Gene Regulation
Gene Regulation
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
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!
Only a Subset of Genes is Expressed at any Given Time
It takes lots of energy to express genesThus it would be wasteful to express all
genes all the timeBy 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.
DNA
Cytoplasm
NucleusG AAAAAA
Export
Degradation etc.G AAAAAA
Control of Gene Expression
G AAAAAA
RNAProcessing
mRNA
RNA
Transcription
Nuclear pores
Ribosome
Translation
Packaging
ModificationTransportation
Degradation
Logical Expression Control Points
DNA packagingTranscriptionRNA processingmRNA ExportmRNA masking/unmasking
and/or modification mRNA degradationTranslationProtein modificationProtein transportProtein degradation
Increasing cost
The logical
place to control
expression is
before the gene
is transcrib
ed
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.
Packaging DNAPackaging DNA
G
C
A
T
Protein scaffold
Metaphase Chromosome
Looped Domains
Nucleosomes
B DNA Helix
Tight helical fiber
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
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:
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
RNA Pol. II
Initiation
T. F.
RNA Pol. II
5’mRNA
Promoter
T. F.
T. F.
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
A “Simple” Eukaryotic Gene
Terminator Sequence
Promoter/Control Region
Transcription Start Site
3’5’
RNA Transcript
Introns
Exon 2 Exon 3Int. 2Exon 1 Int. 1
3’ Untranslated Region5’ Untranslated Region
Exons
Eukaryotic Promoters
5’ Exon 1Promoter
Sequence elements
~200 bp
TATA
~-25
Initiator“TATA Box”
Transcription start site
(Template strand) -1+1SSTATAAAASSSSSNNNNNNNNNNNNNNNNNYYCAYYYYYNN
S = C or G Y = C or T N = A, T, G or C
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
InitiationTFIID Binding
-1+1
Transcription start site
TFIID
“TATA Box”
TBP Associated Factors (TAFs)
TATA Binding Protein (TBP)
InitiationTFIID Binding
TFIID
80o Bend-1+1
Transcription start site
InitiationTFIIA and B Binding
TFIID
TFIIA
-1+1
Transcription start site
TFIIB
InitiationTFIIF and RNA Polymerase Binding
TFIID
TFIIA
-1+1
Transcription start site
TFIIB
RNA PolymeraseTFIIF
InitiationTFIIE Binding
TFIID
TFIIA
-1+1
Transcription start site
RNA PolymeraseTFIIBTFIIF
TFIIE
TFIIE has some helicase activity and may by involved in unwinding DNA so that transcription can start
InitiationTFIIH and TFIIJ Binding
TFIID
TFIIA
-1+1
Transcription start site
RNA PolymeraseTFIIBTFIIF
TFIIE
TFIIH has some helicase activity and may by involved in unwinding DNA so that transcription can start
TFIIH
P PP
TFIIJ
InitiationTFIIH and TFIIJ Binding
TFIID
TFIIA
-1+1
Transcription start site
RNA PolymeraseTFIIBTFIIF
TFIIETFIIH
P PP
TFIIJ
InitiationTFIIH and TFIIJ Binding
-1+1
Transcription start site
RNA PolymeraseP P
P
5’DNA
3’
Enhancers
Enhancer Transcribed Region
3’5’ TF TFTF
3’5’ TF TFTF
5’ RNA
RNAPol.
RNAPol.
Many bases
Promoter