Main Ideas - Gene txn is regulated on many levels!- DNA modifications, histone modifications, specific DNA sequences and transcription factors that bind them!- DNA sequences that influence txn are: core promoter, proximal promoter sequences, and distal promoter sequences (incl. enhancers and silencers)!- Transcription factors contain one or more DNA binding motfi (e.g. helix-turn-helix)!- Gene regulation can be negative (repressor) or positive (activator)!- Examples of prokaryotic gene regulation: Lac operon and tryptophan repressor!- Transcription factors themselves are regulated by different mechanisms!- One transcription factor can control a set of genes!- Combinatorial gene control creates different cell types ! Lecture Objectives 1) Understand main principles of how regulatory proteins control gene transcription 2) Describe the different DNA binding motifs in transcription factors 3) Explain mechanisms of gene activator and gene repressor proteins in prokaryotes and eukaryotes 4) Describe how transcription factors are regulated 5) Understand the described examples of how gene expression can be coordinated 1) Understand main principles of how regulatory proteins control gene transcription - Different cell types contain the same set of genes..but show large diffs in gene expression!- This is because diff. cell types synthesize diff. sets of proteins!- Gene expression in a cell change due to: developmental stage, differentiation, and external stimuli!- Gene txn regulated by:!- Modifications on chromatin: histone and DNA mods!- Specific DNA sequence and transcription factors !- Core promoter sequences: needed for an gene to transcribe. TATA box, INR, BRE, DPE, bound by GTFs - Proximal promotor sequences: CAAT box, GC box, bound by activators - Distal promoter sequences (regulatory elements) - enhancer sequences= binds activators - silencer sequences= binds repressors - insulators= DNA stretch that prevents a gene from being influenced by activation/repression its neighbords 2) Describe the different DNA binding motifs in transcription factors - Gene reg. proteins read DNA on the outside of the DNA double helix--there is a recognition code in the major groove of DNA!- Gene regulatory proteins recognize specific DNA sequences!- Diff. DNA binding motifs once they recognize these sequences.!- also: homeodomain fold, beta sheet, and peptide loop!!- helix-turn-helix motif - zinc finger motif - leucine zipper !!!!!!!!!!!! 3) Explain mechanisms of gene activator and gene repressor proteins in prokaryotes and eukaryotes - Proks have genetic switches Ex. in E. coli= the tryptophan repressor. Genes to make tryptophan are all right next to each other---one gene transcript for all these proteins and its contrlled by an operator= an operon. Euks can't do this.!- Tryptophan repressor (HTH motif)!- operator (above) can be bound by a tryptophan repressor. Repressor can't bind to DNA by itself-->once it binds tryptophan (ligand here) it undergoes a conformational change and can bind the DNA operator-->blocks transcription-->genes are off. Reg. by the gene product of that region.!- if TRP levels are LOW: TRP operon is ON - if TRP levels are HIGH: TRP operon is OFF!- Negative and positive gene regulation - lac operon produces proteins that can break down and utilize lactose in the cell!- fave. sugar of bacteria= glucose!- thus you don't want lac operon on all the time!- Regulators: Lac repressor and CAP (activator protein) - High glucose--> low cAMP - Operon is on when there is low glucose and high lactose! cAMP is bound and repressor is not bound. !- Genetic switches in euks are much more complicated, involve longer DNA stretches, more regulatory proteins, more DNA looping, dozens of signals converge on one promoter--> much morefine tuning of gene expression Eukaryotic Transcriptional Regulation - Several general transcription factors are required!- No operons, each gene= reg. individ!- Euk genes are controlled by a combo of a very large # of diff. regulatory proteins!- Mediator= 24 subunit commplex that mediates communication beween txn factors and RNA polymerases!- Chromatin offers many opportunities for txn regulation - Gene activator proteins= bind to DNA seqs called Enhancers. Have 2 domains: DNA binding and activation domain!- goal= attract, position, and modify the GTFs, RNA pol, or Mediator!- can also alter chromatin structure by recruiting chromatin remodeling complex or histone modifying enzymes!- many diff. orders of events that can lead to txn initiation!- Gene repressor proteins= can either compete for the same site as an activator or mask the surface/get in the way/block the activator, move GTFs out of reach, recruit deactylases !- Each transcription factor can either be a repressor or an activator based on context (who else is present?) and location! 4) Describe how transcription factors are regulated - Aka how any protein can be regulated!!!!!!!!!5) Understand the described examples of how gene expression can be coordinated - one txn factor can coordinate the expression of different genes!- this makes sure that all the components in the pathway will be there at the same time!- Ex. Drosophila Ey gene expressed in leg precursor
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