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

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

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

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

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’
Exon 1
Int. 1
Exon 2
Int. 2
Exon 3
Promoter/
Control Region
Terminator
Sequence
Exons
RNA Transcript

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

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

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

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

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

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

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

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

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

27. The
End