James 4:7 7 Submit yourselves therefore to God. Resist the devil, and he will flee from you

©2000 Timothy G. Standish

James 4:7

7 Submit yourselves therefore to God. Resist the devil, and he will flee from you.


Regulation of Regulation of TranscriptionTranscription

Timothy G. Standish, Ph. D.


Eukaryotic RNA Polymerase II Eukaryotic RNA Polymerase II PromotersPromoters

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


Eukaryotic PromotersEukaryotic Promoters

5’ Exon 1Promoter

~200 bp

TATA

Sequence elements

Some sequence elements are also response elements


Response ElementsResponse 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


Heat Shock Response Heat Shock Response ElementsElements

Sudden changes in the temperature of cells cause stress in response to which heat shock genes are expressed

At least some heat shock genes are thought to be chaperones that help proteins fold correctly

Heat shock genes have Heat Shock Elements (HSEs) in their control regions

Heat Shock Transcription Factors (HSTFs) bind the HSEs up regulating expression of heat shock gene products


The Heat Shock ResponseThe Heat Shock Response

HSTFHot

Cool

Kinase

Heat shock genes

Heat shock response elements



HSTFHot

Cool

KinaseActivation of kinase

Phosphorylation of HSTF





Hot

Cool

Kinase

Activation of HSTF

HSTF

Transcription initiation of all heat shock genes

with HSEs


Metallothionein RegulationMetallothionein Regulation Heat shock protein regulation illustrates how a group

of genes can be regulated by a single transcription factor

Other genes are regulated by a group of transcription factors which allows them to either respond to multiple separate situations, or respond only to a specific combination of situations

Metallothionein is an example of a gene that can be turned on by multiple transcription factors


Metallothionein RegulationMetallothionein Regulation

-260 -240 -220 -200 -180 -160 -140 -120 -100 -80 -60 -40 -20

BLE GC TATAGRE MRE MREMRETREMREBLE

Basal Level Elements(needed for

transcription, act as enhancers)

Glucocorticoid Response Element - Behaves as an

enhancer and allows regulation by steroids

Constitutive Elements

Metallothionein Regulator Elements - Multiple copies

confer greater levels of induction by heavy metals

TGACTCAA consensus sequence to

which AP1 binds conferring a response to phorbol esters


Regulation By TFsRegulation By TFs A single transcription factor (or group of transcription

factors) may regulate expression of a group of genes (i.e., heat shock proteins)

A single gene may be regulated by a number of independent transcription factors (i.e., metallothionein)

Eukaryotic regulation does not seem to involve repression To achieve high levels of expression, several different

transcription factors binding to different response elements may be necessary


How Do TFs Recognize How Do TFs Recognize Response Elements?Response Elements?

Some mechanism must exist for protein transcription factors to recognize the specific sequences of bases found in response elements

There is no known specific relationship between a given amino acid and a base that would allow direct recognition

Groups on bases that are not involved with base pairing have the potential to be recognized by proteins

Some specific sequences are known to influence the gross structure of DNA


DNA Binding DomainsDNA Binding Domains Transcription factors exhibit a number of different

motifs found in the area known to bind DNA: Zinc finger -First found in TFIIIA Helix-turn-helix - First described from phage receptors Amphipathic Helix-loop-helix - Identified in some

development regulators Leucine zipper - Held together by interactions between

leucine amino acids


Zinc FingersZinc Fingers Are found in steroid receptors and are common in other

transcription factors Interaction between cysteine and histidine amino acids

and the divalent zinc ion results in the formation of loops called “fingers”

One side of each loop forms an a-helix which can lie in the major grove of DNA

Interaction between the amino acids in the zinc finger and bases in the DNA allow for sequence recognition


Zinc FingersZinc Fingers

OH

H

H

O

HS

H

H2N

C

C

C

OH

H

H

O

N

H

H2N

C

C

C

CH

C

C

N H


Zinc FingersZinc Fingers

Zn++

H

H

C

C

Zn++

H

H

C

C

Zn++

H

H

C

C

≈ 23Aminoacids

7 - 8 Amino acid linker

2- 4 Aminoacids

≈ 6 Aminoacids


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James 4:7 7 Submit yourselves therefore to God. Resist the devil, and he will flee from you