Differential Gene Expression

1. Differential Gene Expression Turning Genes on or keeping them off?

2. Differential Gene Regulation • Transcriptional regulation • Post-transcriptional regulation • Translational regulation • Post-translational regulation

3. Transcriptional Post-transcriptional Translational Post-translational Transcription factor binding Transcription factor interactions Methylation Nucleosome/chromatin structure Differential Gene Expression

4. Splicing Polyadenylation Stability Transcriptional Post-transcriptional Translational Post-translational Differential Gene Expression

5. Masking Antisense RNA Transcriptional Post-transcriptional Translational Post-translational Differential Gene Expression

6. Glycosylation Acylation Proteolytic processing Transcriptional Post-transcriptional Translational Post-translational Differential Gene Expression

7. Differential Gene Regulation • Hierarchies of transcriptional regulatory proteins • Transcription Factors • Regulators of regulators

8. Transcription Initiation

9. Transcriptional Activation

10. Transcription Control Elements • Promoter • Basal elements (sites) • TATAA box • CCAAT box • GC boxes • Orientation and position dependent • Enhancer • Any combination of transcription factor binding sites • Orientation and position independent • Silencer • Binding site for proteins which make DNA inaccessible to txn factors

11. Transcription Factors • Basal/General Txn Factors • TFIID • TBP - TATA binding protein • TAFs – TBP associated factors • CBP – CCAAT binding protein • SP1 – GGCGGG binding protein • Give a low level of txn • Often found as the only txn control elements of housekeeping genes

12. Gene Specific Txn Factors Classified by DNA binding domains & mechanism of transcriptional activation Transcription Factors

13. Family Representative Homeodomain Hox Hoxa-1, Antp, eve, en POU Pit-1,Unc-86, Oct-2, Brn-5 LIM Lim-1, Isl-1 Paired Box Pax-1,2,6, Prd Forkhead/Winged Helix Fkh, HNF-3 MADS box MEF-1, MCM-1 Basic-helix-loop-helix MyoD, Ac, da, emc Basic leucine-zipper AP1, Myc, C/EBP Zinc-finger standard WT-1, Krox-20, Kr, hb steroid receptors GR, ER, RAR, kni Sox Sry, SoxD, Sox2 Transcription Factor Flavors

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15. Physical Arrangement of Regulatory Elements

16. Cell-Type Specific Transcription • Tissue specificity • Promoter • Enhancer • Tissue specific txn factor and cognizant DNA element (site)

17. Epigenetic Gene Regulation

18. Differential Gene Expression Via Posttranscriptional Regulation Alternative or Differential Splicing

19. Differential Splicing • Differential splicing requires cell-type specific splicing factors • Often one spliced mRNA does not encode a functional protein • When both alternative mRNAs encode functional proteins, one protein typically lacks an entire functional domain

20. Differential Splicing Sex Determination in Drosophila Regulated by Differential Splicing

21. Differential Splicing & Sex Boys Girls

23. 3’ UTR Mediates Stability or Instability U-Rich 3’UTR mediates degradation of

24. Regulation of mRNA Stability

25. RNA masking and Polyadenylation • Factors bind to stored mRNA and prevent translation • smaug protein binds nanos mRNA • mRNAs not polyadenylated • deadenylated transcripts stable in oocyte • Adenylation of transcript allows translation

26. Antisense RNA Regulates Translation Lin-4 RNA is complementary to several regions of lin-14 3’ UTR Formation of dsRNA prevents translation of lin-14