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
08_01_same.genome.jpg

7. 08_02_genetic.instruc.jpg
08_02_genetic.instruc_Part1.jpg

8. 08_02_genetic.instruc_Part2.jpg

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 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
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

17. 05_07_base pairing.jpg
05_07_base pairing.jpg

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

20. 04_10_1_alpha h. beta s.jpg
04_10_1_alpha h. beta s.jpg

21. 04_10_2_alpha h. beta s.jpg
04_10_2_alpha h. beta s.jpg

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

23. × 08_06_single.promot.jpg operon
tryptophan
tryptophan repressor
block access of RNA polymerase
operon ×
(15 nt)
08_06_single.promot.jpg
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 (activating) (repressing)
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. 08_08_activator.prot.jpg activator
(CAP)
(cAMP)
08_08_activator.prot.jpg
marginally functional in binding and positioning RNA polymerase
that helps it initiate transcription

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

27. 08_09_lac operon.jpg
08_09_lac operon.jpg

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

29. 08_10_transcr.factors.jpg General transcription factors:
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
(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
08_10_transcr.factors.jpg
p. 277

30. 08_11_TATA-BP.jpg
TBP
08_11_TATA-BP.jpg

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

32. 08_13_gene.activation.jpg
08_13_gene.activation.jpg

33. 08_14_chromatin.struc.jpg
08_14_chromatin.struc.jpg

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

35. 08_15_Reg. proteins.jpg
08_15_Reg. proteins.jpg

36. 08_16_anterior_posteri.jpg
08_16_anterior_posteri.jpg

37. 08_17_4.gene.reg.prot.jpg
08_17_4.gene.reg.prot.jpg

38. 08_18_reporter.gene.jpg
08_18_reporter.gene.jpg

39. 08_19_eve.stripe.2.jpg
08_19_eve.stripe.2.jpg

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

41. 08_20_coord.expressio.jpg
08_20_coord.expressio.jpg

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

44. 08_21_Fibroblasts.jpg
08_21_Fibroblasts.jpg

45. 08_22_cell.types.jpg
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

47. 08_23_cell.memory.jpg
08_23_cell.memory.jpg

48. 05_28_inactivated X.jpg
05_28_inactivated X.jpg

49. 08_24_chromatin.state.jpg
08_24_chromatin.state.jpg

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

51. 08_25_eye.on.leg.jpg
08_25_eye.on.leg.jpg