Control of Gene Expression

1. Control of Gene Expression ECB Ch 8

2. An overview of gene expression • The different cell types of a multicellular organism contain the same DNA • Different cell types produce different sets of proteins • A cell can change the expression of its genes in response to external signals • Gene expression can be regulated at many of the steps in the pathway from DNA to RNA to protein

3. How transcriptional switches work • Transcription is controlled by proteins binding to regulatory DNA sequences • Repressor turn genes off, activators turn them on • An activator and a repressor control the lac operon • Initiation of eucaryotic gene transcription is a complex process • Eucaryotic RNA polymerase requires general transcription factors • Eucaryotic gene regulatory proteins control gene expression from a distance • Packing of promoter DNA into nucleosomes can affect initiation of transcription

4. The molecular mechanisms that create specialized cell types • Eucaryotic genes are regulated by combinations of proteins • The expression of different genes can be coordinated by a single protein • Combinatorial control can create different cell types • Stable patterns of gene expression can be transmitted to daughter cells • The formation of an entire organ can be triggered by a single gene regulatory protein

5. An overview of gene expression • The different cell types of a multicellular organism contain the same DNA • Different cell types produce different sets of proteins • A cell can change the expression of its genes in response to external signals • Gene expression can be regulated at many of the steps in the pathway from DNA to RNA to protein

6. 08_01_same.genome.jpg

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9. Different cell types produce different sets of proteins • ex: hemoglobin is made only in reticulocytes, but it cannot be detected in any other cell type • housekeeping proteins: • proteins are common to all the cells of a multicellular organism • ex: structural proteins of chromosomes, RNA polymerases, DNA repair enzymes, ribosomal proteins, enzymes involved in glycolysis and other basic metabolic process, … • reveal by • two-dimensional gel electrophoresis • or detecting the expressions of mRNA • at any one time, a typical differentiated human cell expresses perhaps 10000-20000 genes from a repertoire of about 30000

10. A cell can change the expression of its genes in response to external signals • most of the specialized cells in a multicellular organism are capable of altering their patterns of gene expression in response to extracellular cues • different cell types often respond in different ways to the same extracellular signal • ex: glucocorticoid hormone stimulation: • in liver cell: to increase the production of glucose from amino acids and other small molecules (ex: tyrosine aminotransferase ↑) • fat cells: (ex: tyrosine aminotransferase ↓) • some other cells: no response * glucocorticoids are released in the body during periods of starvation or intense exercise

11. Gene expression can be regulated at many of the steps in the pathway from DNA to RNA to protein

12. A cell can control the proteins it makes by • controlling when and how often a given gene is transcribed (DNA level) • controlling how the primary RNA transcript is spliced or otherwise processed (RNA level) • selecting which mRNAs are translated by ribosomes (RNA level) • selectively activating or inactivating proteins after they have been made (protein level)

13. 08_03_control.steps.jpg main site of control

14. How transcriptional switches work • promoter • both in bacteria and eucaryotic genes, including: • an initiation site (transcription actually begins) • a RNA polymerase binding site (a sequence of ~50 nt upstream from the initiation site) • in addition to the promoter, nearly all genes, have regulatory DNA sequences that are used to switch the gene on or off

15. How transcriptional switches work (gene regulatory proteins) • transcription is controlled by proteins binding to regulatory DNA sequences; repressor turn genes off, activators turn them on • an activator and a repressor control the lac operon • initiation of eucaryotic gene transcription is a complex process • eucaryotic RNA polymerase requires general transcription factors • eucaryotic gene regulatory proteins control gene expression from a distance • packing of promoter DNA into nucleosomes can affect initiation of transcription (Text book p271)

16. How transcriptional switches work • gene regulatory proteins-the proteins specialized for switching genes on and off • gene regulation in higher organisms, combined with the packaging of their DNA into chromatin

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18. 05_08_major_minor_gr.jpg 10 base per helical turn Energetically favorable

19. 08_04_gene.reg.prot.jpg protein α helix In most cases, gene regulatory proteins inserts into the major groove of the DNA helix Frequently, DNA-binding proteins bind in pairs (dimers) to the DNA ※P271 the last two paragraphs

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22. DNA-binding motifs 08_05_binding motifs.jpg homeodomain (a member of the helix-turn-helix family) helix 3 contacts with DNA bases leucine zipper (two α helix) zinc finger (α helix-Zn-β sheet)

23. 08_06_single.promot.jpg tryptophan block access of RNA polymerase tryptophan repressor operon × (15 nt) operon: a set of genes that is transcribed into a single mRNA operons are common in bacteria but are not found in eucaryotes

24. 08_07_repress.protein.jpg (repressing) (activating) tryptophan repressor is an allosteric protein in cells, the tryptophan repressor gene is continuously transcribed at a low level, a small amount of the repressor protein is always present (constitutive gene expression: unregulated gene expression, p274)

25. activator 08_08_activator.prot.jpg (CAP) (cAMP) marginally functional in binding and positioning RNA polymerase that helps it initiate transcription

26. β-galctosidase • Encodes by lac operon Lactose galactose+glucose β-galctosidase

27. 08_09_lac operon.jpg

28. Bacteria contain a single type of RNA polymerase *Regulation of transcription in eucaryotes vs. in bacteria, p276

29. 25 nt • General transcription factors: • position the RNA polymerase correctly at the promoter • aid in pulling apart the two strands of DNA to allow transcription to begin • allow RNA polymerase to leave the promoter as transcription begins 08_10_transcr.factors.jpg (bind TATA box) partly unwind DNA as a landmark pry apart the double helix phosphorylate RNA polymerase II: (relase general transcription factors) Transcription initiation complex: general transcription factors+RNApol II p. 277

30. 08_11_TATA-BP.jpg TBP

31. 08_12_Phosphoryltn.jpg Phosphorylation of RNApol II allows RNA-processing proteins to assemble

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34. Eucaryotic genes are regulated by combinations of proteins • Combinatorial control

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40. The expression of different genes can be coordinated by a single protein • Coordinate gene expression in bacteria: operon • Coordinate gene expression in eucaryotes: a committee of regulatory proteins • Expression of different genes coordinated by a single protein • The final number of combination locks • glucocorticoid receptor protein

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42. Combinatorial control can create different cell types • Expression of different genes coordinated by a single protein useful in • The day-to-day regulation of cell function • One of the means by which eucaryotic cells differentiation into particular types of cells during embryonic development • Ex: mammalian skeletal muscle cell Formed by the fusion of many muscle precursor cells: myoblasts

43. mammalian skeletal muscle cell • Formed by the fusion of many muscle precursor cells: myoblasts • Production a large number of characteristic proteins • Fibroblasts from skin connective tissue ↓ MyoD • Start to behave like Myoblast ↓ • Fuse to form musclelike cells

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45. 08_22_cell.types.jpg

46. Stable patterns of gene expression can be transmitted to daughter cells • Remember and pass on • Positive feedback loop • Ex: MyoD gene regulatory protein • Condensed chromatin structure • Ex: X chromosome

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50. The formation of an entire organ can be triggered by a single gene regulatory protein • Ey (in flies), Pax-6 (in vertebrates): a single gene regulatory protein for eye development