Chapter 7 Regulation of Eukaryotic Gene Expression

1. Chapter 7Regulation of Eukaryotic Gene Expression

2. 7.1 Multilevel Eukaryotic Gene Regulation 1. The types of regulation in eukaryotes2. Gene structure of eukaryotes 3. Features of Eukaryotic Genomes 4. Multi-level of gene expression and regulation

3. 7.2 Gene Regulation at DNA Level Chromatin Remodeling 1. Changes of DNA Topo structure Formation of ssDNA DNase I hypersensitive site

4. 2. DNA Methylation DNA Methylation

5.  CpG islands ----- are genomic regions that contain a high frequency of CG dinucleotides. ----- CpG islands particularly occur at or near the transcription start site of housekeeping genes.

6. TF RNA pol Unmethylated CpG island TF RNA pol CH3 CH3 CH3 Methylated CpG island Active transcription Repressed transcription

7. Housekeeping gene-A gene involved in basic functions is required for the sustenance of the cell. Housekeeping genes are constitutively expressed Luxury gene - are those coding for specialized functions synthesized (usually) in large amounts in particular cell types.

8. TF 3. Histone modification  methylation  acetylation

9. 4. Changes of nucleosome High Mobility Group (HMG) Protein • non-histone chromatin proteins • high mobility in PAGE • soluble in 2-5% TCA • small < 30 kDa • high content of charged amino acids: Asp, Glu

10. 5. Other gene regulation at DNA Level (1) Gene Deletion (2) Gene Duplication (3) DNA Rearrangement (4) Gene Amplification (5) Chemical Activator (6) Environmental Activator

11. 7.3 Transcriptional Regulation 1. Cis-acting element (1) What is cis-acting element?  Concept Cis-acting elements - DNA sequences close to a gene that are required for gene expression

12. Features of cis-acting elements (1) Promoter Core promoter  in eukaryote: TATA-box, Initiator (Inr)  in prokaryote: -10 region, Inr

13. Proximal elements of promoter  in prokaryote: -35 region  in eukaryote: CAAT-box, GC-box UPE: upstream promoter element UAS: upstream activating sequence (2) Terminator A DNA sequence just downstream of the coding segment of a gene, which is recognized by RNA polymerase as a signal to stop transcription.

14. (3) Enhancer A regulatory DNA sequence that greatly enhances the transcription of a gene. (4) Silencer A DNA sequence that helps to reduce or shut off the expression of a nearby gene.

15. Animation

16. (5) Insulators

17. No transcription

18. 2. What is trans-acting factor?  Concept trans-acting factors - usually they are proteins, that bind to the cis-acting elements to control gene expression.

19. These trans-acting factors can control gene expression in several ways: may be expressed in a specific tissue may be expressed at specific time in development may be required for protein modification may be activated by ligand binding

20. (1) RNA polymerase prokaryotic RNA Pol eukaryotic RNA Pol (2) Transcription factors  Basal/general TFs  Specific TFs

21. (3) Domains of trans-acting factors  DNA binding domain DBD DNA结合结构域  transcription activating domain 转录活化结构域

22. a. HTH (helix-turn-helix) α-helix (N-terminus)----specific α-helix (C-terminus)----non-specific

23. b. homeodomain --60 aa long DNA binding protein motif α-helix 1 α-helix 2 α-helix 3 ---- DNA major groove

24. helix turn helix motif: binds to DNA

25. c. Leu zipper

27. d. Zinc finger

28. GAL4 SP1

29. e. Helix-loop-helix

31. f. Bromodomain g. Chromodomain Ribbon diagram of the GCN5 bromodomain from Saccharomyces cerevisiae

32. Transcription Activation Domains 􀂄  Acidic domains 􀂄  Glutamine-rich domains 􀂄  Proline-rich domains

33. 7.4 Post-Transcriptional Regulation 1. Gene Regulation of mRNA Processing exon shuffling alternative gene splicing

34. 2. Gene Regulation of mRNA Editing • 3. mRNA Longevity • mRNA Transport Control • RNA Interference (RNAi) • miRNA • siRNA

35. The left petunia is wild-type; the right petunias contain transgenes that induce suppression of both transgene and endogenous gene expression, giving rise to the unpigmented white areas of the flower.

36. RNA沉默(RNA silencing)是普遍存在于植物、动物(RNAi)和真菌(quelling)等真核生物细胞中的一种抵抗外源遗传因子(病毒、转座子或转基因)及调控基因表达的防御机制，可特异而高效的降解靶mRNA，以保持生物体自身基因组的完整和稳定。

38. 7.5 Translational and Post-translational Regulation 1. Translation Control Blocking mRNA Attachment to Ribosomes 2. Regulation of Protein Processing Protein Modification

39. Amino acid residus phosphorylated  Ser/Thr type  Tyr type  Catalysis Features of Actions Reversible Integrated signals from different pathways effectively  The same kind kinase or phosphatase is multible-substrates. modified different amino acids, different influences

40. 3. Regulation of Protein Stability

41. 1. Features of Cancer Cells 7.6 Gene Regulation & Cancer

42. 2. Causes of Cancer: Viruses Tobacco smoke Food Radiation Chemicals Pollution

43. 3. Proto-oncogene & Oncogene  Proto-oncogene - is a normal gene that can become an oncogene due to mutations or increased expression.  Oncogene - is a protein encoding gene, which - when deregulated - participates in the onset and development of cancer. Tumour suppressor gene - or antioncogene is a gene that protects a cell from being cancer.

44. ① ② ③ ③ ⑤ ⑤ ④ ④ ⑥

45. 4. Proto-oncogene activation

46. 5. p53 and cancer It can activate DNA repair proteins when DNA has sustained damage.  It can also hold the cell cycle at the G1/S regulation point on DNA damage recognition  It can initiate apoptosis, the programmed cell death, if the DNA damage proves to be irreparable.

48. Summary 1. Genomic structure of eukaryotes 2. Regulation levels of eukaryotic gene expression. 3. Regulation at DNA level 4. Regulation at transcritional level 5. Transcriptional regulation 6. The mechanism of RNAi 7. Translational and post-translational regulation: 8. Protein phosphorylation and its mechanism

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