more regulating gene expression

1. more regulating gene expression

2. We looked at the mechanisms of gene expression, now we will look at its regulation. Combinations of 3 nucleotides code for each 1 amino acid in a protein.

3. Gene Expression is controlled at all of these steps: • DNA packaging • Transcription • RNA processing and transport • RNA degradation • Translation • Post-translational Fig 15.1 Fig 16.1

4. Gene Expression is controlled at all of these steps: • DNA packaging • Transcription • RNA processing and transport • RNA degradation • Translation • Post-translational Fig 15.1 Fig 16.1

5. Eukaryotic transcription must be activated by binding of transcription factors Fig 12.14

6. Mutations in the promoter show critical nucleotides

7. Fig 15.12 Enhancers are regulatory regions located some distance away from the promoter

8. Proteins that help bend DNA can play an important role in transcription Fig 15.12

9. Fig 15.12 DNA bends to bring different areas in to close contact.

10. How do eukaryotic cells jointly express several proteins (without operons)?

11. Promoter sequences where transcription factors can bind activating multiple gene in response to the environment

12. Fig 12.13 Promoters typically have several regulatory sequences

13. Steroid response element

14. Fig 15.6 • Steroids bind to receptors/transcription factors inside cell • get translocated to the nucleus • bind to promoters andactivate transcription. cytoplasm

15. Gene Expression is controlled at all of these steps: • DNA packaging • Transcription • RNA processing and transport • RNA degradation • Translation • Post-translational Fig 15.1 Fig 16.1

16. Fig 23.25 Alternate Splicing in Drosophila Sex Determination

17. Fig 23.25 Alternate splicing leads to sex determination in fruit flies

18. Mammalian mRNA Splice-Isoform Selection Is Tightly Controlled • Jennifer L. Chisa and David T. Burke • Genetics, Vol. 175: 1079-1087, March 2007 • Regulation of gene expression is often in response to a changing environment. • But how stable can alternative splicing be, and does it play a role in maintaining homeostasis?

19. Alternative splicing modifies at least half of all primary mRNA transcripts in mammals. • More than one alternative splice isoform can be maintained concurrently in the steady state mRNA pool of a single tissue or cell type, and changes in the ratios of isoforms have been associated with physiological variation and susceptibility to disease. • Splice isoforms with opposing functions can be generated; for example, different isoforms of Bcl-x have pro-apoptotic and anti-apoptotic function. Chisa, J. L. et al. Genetics 2007;175:1079-1087 Fig. 1

20. Alternatively spliced versions of different genes were identified Chisa, J. L. et al. Genetics 2007;175:1079-1087 Fig. 1

21. variation in splice-isoform ratios is conserved in two genetically diverse mouse populations Black= genetically heterogeneous population UMHET3 Red= a population of hybrid females Chisa, J. L. et al. Genetics 2007;175:1079-1087 Fig. 4

22. In different individuals splice isoforms in different tissues are conserved Chisa, J. L. et al. Genetics 2007;175:1079-1087 Fig. 5

23. Conclusions: • Alternate splicing for some genes is tightly regulated between different individuals. • Slight differences in alternative splicing may be indicative of abnormalities (disease).

24. mRNA transport is an important regulatory step Molecular Biology of the Cell 4th ed. Alberts et al. Fig 6.40 http://www.ncbi.nlm.nih.gov/books/bv.fcgi?rid=mboc4.TOC&depth=2

25. mRNA can be localized to a specific parts of a cell (from Drosophila embryo) Molecular Biology of the Cell 4th ed. Alberts et al. Fig 7.52 http://www.ncbi.nlm.nih.gov/books/bv.fcgi?rid=mboc4.TOC&depth=2

26. At least 3 mechanisms are involved: Molecular Biology of the Cell 4th ed. Alberts et al. Fig 7.98 Directed transport via cytoskeleton Random diffusion and trapping Degradation and local protection

27. A processed mRNA ready for translation 5’ untranslatedregion 3’ untranslatedregion Protects from degradation/ recognition for ribosome Protects from degradation/ transport to cytoplasm

28. mRNA with 3’ UTR properly localized mRNA without 3’ UTR improperly localized Molecular Biology of the Cell 4th ed. Alberts et al. Fig 7.99 http://www.ncbi.nlm.nih.gov/books/bv.fcgi?rid=mboc4.TOC&depth=2

29. Gene Expression is controlled at all of these steps: • DNA packaging • Transcription • RNA processing and transport • RNA degradation • Translation • Post-translational Fig 15.1 Fig 16.1

30. Seeds germinated underground begin growing in darkness then emerge into light and begin photosynthesis energy from seed energy from sun

31. The level of this mRNA increases after plants are exposed to light. • How might the cell accomplish this?

32. The level of this mRNA increases after plants are exposed to light. • How might the cell accomplish this?Increased transcription and/or decreased mRNA degradation

33. Northern blot analysis: The level of this mRNA increases after plants are exposed to light. • How might the cell accomplish this? • Does this necessarily lead to increased protein production?

34. Gene Expression is controlled at all of these steps: • DNA packaging • Transcription • RNA processing and transport • RNA degradation • Translation • Post-translational Fig 15.1 Fig 16.1

35. Fig 15.25 Regulation of iron assimilation in mammals: Regulating of Translation

36. Fig 15.26 Ferritin is regulated at translation

37. C. elegans is commonly used to study development

38. C. elegans development

39. C. elegans mutants with cells that do not develop properly.

40. C. elegans mutants with cells that do not develop properly. The product of these genes was found to be RNA?

41. MicroRNAs (miRNA) are ~22nt RNAs that play important regulatory roles Cell vol. 116, 281-297 2004

42. miRNA expressed How do microRNAs control gene expression? miRNA processed to ~22nt RNA Mature miRNA Fig 15.23 and

43. A processed mRNA ready for translation: microRNAs inhibit translation by binding to the 3’ end of mRNA microRNA bind to 3’-UTR 5’-UTR 3’-UTR

44. miRNA expressed the 3’ end with attached microRNA interacts with the 5’ end, blocking translation miRNA processed to ~22nt RNA Mature miRNA Fig 15.23 and

45. miRNAs can lead to methylation of DNA that leads to inhibition of transcription

46. microRNAs primarily target gene products that function during development Tbl 1

47. tissue specific expression of mouse microRNA PNAS vol. 101 #1 pg 360-365, 2004

48. Silencing RNAs (siRNA) are artificially induced dsRNA Fig 15.21

49. siRNA with exact matches to the target mRNA causes degradation of the mRNA

50. microRNA siRNA mRNA degraded Translation inhibited