1. Chapter 11 Molecular Mechanisms of Gene regulation Jones and Bartlett Publishers © 2005

2. Outline of topics Transcriptional regulation in eukaryotes Epigenetics Regulation through RNA processing and decay Translational control Programmed DNA rearrangements

3. Transcriptional Enhancers (Silencers – opposite of enhancers)

4. Deletion scanning

6. Transcriptional activation by recruitment (DNA looping)

7. Transcription factors: TFIIB, TFIID, TFIIE, TFIIF, TFIIH, PolII, and TFIIA. TFIID contains a TATA box-binding protein (TBP) 10 TAFs- TBP-associated factors PolII RNA polymerase- 12 subunits PolII holoenzyme- PolII RNA polymerase plus most basal transcription factors. Basal transcription factors

8. Transcriptional activation in Drosophila development

9. Chromatin remodeling complexes Purified chromatin + components of transcription don’t result in transcription. CRCs: SWI-SNF, RSC (remodels the structure of chromatin), NURF (nucleosome remodeling factor), CHRAC (chromatin accessibility complex, and ACF (ATP-dependent chromatin assembly and remodeling factor). CRCs are part of PolII holoenzyme.

10. Chromatin remodeling complexes

11. How are genes regulated during different stages of development in an organism? –Use of alternative promoter

12. Alternative promoters

13. CG doublets can be methylated. 5-methylcytosine can make up 2-7% of C in vertebrate DNA and up to 30% of plant DNA. Both Cs in the CG doublet are methylated. Maintenance methylase preserves this. Epigenetic methods of transcriptional regulation

17. Transcriptional cosuppression Inserted gene copies can result in transcriptional silencing. Chalcone synthase gene in petunia. Methylation is involved here. Drosophila have no methylation (no DNA methylase), but still have transcriptional silencing.

18. Genomic Imprinting Imprinting occurs in the germ line. Affects a few hundred genes, in clusters. Heavy methylation is involved. Imprinted genes are methylated differently in female and male germ lines. Once imprinted and methylated, a silenced gene remains transcriptionally inactive during embryogenesis. Imprints are erased early in germ-line development, then re-established according to sex- specific pattern.

19. Some human diseases are due to loss of sites involved in genomic imprinting

20. Alternative splicing of the primary transcript

21. Regulation through RNA processing and decay Alternative splicing mRNA stability (poly-A tail is trimmed) Posttranscriptional cosuppression RNA interference: a few hundred pairs of double stranded RNA triggers RNA transcript degradation. –RISC (RNA-induced silencing complex) –Plus 21- or 22-mer oligonucleotides (chopped dsRNA) as templates to recognize complementary sequences.

22. Anti-sense RNA

23. Structure of an immunoglobulin G (IgG) molecule

24. The distribution of variable, joining and constant sequences which are spliced to create many different light chain proteins

25. Antibody diversity in humans

26. Mating type switching during the life cycle of some strains of Saccharomyces

27. Both mating type genes are located on chromosome III of Saccharomyces. The mating type of the cell is determined by the sequence present at the MAT site

28. Regulation of a-specific,  -specific and haploid-specific genes in Saccharomyces Three proteins (a1,  1 and  2) are involved in regulating the expression of these 3 classes of genes.