GCD 3022 1st Edition Lecture 21 Outline of Last Lecture I Introduction a Gene regulation b Unregulated genes c Benefit of regulating genes II Overview of transcriptional regulation a Timing of regulation in bacteria b Regulatory proteins i Repressors ii Activators c Negative and positive control d Effector molecules i Inducers ii Corepressors iii Inhibitors III Regulation of the lac operon a Operon b Transcriptional units i lac operon These notes represent a detailed interpretation of the professor s lecture GradeBuddy is best used as a supplement to your own notes not as a substitute 1 DNA elements 2 Structural genes ii lacI gene c Regulation by a repressor protein i Transcriptional regulation ii Inducible negative control d lacI gene experiment i problem ii set up iii hypothesis iv conclusion Outline of Current Lecture I Introduction a Eukaryotes and gene regulation b Necessity of gene regulation II Transcriptional Factors a General Transcription factors b Regulatory Transcription factors i Control elements ii Activators and repressors iii Enhancers and silencers c Combinatorial control i Common factors that contribute to combinatorial control d Structural features of regulatory transcription factors i Domains ii Motifs e Variation in regulatory transcription factor functions i Three main functions f Steroid receptors i Action of steroid hormones ii Response of the cell to steroid hormones 1 Glucocorticoids 2 Gonadocorticoids g CREB protein i Mechanism ii cAMP response element CRE III Chromatin remodeling and histones a Purpose b Structure of chromatin i Closed conformation ii Open conformation iii Nucleosomes c ATP dependent chromatin remodeling d Histones i 5 histone genes ii Humane histone genes iii Specialized chromatin e Histone code i Modification of histones in mammals ii Protein recognition and binding IV DNA methylation a DNA methylation in eukaryotes b CpG islands i Housekeeping genes ii Tissue specific genes c Heritability V Insulators a Purpose b Mechanism Current Lecture I Introduction a Eukaryotes and gene regulation allows eukaryotes to respond to environmental changes and nutrient availability Multicellularity and complexity demand a high level of gene regulation doma b Necessity of gene regulation ensures expression of genes in an accurate pattern during the various developmental stages of the life cycle and differences among distinct cell types II Transcriptional Factors regulate gene transcription in initiation and elongation phases a General Transcription factors required for binding of RNA polymerase to the core promoter and its progression to the elongation stage Necessary for basal transcription b Regulatory Transcription factors regulate transcription of target genes by influencing the ability of RNA polymerase to begin transcription of a particular gene i Control elements regulatory transcription factors that recognize cis regulatory elements located near the core promoter Also called regulatory elements or regulatory sequences ii Activators and repressors regulatory proteins that increase or decrease the rate of transcription by binding to control elements iii Enhancers and silencers bind to activators cause up regulation of transcription and repressors cause down regulation of transcription Orientation dependent bidirectional they can function in the forward or reverse orientation Most are located within a few hundred nucleotides upstream of the promoter although some are found thousands of nucleotides away downstream from the promoter or within introns c Combinatorial control eukaryotic genes are regulated to many factors Various combinations can contribute to the regulation of a single gene i Common factors that contribute to combinatorial control one or more activator proteins can stimulate transcription or inhibit transcription Activators and repressors can also be regulated as can nucleosomes near the promoter DNA methylation is another factor that can contribute to combinatorial control d Structural features of regulatory transcription factors i Domains regions in transcription factor proteins that have specific functions ex DNA binding effector molecule binding etc ii Motifs domain or portion of a domain that has a very similar structure in many different proteins e Variation in regulatory transcription factor functions i Three main functions binding of a small effector molecule proteinprotein interactions and covalent modification f Steroid receptors regulatory transcription factors that respond to steroid hormones i Action of steroid hormones ultimate action is to affect gene transcription Produced by endocrine glands and released into the bloodstream to travel to target cells ii Response of the cell to steroid hormones cells respond differently to steroid hormones 1 Glucocorticoids promote glucose utilization fat mobilization and protein breakdown 2 Gonadocorticoids influence growth and function of gonads include estrogen and testosterone g CREB protein cAMP response element binding i Mechanism CREB protein becomes activated in response to cell signaling molecules that cause an increase in cytoplasmic concentration of cAMP cyclic adenosine monophosphate ii cAMP response element CRE consensus sequence that is recognized by the CREB protein Sequence is 5 TGACGTCA 3 III Chromatin remodeling and histones a Purpose used to regulate transcription Carried out by diverse multi protein machines that reposition and restructure nucleosomes b Structure of chromatin 3 D packing of chromatin is important to gene expression i Closed conformation chromatin is tightly packed no transcription can take place or is at least difficult ii Open conformation when chromatin is accessible to transcription factors iii Nucleosomes can change position due to chromatin remodeling c ATP dependent chromatin remodeling when the energy of ATP hydrolysis is used to drive change in location and or composition of nucleosomes Makes the DNA more or less amenable to transcription d Histones i 5 histone genes H1 H2A H2B H3 and H4 ii Human histone genes human genome contains over 70 histone genes Most encode standard histones and a few have accumulated mutations that changes the amino acid sequence called histone variants iii Specialized chromatin some histone variants are incorporated into a subset of nucleosomes to create specialized chromatin e Histone code i Modification of histones in mammals over 50 enzymes have been identified in mammals that selectively modify the amino