1. MCB 317 Genetics and Genomics MCB 317 Topic 10, part 4 A Story of Transcription

2. Deletion and Linker Scanner Analysis In vitro Txn Assay Promoter sufficient in vitro Identification of Enhancers Identify and define TBP and basal factors Extract + Prom.-Enh. Basal Facts. + Prom.-Enh. Activated Txn (Enhanced) & Regulated Txn Extract + Prom.-Enh. Activators Co-activators + Enhancer & TBP & TAFs Promoter “Activated” txn & Regulated txn In vivo Txn Assay Promoter not Sufficient

3. Co-activators and Chromatin Remodeling Complexes

4. Co-activators & chromatin remodeling complexes not shown

5. How could we have missed Co-activators and Chromatin Remodelling Complexes for 20+ years? How to study what’s going on and what’s important in vivo?

6. Purify Polymerases Immuno-affinity Purification, Mass Spec Mediator In vitro “chromatin” Assembly Genetic Screens In vitro txn of in vitro “chromatin” Coactivators Chromatin Remodeling Complexes “Histone” Biochemistry Activators

7. Strength of Genetics as a Tool Strength of Genetics: Is a Gene Important in vivo? Limitation of biochemistry: Does an in vitro assay recapitulate the entire in vivo process?

8. Concept: Comprehensive view of a molecular process requires both Genetics and Biochemistry

9. Genetic Screens (Yeast mostly) Coactivators Chromatin Remodeling Complexes Basal Factors Activators Mediator RNAP II

10. Purify Polymerases Immuno-affinity Purification, Mass Spec Mediator In vitro “chromatin” Assembly Genetic Screens In vitro txn of in vitro “chromatin” Coactivators Chromatin Remodeling Complexes “Histone” Biochemistry Activators

14. Coding RegionPrUAS Enzyme involved in sucrose metabolism

15. Coding RegionPrUAS Enzyme involved in sucrose metabolism

17. Genetic Screens: Primary screen and initial characterization of mutants 1. Screen for mutants 2. Phenotype due to a single mutation? 3. Dominant or Recessive? 4. Complementation tests

18. Our snf- screen = many complementation groups = many genes snf1 snf2 snf3 snf4 snf5 snf6 snf7 snf8….. Which, if any encode txn factors? Secondary screen to identify possible txn factors

19. Genetic Screens: Primary screen Secondary screen(s)

20. SUC2 encodes an enzyme that metabolizes sucrose. SUC2 txn is induced in response to sucrose Transform Reporter into each of our mutant strains: snf1-, snf2-, snf3-, snf4-, snf5-, snf6-, etc. Three key complementation groups identified: SNF2, SNF5 and GCN5

22. Raise antibodies to Snf2 and Snf5 proteins and use them to purify the native proteins from wild-type yeast cells Snf2 and Snf5 are part of the same large protein complex

23. Nuclease Protection Assay = variation on footprinting that provides information on where histones bind and on which bases and strands of the DNA faces outward on the nucleosome surface and which face inward

27. Purify Polymerases Immuno-affinity Purification, Mass Spec Mediator In vitro “chromatin” Assembly Genetic Screens In vitro txn of in vitro “chromatin” Coactivators Chromatin Remodeling Complexes “Histone” Biochemistry Activators

28. Back to GCN5

29. Continuing Concept: Comprehensive view of a molecular process requires both Genetics and Biochemistry

30. Histone Modification Histone Code

33. Lodish 11-32 UAS = Upstream Activation Site = Yeast Enhancer Gcn4 is an Activator Gcn5 is a subunit of a co-activator (SAGA) that has histone acetylase activity

34. Activators One function of activators is to act as a “platform” that recruits (binds) Co-activators

35. Purify Polymerases Immuno-affinity Purification, Mass Spec Mediator In vitro “chromatin” Assembly Genetic Screens In vitro txn of in vitro “chromatin” Coactivators Chromatin Remodeling Complexes “Histone” Biochemistry Activators

36. How could we have missed Co-activators and Chromatin Remodelling Complexes for 20+ years? How to study what’s going on and what’s important in vivo?

39. Purify Polymerases Immuno-affinity Purification, Mass Spec Mediator In vitro “chromatin” Assembly Genetic Screens In vitro txn of in vitro “chromatin” Coactivators Chromatin Remodeling Complexes “Histone” Biochemistry Activators