Download 17. Gene regulation

BIOL 311 Human Genetics
Fall 2006
Lecture: Regulation of Gene Expression
Reading: Chap. 10
Lecture outline:
1. Levels of control
2. Histone modification
3. RNA polymerase II transcription
4. Transcription factors
5. Steroid receptors
6. Alternate promoters and alternate splicing
7. Epigenetic mechanisms
Lecture:
1. Levels of control of gene expression
transcriptional control
 control determines whether or not transcription is initiated
 requires promoter of gene
 transcription factors bind to promoter and recruit RNA polymerase to initiate
transcription
post-transcriptional regulation of gene expression
 control after pre-mRNA synthesis
 can involve control of RNA processing, mRNA transport, translation, mRNA
stability, protein processing, protein targeting, protein stability
epigenetic mechanisms
 changes that are heritable, but not due to changes in the order of bases on DNA
 main mechanism is DNA methylation. Methylation represses gene expression
and determines which allele of a gene is expressed for certain genes
(immunoglobulin genes, genes on X-chromosome, etc.)
2. Histone modification
 histones are basic proteins that help compact DNA
 act as generalized repressors of transcription
 dense packed chromatin: transcriptionally inactive
 to open up the chromatin structure, chemical groups are added to histones to make
conditions more favorable for transcription
Histone acetylation:
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Add acetyl group to epsilon-NH2 group of lysines on histone H3 and H4. Acetylation
reduces the positive charge of histone side chains.
HATs
Histone ---------- acetylated histone
-------HDACs (histone deacetylases)
Many other types of modifications of histones occur: methylation, phosphorylation,
ubiquitination, ADP-ribosylation.
Fig. 10.1 Some histone modifications shown; "histone code"
3. RNA polymerase II transcription
Eukaryotes have different RNA polymerases to transcribe different categories of gene.
rRNA genes: RNA polymerase I transcribes 18S, 5.8S, 28S rRNA genes
tRNAs, 5S rRNA, some snRNAs: transcribed by RNA polymerase III
protein coding genes and some snRNAs: transcribed by RNA polymerase II
RNA polymerase II
12 subunits catalyzes RNA synthesis
associates with about 40 other subunits that are transcription factors
TFIID: TATA binding protein
Also TFIIB, A, F, E, H
4. Transcription factors


basal transcription factors: proteins that assist transcription in many tissues
tissue-specific transcription factors: proteins only present in certain tissues that
enhance or repress transcription


bind DNA
may activate transcription directly or bind to other proteins (coactivators) that
activate transcription
transcription factors often have conserved domains that mediate protein
interactions

DNA binding domains
 Zinc fingers, Fig. 10.6 cys2his2 type and cys4 type
 Homeodomain (helix-turn-helix) Fig. 10.8
 Helix-loop-helix Fig. 10.8
Protein interaction domain
 Leucine zipper
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Activation domains--more difficult to define
 Glutamine rich
 Proline rich
5. Steroid receptors
Respond to small molecules (ligands) in environment
Fig. 10.10
Ligand
Glucocorticoids
Estrogen
Thyroid hormone
Vitamin D
Retinoic acid
Receptor
GR
ER
TR
VDR
RAR
Have similar DNA binding domains: cys4 zinc fingers
Ligand binding activates receptor
Recognition sites on DNA are similar
Receptor--ligand interactions mostly occur in the cytoplasm
Other transcription factors mediate environmental responses
Chemical signal
cAMP
Serum growth factor
Phorbol esters
Transcription factor
CREB/ATF
SRF=serum response factor
AP-1 (dimer of fos/jun)
Transcription factors often carry out the final stage of activation, triggered by an
environmental signal.
Signal + receptor  cell signaling (i.e. kinase cascade) activate transcription factor
moves to nucleus to activate gene expression.
6. Alternate promoters and alternate splicing
human genome project
 ~35,000 human genes initial predictions were for 80,000-100,000
 why the discrepancy?
 Single gene can have:
multiple transcription start sites (some genes)
alternate splicing (many genes): when different selections of exons are used in making
different mRNAs from the same gene
Example of multiple promoters:
 Dystrophin gene
79 exons/2.4 Mb/Xp21 location
 Altered in two forms of muscular dystrophy
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

Duchenne's MD: severe form, usually due to large deletions in gene
Becker's MD: milder form, usually due to small mutations in gene



At least 7 distinct promoters for dystrophin gene
Active in different tissues
First three promoters when used produce large transcript encoding 427 kDa
protein
Alternate splicing and alternate poly(A) addition sites produce many different premRNAs encoding different proteins.
Various alternate splicing scenarios: Fig. 10.15
Alternate splicing of Wilms tumor protein
 Wilms tumor=kidney tumor
 WT1 gene altered in some inherited kidney cancers
 Single gene encodes 24 isoforms
o Three possible start codons
o RNA editing in exon 6: some RNA bases altered in pre-mRNA
o Alternative splicing
 Produces isoforms with different functions
DsCam: Drosophila gene with 38,000 possible isoforms
7. Epigenetic mechanisms
Heritable states which do not depend on DNA sequences
Examples:
 DNA methylation
 Chromatin remodeling
 Histone modification
Fig. 10.18
Mechanism of DNA methylation
 CpG target sequence
 Keep the same pattern of methylation as DNA is replicated and passed on
Why is DNA methylated?
 Protect from transposons? NO
 Regulate gene expression
 Generally silences gene expression
 Recruits HDAC  leads to deactylation of histone, helping to shut off gene
expression
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