Biochemistry Sixth Edition Chapter 31 The Control of Gene Expression Part II: Eukaryotes (cis vs. trans) Copyright © 2007 by W. H. Freeman and Company Berg Tymoczko Stryer

Transcriptional regulation: prokaryotes vs. eukaryotes Greater complexity of genomes E coliyeast human One Mb Mb Mb 2000 proteins600025,000 Chromosome Size Eukaryotes: * Different cell types * No operons * nuleosome/chromatin structure

RNA polymerase II promoter: 3 common elements Mutagenesis exp’ts, footprinting, and sequence comparisons Initiator element (-3 ~ +5) Downstream core promoter element (+28 ~ +32)

Combinatorial control !!

DNA: proteins  ionic interaction

* Sequence-specific * Promoter-proximal or enhancer sites (conserved recognition seq.) * motifs? Initiates txn by interacting with RNA pol II & co. Prevents DNA binding Homo-dimer or hetero-dimer

Activation domains recruit: * Proteins that promote transcription (co-factors) * RNA pol. II * ex. intermediary proteins (ex. mediator)

25-30 subunits

Activation domains: * Less conserved than DNA-binding (acidic, hydrophobic, Q-rich, P-rich) 1.Redundant 2.Modular 3.Act synergistically

Homo-dimer or hetero-dimer

Prevents (or regulate) DNA binding

Steroid hormone system of gene expression *cholesterol derived *hydrophobic molecules *membrane permeable *bind to nuclear receptors & progesterone

Steroid hormone system of gene expression Nuclear hormone receptors: *large protein family (>50 in human) *binds signaling molecule (or “ligand”) *binds specific DNA sites with consensus sequence -> gene expression *modular domains

Ligand binding induces conformational change However, DNA binding is not altered

Coactivator recruitment by estrogen receptor Coactivator modifies chromatin structure

Steroid-hormone receptors are drug targets Agonists: molecules that bind receptor and trigger signaling pathway Anabolic steroids

Antagonists: molecules that bind receptor and do not trigger signaling pathway -> competitive inhibitors SERMs: selective estrogen receptor modulators -> treatment of breast cancer

Binding but no conformation changes: *blocking coactivator recruitment *inhibiting gene expression

Enhancers: * No promoter activity * Increase txn * Long range  Binding sites for cell type-specific regulatory proteins  Regulation through chromatin structure (not directly on pol.)

Enhancer of muscle-specific enzyme  non-muscle gene

 -galactosidase activity can be monitored by X-Gal Application: reporter assay TA cloning