Gene Regulation

  1. Eukaryotic Chromatin and Epigenetic Regulation
    1. Chromatin Structure and Organization
      1. Nucleosome Structure
        1. Histone Octamer Composition
          1. DNA Wrapping Around Histones
            1. Nucleosome Core Particle
            2. Higher-Order Chromatin Structure
              1. 30-nm Fiber Formation
                1. Chromatin Loops and Domains
                  1. Nuclear Organization
                  2. Euchromatin versus Heterochromatin
                    1. Structural Differences
                      1. Transcriptional Activity States
                        1. Chromosomal Territories
                        2. Chromatin Remodeling Complexes
                          1. ATP-Dependent Remodeling
                            1. SWI/SNF Complex Family
                              1. Nucleosome Sliding and Ejection
                                1. Chromatin Accessibility Changes
                              2. Histone Modifications
                                1. Histone Acetylation
                                  1. Histone Acetyltransferases (HATs)
                                    1. Histone Deacetylases (HDACs)
                                      1. Lysine Acetylation Sites
                                        1. Transcriptional Activation Effects
                                        2. Histone Methylation
                                          1. Histone Methyltransferases
                                            1. Histone Demethylases
                                              1. Methylation States
                                                1. Monomethylation
                                                  1. Dimethylation
                                                    1. Trimethylation
                                                    2. Activating and Repressive Marks
                                                    3. Histone Phosphorylation
                                                      1. Kinases and Phosphatases
                                                        1. Cell Cycle Regulation
                                                          1. Chromatin Condensation
                                                          2. Histone Ubiquitination
                                                            1. Ubiquitin Ligases
                                                              1. Transcriptional Effects
                                                                1. DNA Repair Signaling
                                                                2. The Histone Code Hypothesis
                                                                  1. Combinatorial Modifications
                                                                    1. Reader Proteins
                                                                      1. Chromatin State Determination
                                                                      2. Histone Variants
                                                                        1. H3 Variants
                                                                          1. H2A Variants
                                                                            1. Specialized Functions
                                                                          2. DNA Methylation
                                                                            1. CpG Dinucleotides and CpG Islands
                                                                              1. Genome Distribution
                                                                                1. Promoter Region Methylation
                                                                                  1. CpG Island Shores
                                                                                  2. DNA Methyltransferases
                                                                                    1. DNMT1 Maintenance Activity
                                                                                      1. DNMT3A and DNMT3B De Novo Activity
                                                                                        1. Methylation Establishment
                                                                                        2. Gene Silencing Mechanisms
                                                                                          1. Transcriptional Repression
                                                                                            1. Methyl-CpG Binding Proteins
                                                                                              1. Chromatin Compaction
                                                                                              2. Methylation Inheritance
                                                                                                1. Hemimethylated DNA Recognition
                                                                                                  1. Replication-Coupled Maintenance
                                                                                                  2. Genomic Imprinting
                                                                                                    1. Parent-of-Origin Gene Expression
                                                                                                      1. Imprinting Control Regions
                                                                                                        1. Imprinting Disorders

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                                                                                                    2. Prokaryotic Gene Regulation

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                                                                                                    4. Eukaryotic Transcriptional Regulation