1. Gene Expression Expression of different set of genes in each cell type

2. Steps For Regulating Gene Expression Transcriptional control is most common

3. Components For Regulating Transcription Short DNA segments of defined sequence Gene regulatory proteins that bind to a specific sequence Gene regulatory protein

4. Specific Binding of Gene Regulatory Proteins Structural motifs recognize specific DNA sequences Amino acids interact with outside of bases

5. Trp Operon Multiple genes transcribed as one mRNA molecule Transcribed from a single promoter

6. Regulation Of Tryptophan Operon On only when tryptophan is absent Negative regulation by tryptophan repressor Repressor is active only when tryptophan is bound to it

7. Regulation Of Lac Operon On only when lactose is present and glucose is absent Positive regulation by CAP in response to glucose Negative regulation by lac repressor in response to lactose

8. Transcriptional Control Region Of Eucaryotic Gene Multiple binding sites for gene regulatory proteins Regulatory sequences known as enhancers can be thousands of nucleotides from promoter

9. Eucaryotic Gene Activator Proteins Recruitment of RNA polymerase II holoenzyme complex Assembly of general transcription factors Alterations in chromatin structure Can facilitate: General function:promote assembly of RNA polymerase II and general transcription factors at the promoter to allow transcription to begin

10. Recruitment Of RNA Polymerase II Holoenzyme Gene activators attract holoenzyme complex to promoter

11. Assembly Of General Transcription Factors Gene activators promote assembly of some general transcription factors

12. Alterations In Chromatin Structure Recruitment of histone modifying proteins, histone chaperones, and chromatin remodeling complexes Can make chromatin more accessible to transcription machinery

13. Histone Code Proteins recognize specific patterns of histone modification Acetylation promotes activation Methylation: some residues promote activation some residues promote repression

14. An example of writing and reading the histone code

15. Gene Repressor Proteins

16. TFs in Human Genome 1962 estimated (8% of genome) Gene regulatory proteins, general transcription factors, coactivators, corepressors, chromatin and histone modifiers Common structural classes of gene regulatory proteins Zinc finger (762) Homeobox (199) Basic helix-loop-helix (117) Beta-scaffold (87) Basic-leucine zipper (72) Nuclear hormone receptor (49) Forkhead (40) Ets (31)

17. Examples of TF Classes Zinc fingerBasic helix-loop-helix Classes have common motif for DNA binding Differences within a class determine specificity

18. Regulating Activity Of Gene Regulatory Proteins Modulates pattern of gene expression in response to cell’s environment

19. DNA Methylation Methylation of C at certain CG Pattern maintained by maintenance methyl transferases

20. Effect Of DNA Methylation Reinforce inactivation of genes that are not expressed

21. Genomic Imprinting Expression of few genes occurs only from paternal or maternal allele Methylation pattern established in germ cells and maintained in offspring

22. CG Islands CG Methyl group Many CG lost during vertebrate evolution due to accidental deamination, inefficient repair of methylated CG found at inactive DNA in germ cells Promoters of active (often housekeeping) genes in germ cells not methylated, deamination repaired accurately, preserved as CG islands CG dinucleotides deficient, preferentially found at promoters of many genes

23. Epigenetic Mechanisms Epigenetic inheritance- daughter cells maintain memory of gene expression pattern of parent cells Histone modifications, DNA methylation, and positive feedback loops contribute to epigenetic inheritance

24. Epigenetic Mechanisms Histone reader-writers that recognize same histone modification they catalyze Gene regulatory proteins that activate their own expression

25. Coordinating Gene Expression Decisive event within combinatorial control Single gene regulatory protein can be decisive, can control set

26. Generate Specialized Cell Types Myogenic helix-loop-helix proteins (MyoD, etc.) and skeletal muscle Trigger becoming muscle cell Muscle-specific expression Coordinately activate muscle genes Specific for muscle genes

27. Transcription Attenuation Coupled to translation Depends upon levels of tryptophan Attenuation of trp operon:

28. Alternative Splicing Alternative choices for certain splice sites in primary RNA transcript

29. Regulation Of Alternative Splicing Splicing decision controlled by regulatory protein that binds primary RNA transcript

30. Regulation Of RNA Cleavage In Antibody Genes First cleavage site encountered is suboptimal and skipped in unstimulated cells Antigen stimulation increases CstF levels to promote cleavage at first site

31. RNA Editing A to I editing ADAR recognizes RNA structure C to U editing ApoB example

32. HIV Genome Several products through alternative splicing Some have introns that normally cannot be exported

33. Regulation Of Nuclear Export Of HIV RNA Rev directs export of viral RNAs that contain introns Rev levels sufficient to promote export late in infection

34. Gene Silencing by microRNAs miRNAs are dsRNAs processed from hairpin precursors miRNA complex binds 3’ UTR of mRNA targets Translation repression / mRNA degradation

35. Translational Repressors Bind specific sequences in 5’ or 3’ UTR of RNA

36. Phosphorylation Of eIF-2 Activation of specific protein kinases Reduction of overall protein synthesis by inhibiting eIF-2B-mediated exchange of GDP→GTP on eIF-2

37. Regulation Of Translation In Reticulocytes Globin translation coordinated with Heme levels HRI phosphorylates eIF-2 HRI active in absence of heme, inactive in presence of heme

38. Mechanisms Of mRNA Decay Deadenylation-dependent- gradual polyA shortening followed by rapid degradation Deadenylation-independent- endonucleolytic removal of polyA

39. Iron-Mediated Post- Transcriptional Regulation Protein that binds to ferritin & transferrin receptor mRNAs Disassociates from RNA when bound to iron Blocks translation when bound to 5’ UTR of ferritin mRNA Stabilizes mRNA when bound to 3’ UTR of transferrin receptor Aconitase: