Hebrews 1

1. Hebrews 1 1 God, who at sundry times and in divers manners spake in time past unto the fathers by the prophets, 2 Hath in these last days spoken unto us by his Son, whom he hath appointed heir of all things, by whom also he made the worlds;

2. Gene Regulation - Eukaryotes Timothy G. Standish, Ph. D.

3. Control Of Expression In Eukaryotes • Some of the general methods used to control expression in prokaryotes are used in eukaryotes, but nothing resembling operons is known • Eukaryotic genes are controlled individually and each gene has specific control sequences preceding the transcription start site • In addition to controlling transcription, there are additional ways in which expression can be controlled in eukaryotes

4. Eukaryotes Have Large Complex Geneomes • The human genome is about 3 x 109 base pairs or ≈ 1 m of DNA • Because humans are diploid, each nucleus contains 6 3 x 109 base pairs or ≈ 2 m of DNA • That is a lot to pack into a little nucleus!

5. Only a Subset of Genes is Expressed at any Given Time • It takes lots of energy to express genes • Thus it would be wasteful to express all genes all the time • By differential expression of genes, cells can respond to changes in the environment • Differential expression, allows cells to specialize in multicelled organisms. • Differential expression also allows organisms to develop over time.

6. Cytoplasm Nuclear pores Degradation AAAAAA AAAAAA DNA Transcription Modification RNA RNA Processing G G Degradation etc. Ribosome mRNA G AAAAAA Export Translation Nucleus Control of Gene Expression Packaging Transportation

7. Increasing cost Logical Expression Control Points The logical place to control expression is before the gene is transcribed • DNA packaging • Transcription • RNA processing • mRNA Export • mRNA masking/unmasking and/or modification • mRNA degradation • Translation • Protein modification • Protein transport • Protein degradation

8. Eukaryotic DNA Must be Packaged • Eukaryotic DNA exhibits many levels of packaging • The fundamental unit is the nucleosome, DNA wound around histone proteins • Nucleosomes arrange themselves together to form higher and higher levels of packaging.

9. Nucleosomes T Looped Domains Tight helical fiber G C A Protein scaffold B DNA Helix Packaging DNA Metaphase Chromosome

10. Highly Packaged DNA Cannot be Expressed • The most highly packaged form of DNA is “heterochromatin” • Heterochromatin cannot be transcribed, therefore expression of genes is prevented • Chromosome puffs on some insect chomosomes illustrate where active gene expression is going on

11. Eukaryotic RNA Polymerase II • RNA polymerase is a very fancy enzyme that does many tasks in conjunction with other proteins • RNA polymerase II is a protein complex of over 500 kD with more than 10 subunits:

12. Eukaryotic RNA Polymerase II Promoters • Several sequence elements spread over about 200 bp upstream from the transcription start site make up RNA Pol II promoters • Enhancers, in addition to promoters, influence the expression of genes • Eukaryotic expression control involves many more factors than control in prokaryotes • This allows much finer control of gene expression

13. Promoter T. F. RNA Pol. II T. F. RNA Pol. II mRNA 5’ Initiation T. F.

14. Eukaryotic RNA Polymerase II Promoters • Eukaryotic promoters are made up of a number of sequence elements spread over about 200 bp upstream from the transcription start site • In addition to promoters, enhancers also influence the expression of genes • Control of gene expression in eukaryotes involves many more factors than control in prokaryotes • This allows much finer control of gene expression

15. A “Simple” Eukaryotic Gene Transcription Start Site 3’ Untranslated Region 5’ Untranslated Region Introns 5’ 3’ Int. 1 Int. 2 Exon 1 Exon 2 Exon 3 Promoter/ Control Region Terminator Sequence Exons RNA Transcript

16. Exon 1 Promoter 5’ Sequence elements TATA ~200 bp Transcription start site “TATA Box” Initiator SSTATAAAASSSSSNNNNNNNNNNNNNNNNNYYCAYYYYYNN -1+1 S = C or G Y = C or T N = A, T, G or C Eukaryotic Promoters (Template strand) ~-25

17. Response Elements • Response elements are short sequences found either within about 200 bp of the transcription start site, or as part of enhancers • Different genes have different response elements • Binding of transcription factors to response elements determines which genes will be expressed in any cell type under any set of conditions

18. TFIID TBP Associated Factors (TAFs) Transcription start site InitiationTFIID Binding “TATA Box” -1+1 TATA Binding Protein (TBP)

19. 80o Bend Transcription start site InitiationTFIID Binding TFIID -1+1

20. TFIIB Transcription start site InitiationTFIIA and B Binding TFIID -1+1 TFIIA

21. TFIIB Transcription start site InitiationTFIIF and RNA Polymerase Binding TFIID -1+1 TFIIA RNA Polymerase TFIIF

22. TFIIB Transcription start site InitiationTFIIE Binding TFIIE TFIID RNA Polymerase TFIIF -1+1 TFIIA TFIIE has some helicase activity and may by involved in unwinding DNA so that transcription can start

23. TFIIH TFIIB P P P Transcription start site InitiationTFIIH and TFIIJ Binding TFIIJ TFIIE TFIID RNA Polymerase TFIIF -1+1 TFIIA TFIIH has some helicase activity and may by involved in unwinding DNA so that transcription can start

24. TFIIH TFIIB P P P Transcription start site InitiationTFIIH and TFIIJ Binding TFIIJ TFIIE TFIID TFIIF RNA Polymerase -1+1 TFIIA

25. P P P Transcription start site InitiationTFIIH and TFIIJ Binding RNA Polymerase -1+1

26. DNA 5’ 3’ Enhancer Promoter Transcribed Region 3’ 5’ TF 3’ 5’ TF TF RNA Pol. RNA Pol. RNA 5’ Enhancers Many bases TF TF TF

27. The End