Gene Regulation

  1. Eukaryotic Transcriptional Regulation
    1. Cis-Regulatory Elements
      1. Core Promoter Elements
        1. TATA Box
          1. Sequence Characteristics
            1. TATA-Binding Protein Recognition
              1. Transcription Start Site Positioning
              2. Initiator Elements
                1. TFIID Recognition
                  1. Alternative Core Promoters
                  2. Downstream Promoter Elements
                    1. DPE Sequences
                      1. TFIID Interactions
                    2. Proximal Promoter Elements
                      1. CAAT Box
                        1. GC Box
                          1. Sp1 Binding Sites
                          2. Distal Regulatory Elements
                            1. Enhancers
                              1. Distance and Orientation Independence
                                1. Tissue-Specific Activity
                                  1. Enhancer-Promoter Looping
                                  2. Silencers
                                    1. Transcriptional Repression
                                      1. Chromatin-Mediated Silencing
                                      2. Insulators
                                        1. Boundary Element Function
                                          1. Enhancer Blocking Activity
                                            1. Loop Domain Formation
                                        2. Trans-Acting Factors
                                          1. General Transcription Factors
                                            1. TFIID Complex
                                              1. TFIIB Function
                                                1. TFIIE and TFIIF Roles
                                                  1. TFIIH Kinase Activity
                                                    1. Pre-Initiation Complex Assembly
                                                    2. Sequence-Specific Transcription Factors
                                                      1. DNA-Binding Domains
                                                        1. Helix-Turn-Helix Motif
                                                          1. Zinc Finger Domains
                                                            1. Leucine Zipper Structure
                                                              1. Helix-Loop-Helix Motif
                                                                1. Basic Helix-Loop-Helix
                                                                2. Activation Domains
                                                                  1. Acidic Activation Domains
                                                                    1. Glutamine-Rich Domains
                                                                      1. Proline-Rich Domains
                                                                      2. Repression Domains
                                                                        1. Active Repression Mechanisms
                                                                          1. Corepressor Recruitment
                                                                        2. Mediator Complex
                                                                          1. Subunit Organization
                                                                            1. Transcription Factor Bridging
                                                                              1. RNA Polymerase II Regulation
                                                                                1. Kinase Module Function
                                                                              2. Transcription Initiation Complex
                                                                                1. RNA Polymerase II Structure
                                                                                  1. Subunit Composition
                                                                                    1. C-Terminal Domain
                                                                                      1. Active Site Organization
                                                                                      2. Promoter Recognition and Binding
                                                                                        1. Sequential Factor Assembly
                                                                                          1. DNA Melting and Open Complex Formation
                                                                                            1. Transcription Start Site Selection
                                                                                            2. Promoter Clearance and Elongation
                                                                                              1. CTD Phosphorylation
                                                                                                1. Elongation Factor Recruitment
                                                                                                  1. Pausing and Anti-Pausing Factors
                                                                                                2. Combinatorial Gene Regulation
                                                                                                  1. Transcription Factor Interactions
                                                                                                    1. Cooperative DNA Binding
                                                                                                      1. Synergistic Activation
                                                                                                        1. Competitive Binding
                                                                                                          1. Antagonistic Effects
                                                                                                          2. Regulatory Networks
                                                                                                            1. Feed-Forward Loops
                                                                                                              1. Feedback Circuits
                                                                                                                1. Bistable Switches
                                                                                                                2. Cell Type-Specific Expression
                                                                                                                  1. Master Regulatory Factors
                                                                                                                    1. Tissue-Specific Enhancers
                                                                                                                      1. Developmental Gene Cascades

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                                                                                                                  3. Eukaryotic Chromatin and Epigenetic Regulation

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                                                                                                                  5. Post-Transcriptional Regulation in Eukaryotes