gene regulation eukaryotes

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


TFIID

“TATA Box”

TBP Associated Factors (TAFs)

TATA Binding Protein (TBP)

InitiationTFIID Binding

TFIID

80o Bend-1+1


InitiationTFIIA and B Binding

TFIID

TFIIA

-1+1


TFIIB

InitiationTFIIF and RNA Polymerase Binding

TFIID

TFIIA

-1+1


TFIIB

RNA PolymeraseTFIIF

InitiationTFIIE Binding

TFIID

TFIIA

-1+1


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



TFIIE

TFIIH has some helicase activity and may by involved in unwinding DNA so that transcription can start

TFIIH

P PP

TFIIJ


TFIID

TFIIA

-1+1



TFIIETFIIH

P PP

TFIIJ


-1+1


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

gene regulation eukaryotes

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