Lecture 16: Regulation of Gene Expression PDF

Lecture 16 Regulation of gene expression I Reading: ECB6 243-247 &277-286 Learning objectives: Understand that gene expression can be regulated at many different levels Understand the concept of promoter Understand that transcriptio...

Lecture 16 Regulation of gene expression I Reading: ECB6 243-247 &277-286 Learning objectives: Understand that gene expression can be regulated at many different levels Understand the concept of promoter Understand that transcriptional regulators are DNA binding proteins that can act as activators or repressors Understand how the Lac operon is regulated in bacteria Appreciate the complexity of homeodomain transcription factor eukaryotic transcriptional binding to DNA regulation Understand Login now to https://pollev.com/biomg1350fall24 the definition of Cell-cell communication in animal development is mediated by only a small number of conserved cell-cell signaling pathways, including Transforming growth factor-ß (TGFß) Wnt Hedgehog (Hh) Notch Receptor tyrosine kinase (RTKs) … Yet, there is enormous cell diversity in animals The same inductive signal can generate different responses Sequential induction  How is gene expression regulated? Ectoderm Mesoderm Endoderm The genome is constant in all somatic cells. Only a fraction of the genome is expressed in any cell type Each cell type expresses a different combination of genes Thousands of genes turn on and off at each step of commitment Differential gene expression makes cells different Gene expression: the process by which the information encoded in a DNA sequence is translated into a product that has some effect on a cell or  Gene expression can be controlled at many levels posttranscriptional controls relatively slow acting most energy efficient most common control point for long term fast acting regulation readily reversible Figure 8-3 ECB5  Gene expression can be controlled at many levels posttranscriptional controls most common control point in development Figure 8-3 ECB5  Transcription Figure 7-6 Essential Cell Biology  Elements of prokaryotic transcriptional regulation caryotes served as useful model systems to derstand regulation of gene expression  The role of promoters in prokaryotic transcriptional regulation upstream downstream a promoter contains sequences recognized and bound by RNA polymerase is located upstream of the transcription start site Figure 7-9 ECB5  Elements of prokaryotic transcriptional regulation promoters vary in their strength of binding to RNA polymerase promoter activity is enhanced by transcriptional activators promoter activity is inhibited by transcriptional repressors activators and repressors can act in concert to Figure 7-9 ECB5 provide highly sensitive transcriptional regulation  Transcriptional regulators (activators and repressors) are proteins that have DNA binding domains The DNA binding domain of a transcription factor binds a stretch of unique DNA sequences Different DNA binding domains can bind to different DNA sequences, allowing for specificity Figure 8-5 Essential Cell Biology 5 Lecture 16 Homeodomain transcription factor binding to DNA  The Lac operon provides a simple example of gene regulation by transcriptional activators and repressors RNA start of transcription CAP- polymera bindin se g site binding site LacZ LacY LacA (promote r) operator mRNA An operon = a cluster of bacterial genes hat can be transcribed from a single promoter Figure 8-9 ECB5 modified  Transcription of the Lac operon genes allow E. coli to utilize lactose when glucose is absent RNA start of transcription CAP- polymera bindin se g site binding site LacZ LacY LacA (promote r) operator mRNA E. coli use glucose as an energy source but enzymes for if there is no glucose available, they can lactose utilization get it by breaking down lactose ß-galactoside (disaccharide of glucose and galactose). E. coli wants to express Lac genes only lactose glucose + galactose when: Figure 8-9 ECB5 modified  Transcription of the Lac operon genes allow E. coli to utilize lactose when glucose is absent RNA start of transcription CAP- polymera bindin se g site binding site LacZ LacY LacA (promote r) operator Lac genes glucose only off lactose only on glucose & lactose Figure 8-9 ECB4 off  Lac repressor inhibits transcription when lactose is not present - LACTOSE allolactose is a metabolite of allolactose lactose; its levels reflect Inhibiting lactose levels repressor binding + LACTOSE is not sufficient to allow transcription because the promoter is weak Figure 8-9 ECB5  CAP activates transcription when glucose is not present + GLUCOSE when glucose levels are low, cAMP levels go up CAP activator - GLUCOSE helps to recruit RNA polymerase to the promoter Figure 8-9 ECB5  An activator and a repressor work together to regulate the Lac operon Figure 8-9 ECB5  Regulation of eukaryotic transcription is complex Eukaryotic cells contain three distinct RNA polymerases: I, II, III. We will focus on RNA Pol II which transcribes all mRNAs. The promoter contains a TATA Box bound by the TATA Box Binding Protein or TBP, which helps recruit general transcription factors (GTFs) This results in RNA Pol II recruitment at the promoter, which opens up the DNA double helix in preparation for transcription GTF TBP TATA Box RNA Pol II ut this is still not enough to start transcription!  TATA-binding protein Animation 7.4 ECB5 Regulation of eukaryotic transcription is complex Eukaryotic cells contain three distinct RNA polymerases: I, II, III. We will focus on RNA Pol II which transcribes all mRNAs. The promoter contains a TATA Box bound by the TATA Box Binding Protein or TBP, which helps recruit general transcription factors (GTFs) This results in RNA Pol II recruitment at the promoter, which opens-up the DNA double helix in preparation for transcription GTF TBP TATA Box RNA Pol II But this is still not enough to start transcription! Eukaryotic DNA regulatory elements and transcription activators act at a distance Enhancers: are regulatory DNA sequences that function to allow the transcription of a given gene bind activator proteins can be located either upstream or downstream of the gene they regulate can be located either close to or far away (up to tens of thousands of nucleotides) from the transcription start site Allows regulation of gene express Figure 8-10 ECB5 in the context of chromatin DNA looping and protein-protein interaction allows the activators to help RNA polymerase initiate transcription promoter Mediator A 24-subunit complex that serves as an intermediary between transcription regulators and RNA DNA looping polymerase. Enhancer function confers Figure 8-10 Essential Cell Biology 4e gene and cell type  Shh (sonic hedgehog) regulates anterior-posterior patterning of the limb by acting as a morphogen Shh (sonic hedgehog) mRNA in the chick limb bud Expression of Shh in the limb is controlled by a limb-specific enhancer  A single base pair change that causes ectopic expression of Shh in the limb results in digit duplication in mouse (hemimelic-extra toes) This G to A change is located 1x106 base pair away from the Shh start codon (ATG)! The Shh limb enhancer is conserved in mouse, human and fish, but not in limbless reptiles From Kvon et al (2016) Cell ZRS enhancer = Shh limb enhancer 167: 633  Testing the function of the Shh limb enhancers in mouse Substitute the mouse Make the snake enhancer with the enhancer more like the snake enhancer human enhancer Loss of the limb enhancer for Shh is associated with the loss of limb in advanced snakes re about patterning and gene expression Lecture 20 and Section 10 From Kvon et al (2016) Cell Why do we need such complexity of gene expression regulation in multicellular organisms? Enhancers, others More about gene expression regulation in lecture 17