8. Tumor-Suppressor Genes
T antigen, p53, and Rb
Box 7-9. p53 and Human Tumors
Box 7-10. Hereditary Colorectal Cancer
Cancer Therapy and Checkpoints
Apoptosis
The Genetic Basis of Apoptosis
Box 7-11. Lineage Analysis in Caenorhabditis elegans
Box 7-12. Caspases
Activating the Suicide Machinery
Box 7-13. Death Receptors
Summary
References

8. MEIOSIS AND RECOMBINATION

Overview
Meiosis
The Synaptonemal Complex
Chiasmata and Chromosome Segregation
The Production of Gametes
Recombination
Principles Involved in Strand Exchange
Gene Conversion
Box 8-1. RecBCD, RecA, and General Recombination
General Recombination in Eukaryotes
Box 8-2. The ARG4 Recombination Site in Budding Yeast
Chromosome Pairing
Summary
References

Appendix 1: Some Websites
Index

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