Plant Molecular Biology

  1. Gene Expression and Its Regulation
    1. Transcription
      1. RNA Polymerases in Plants
        1. RNA Polymerase I
          1. rRNA Transcription
            1. Nucleolar Localization
            2. RNA Polymerase II
              1. mRNA Transcription
                1. Promoter Recognition
                2. RNA Polymerase III
                  1. tRNA and 5S rRNA Transcription
                  2. RNA Polymerase IV
                    1. Silencing Pathway
                    2. RNA Polymerase V
                      1. Transcriptional Silencing
                    3. Promoter Elements and Structure
                      1. Core Promoter Elements
                        1. TATA Box
                          1. Initiator Elements
                            1. CAAT Box
                            2. Proximal Regulatory Elements
                              1. Upstream Activating Sequences
                                1. Repressor Binding Sites
                                2. Distal Regulatory Elements
                                  1. Enhancers
                                    1. Silencers
                                  2. Transcription Factors
                                    1. Major Transcription Factor Families
                                      1. MADS-box Family
                                        1. bZIP Family
                                          1. MYB Family
                                            1. AP2/ERF Family
                                              1. NAC Family
                                                1. WRKY Family
                                                  1. bHLH Family
                                                    1. Homeodomain Proteins
                                                    2. DNA-Binding Domains
                                                      1. Helix-Turn-Helix
                                                        1. Zinc Fingers
                                                          1. Leucine Zippers
                                                          2. Transcriptional Activation and Repression
                                                            1. Activation Domains
                                                              1. Repression Domains
                                                              2. Combinatorial Control
                                                                1. Cooperative Binding
                                                                  1. Competitive Binding
                                                                  2. Post-Translational Regulation
                                                                    1. Phosphorylation
                                                                      1. Protein-Protein Interactions
                                                                    2. Transcriptional Regulation Mechanisms
                                                                      1. Chromatin-Level Regulation
                                                                        1. Promoter-Specific Regulation
                                                                          1. Long-Range Regulation
                                                                        2. Post-Transcriptional Processing and Regulation
                                                                          1. 5' Capping
                                                                            1. Capping Enzymes
                                                                              1. Cap Structure
                                                                                1. Role in mRNA Stability
                                                                                  1. Role in Translation Initiation
                                                                                  2. 3' End Processing
                                                                                    1. Polyadenylation Signals
                                                                                      1. Cleavage and Polyadenylation
                                                                                        1. Poly(A) Tail Function
                                                                                        2. Pre-mRNA Splicing
                                                                                          1. Spliceosome Assembly
                                                                                            1. U1 snRNP
                                                                                              1. U2 snRNP
                                                                                                1. U4/U6•U5 tri-snRNP
                                                                                                2. Splicing Signals
                                                                                                  1. 5' Splice Site
                                                                                                    1. 3' Splice Site
                                                                                                      1. Branch Point
                                                                                                      2. Alternative Splicing
                                                                                                        1. Exon Skipping
                                                                                                          1. Intron Retention
                                                                                                            1. Alternative 5' and 3' Sites
                                                                                                              1. Mutually Exclusive Exons
                                                                                                                1. Functional Consequences
                                                                                                              2. mRNA Quality Control
                                                                                                                1. Nonsense-Mediated Decay
                                                                                                                  1. No-Go Decay
                                                                                                                    1. Non-Stop Decay
                                                                                                                    2. mRNA Stability and Turnover
                                                                                                                      1. Deadenylation
                                                                                                                        1. Decapping
                                                                                                                          1. 5' to 3' Degradation
                                                                                                                            1. 3' to 5' Degradation
                                                                                                                              1. RNA-Binding Proteins
                                                                                                                              2. mRNA Transport and Localization
                                                                                                                                1. Nuclear Export
                                                                                                                                  1. Export Factors
                                                                                                                                    1. Nuclear Pores
                                                                                                                                    2. Cytoplasmic Localization
                                                                                                                                      1. Localization Signals
                                                                                                                                        1. Transport Machinery
                                                                                                                                    3. Translation
                                                                                                                                      1. Ribosome Structure and Function
                                                                                                                                        1. Ribosomal RNA
                                                                                                                                          1. Ribosomal Proteins
                                                                                                                                            1. Ribosome Assembly
                                                                                                                                              1. Polysome Formation
                                                                                                                                              2. Translation Initiation
                                                                                                                                                1. Initiation Factors
                                                                                                                                                  1. Start Codon Recognition
                                                                                                                                                    1. Ribosome Binding
                                                                                                                                                    2. Translation Elongation
                                                                                                                                                      1. Elongation Factors
                                                                                                                                                        1. Peptide Bond Formation
                                                                                                                                                          1. Translocation
                                                                                                                                                          2. Translation Termination
                                                                                                                                                            1. Stop Codon Recognition
                                                                                                                                                              1. Release Factors
                                                                                                                                                                1. Ribosome Recycling
                                                                                                                                                                2. Translational Regulation
                                                                                                                                                                  1. Upstream Open Reading Frames
                                                                                                                                                                    1. Internal Ribosome Entry Sites
                                                                                                                                                                      1. Ribosome Profiling
                                                                                                                                                                        1. Small RNA Regulation
                                                                                                                                                                      2. Post-Translational Modifications
                                                                                                                                                                        1. Protein Folding and Quality Control
                                                                                                                                                                          1. Molecular Chaperones
                                                                                                                                                                            1. Heat Shock Proteins
                                                                                                                                                                              1. Chaperonins
                                                                                                                                                                              2. Protein Disulfide Isomerases
                                                                                                                                                                                1. Unfolded Protein Response
                                                                                                                                                                                2. Proteolytic Processing
                                                                                                                                                                                  1. Signal Peptide Cleavage
                                                                                                                                                                                    1. Propeptide Removal
                                                                                                                                                                                      1. Protein Maturation
                                                                                                                                                                                      2. Chemical Modifications
                                                                                                                                                                                        1. Glycosylation
                                                                                                                                                                                          1. N-linked Glycosylation
                                                                                                                                                                                            1. O-linked Glycosylation
                                                                                                                                                                                            2. Phosphorylation
                                                                                                                                                                                              1. Protein Kinases
                                                                                                                                                                                                1. Protein Phosphatases
                                                                                                                                                                                                  1. Signal Transduction
                                                                                                                                                                                                  2. Acetylation
                                                                                                                                                                                                    1. Methylation
                                                                                                                                                                                                      1. SUMOylation
                                                                                                                                                                                                      2. Protein Degradation
                                                                                                                                                                                                        1. Ubiquitin-Proteasome System
                                                                                                                                                                                                          1. Ubiquitin Conjugation
                                                                                                                                                                                                            1. 26S Proteasome
                                                                                                                                                                                                            2. Autophagy
                                                                                                                                                                                                              1. Vacuolar Degradation
                                                                                                                                                                                                            3. Small RNA Pathways
                                                                                                                                                                                                              1. MicroRNAs
                                                                                                                                                                                                                1. Biogenesis Pathway
                                                                                                                                                                                                                  1. Transcription
                                                                                                                                                                                                                    1. Processing by Dicer
                                                                                                                                                                                                                    2. Target Recognition
                                                                                                                                                                                                                      1. Gene Silencing Mechanisms
                                                                                                                                                                                                                      2. Small Interfering RNAs
                                                                                                                                                                                                                        1. Biogenesis
                                                                                                                                                                                                                          1. Transposon Silencing
                                                                                                                                                                                                                            1. Antiviral Defense
                                                                                                                                                                                                                            2. RNA-Induced Silencing Complex
                                                                                                                                                                                                                              1. RISC Assembly
                                                                                                                                                                                                                                1. Argonaute Proteins
                                                                                                                                                                                                                                  1. Target Cleavage
                                                                                                                                                                                                                                  2. Long Non-Coding RNAs
                                                                                                                                                                                                                                    1. Regulatory Functions
                                                                                                                                                                                                                                      1. Chromatin Modification

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                                                                                                                                                                                                                                  4. Molecular Basis of Plant Physiology