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GENE REGULATION
Key control mechanism for dictating cell phenotype
and function
Two kinds of genes
• Housekeeping genes
 Needed for cell metabolism
• Required for nearly all cell types
• Regulated Genes
 Controls cell phenotype and function
Housekeeping Genes
• Pol I 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)
Regulated Genes
• Pol II transcripts
 For e.g.
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Transcription factors
Cytokines
Kinases
Phosphatases
Ubiquitinases
etc., etc., etc.
• Pol III transcripts
• miRNAs (siRNA like molecules that inhibit specific gene
expression)
Multiple Mechanisms of Gene
Regulation
• Transcription
• Initiation
• Elongation
• Post-transcription
 RNA level
• RNA processing (alternative splicing, polyadenylation)
• RNA transport
• mRNA stability
 Protein level
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Translation initiation
Protein transport
Protein stability
Protein processing
• Epigenetic
Transcription
• Housekeeping
 Pol I transcription
• Ribosomal RNA genes (18S, 5.8S, and 28s rRNAs)
 Pol III transcription
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5S rRNA (ribosomal RNA)
tRNAs (translation)
snRNA (splicing)
miRNAs (control of gene regulation)
• Regulated
 Pol II transcription
• Protein encoding transcripts
Pol I Transcription
• 18S, 5.8S, and 28S RNA genes transcribed as
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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 30-40
times
 Helps provide higher expression of these
housekeeping gene products.
Pol I Transcription
Pol I Promoter Function
Pol III Transcription
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)
• Binds regulatory transcription factors involved in activating or
suppressing basal transcription
Pol II Transcription
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)
Pol II Transcription
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
Regulation of promoter function by proximal promoter
factors and enhancer/silencers
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Recruitment of basal factors*
Recruitment of histone acetylases
Recruitment of histone methylases
Recruitment of ATP dependent chromatin remodeling
complexes*
Histone modification
- 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
Promoter Elements Function in Either Orientation
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
Solved DNA Interaction Motifs
DNA Recognition
Regulation of Transcription factor function
• Tissue specific expression of transcription factors
• Translocation of transcription factor to nucleus
• Post-transcriptional modification of transcription factors
Steroid Hormone Receptors
- Zinc fingers
- Bind as dimers
Regulation of Steroid Hormone Receptors
Regulation of CREB
NF-kB Regulation
Other Mechanisms for Regulating Gene
Expression
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Regulation of translation
Regulation of mRNA stability
Alternative promoter usage
Alternative Splicing
Alternative polyadenylation
Translational Control and RNA Stability
Control
Tissue Specific Promoter Usage
Dystrophin Gene
C - Corical
M - Muscle
P - Purkinje
R - Retinal
CNS - Central Nervous System
S - Schwann cell
G - General
Alternative Splicing
Alternative Splicing - Examples