1. GENE REGULATION Key control mechanism for dictating cell phenotype
and function

2. Two kinds of genes Housekeeping genes Regulated Genes
Needed for cell metabolism
Required for nearly all cell types
Regulated Genes
Controls cell phenotype and function

3. Housekeeping Genes Pol I transcripts Some Pol II transcripts
Ribosomal RNA genes (18S, 5.8S, and 28s rRNAs)
Some Pol II transcripts
e.g. Structural Proteins such as Actin
Pol III transcripts
5S rRNA (ribosomal RNA)
tRNAs (translation)
snRNA (splicing)

4. Regulated Genes Pol II transcripts Pol III transcripts For e.g.
Transcription factors
Cytokines
Kinases
Phosphatases
Ubiquitinases
etc., etc., etc.
Pol III transcripts
miRNAs (siRNA like molecules that inhibit specific gene expression)

5. Multiple Mechanisms of Gene Regulation
Transcription
Initiation
Elongation
Post-transcription
RNA level
RNA processing (alternative splicing, polyadenylation)
RNA transport
mRNA stability
Protein level
Translation initiation
Protein transport
Protein stability
Protein processing
Epigenetic

6. Transcription Housekeeping Regulated Pol I transcription
Ribosomal RNA genes (18S, 5.8S, and 28s rRNAs)
Pol III transcription
5S rRNA (ribosomal RNA)
tRNAs (translation)
snRNA (splicing)
miRNAs (control of gene regulation)
Regulated
Pol II transcription
Protein encoding transcripts

7. Pol I Transcription
18S, 5.8S, and 28S RNA genes transcribed as one 13 kb transcript.
This transcript is subsequently processed (cleaved) to give individual 18S, 5.8S and 28S rRNAs.
On chromosome, 13 kb transcription unit (along with a 27kb intergenic region) is repeated times
Helps provide higher expression of these housekeeping gene products.

8. Pol I Transcription
10_02.jpg

9. Pol I Promoter Function
10_03.jpg

10. Pol III Transcription
10_04.jpg

11. Pol II Transcription Three types of cis elements:
Core promoter elements (-45 to +40)
Binds basal factors required for initiation and elongation.
Proximal promoter elements (-1kb to +200)
Binds regulatory transcription factors involved in activating or suppressing basal transcription
Enhancers/Silencers (far up or downstream)

12. Pol II Transcription
10_05.jpg
Core promoter function - facilitates transcription initiation and elongation
- Pol II - Catalyzes RNA synthesis
- TFIID - Provides scaffold for general transcription factors (TBP is at core of this
complex and is associated with TAFs (TBP Associated Factors)
- TFIIB - Binds TBP, selects start site and recruits Pol II
- TFIIA - Stabilizes binding of TFIIB and TBP to promoter
- TFIIF - Binds TFIIB and Pol II
- TFIIE - Recruits TFIIH
- TFIIH - Helicase and kinase (Unwinds DNA phosphorylates C-terminus of Pol II)

13. Pol II Transcription
10_05.jpg
Proximal promoter function - regulates core promoter function
Proximal promoter binding factors activate transcription through multiple mechanisms:
- Recruit basal factors
- Recruit coactivators and mediators (for example, CBP, p300, p/caf, etc)
- helps recruit basal factors
- contain or recruit histone acetyl-transferases
- recruit histone methyl-transferases
- contain or recruit ATP dependent chromatin remodeling enzymes
- helps form stable complexes between multiple proximal transcription
factors

14. Regulation of promoter function by proximal promoter factors and enhancer/silencers
Recruitment of basal factors*
Recruitment of histone acetylases
Recruitment of histone methylases
Recruitment of ATP dependent chromatin remodeling complexes*

15. Histone modification
10_01.jpg
Histone acetylation - generally associated with promoter activation
(histone deacetyleses (HDACs) inhibit transcription
Neutralizes basic charges on lysines and arginine residues - relaxes nucleosome
Allows direct binding of activating proteins to promoter bound histones
Histone methylation
Arginine methylation associated with promoter activation
Lysine methylation associated with promoter inactivation

16. Promoter Elements Function in Either Orientation
10_07.jpg

17. Pol II Promoters Contain Multiple Transcription Factor Binding Sites
Human Insulin Promoter - red, specific for pancreatic beta cells
Reasons?
- Coactivator interactions stabilized by binding to multiple transcription factors at the
same time
- Some factors cannot carry out all steps required for promoter activation (SP1)
- Some elements play a role in signaling activation by different effectors
10_06.jpg

18. Solved DNA Interaction Motifs
10_08.jpg

19. DNA Recognition
10_09.jpg

20. Regulation of Transcription factor function
Tissue specific expression of transcription factors
Translocation of transcription factor to nucleus
Post-transcriptional modification of transcription factors

21. Steroid Hormone Receptors
10_10.jpg
- Zinc fingers
- Bind as dimers

22. Regulation of Steroid Hormone Receptors
10_11.jpg

23. Regulation of CREB
10_12.jpg

24. NF-kB Regulation
10_12_2.jpg

25. Other Mechanisms for Regulating Gene Expression
Regulation of translation
Regulation of mRNA stability
Alternative promoter usage
Alternative Splicing
Alternative polyadenylation

26. Translational Control and RNA Stability Control
10_13.jpg

27. Tissue Specific Promoter Usage
10_14.jpg
Dystrophin Gene
C - Corical
M - Muscle
P - Purkinje
R - Retinal
CNS - Central Nervous System
S - Schwann cell
G - General

28. Alternative Splicing
10_15.jpg

29. Alternative Splicing - Examples
10_16.jpg