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Control of Gene Control of Gene ExpressionExpression

MOLECULAR BIOLOGY OF THE CELL

5TH Edition

Chapter 7Chapter 7

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The rules and mechanisms by The rules and mechanisms by which a subset of the genes is which a subset of the genes is

selectively expressed in each cell selectively expressed in each cell

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Cell DifferentiationCell DifferentiationWhat makes the differences??What makes the differences??The two cells extremely different but

contain the same genome!!DifferentiationDifferentiation = synthesizing and

accumulating different sets of RNA and protein molecules.The DNA sequence is generally not alteredAll the differences are achieved by changes

in gene expression

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CluesClues for genome preservation during for genome preservation during cell differentiation:cell differentiation:

1. From Animal Experiments

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2. From comparing the detailed banding patterns detectable in condensed chromosomes at mitosis

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3. Comparisons of the genomes of different cells based on recombinant DNA technology have shown:

Changes in gene expression that underlie the development of multicellular organisms are not accompanied by changes in the DNA sequences of the corresponding genes.

However, in a few cases DNA rearrangements of the genome take place during development Example:Example: in generating the diversity of the immune system

of mammals

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Different Cell Types Synthesize Different Cell Types Synthesize Different Sets of ProteinsDifferent Sets of Proteins

1.1. Housekeeping proteinsHousekeeping proteins are made in all cells

Like what?? The structural proteins of chromosomes RNA polymerases DNA repair enzymes Ribosomal proteins Enzymes involved in the central reactions of

metabolism Many of the proteins that form the cytoskeleton

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2.2. Specialized proteinsSpecialized proteins are responsible for the cell’s distinctive properties Like what?? ExampleExample: Hemoglobin can be detected only in red

blood cells.

3.3. All other proteinsAll other proteins are expressed to various degrees from one cell type to another A typical human cell expresses 30-60% of its

approximately 25,000 genes

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A cell can change the expression of A cell can change the expression of its genes in response to external its genes in response to external signalssignalsDifferent cells respond in different ways to

the same signalFor example: in response to glucocorticoid glucocorticoid

hormonehormone:liver cell turns up tyrosine aminotransferase (helps to

convert tyrosine to glucose to combat starvation)fat cells turns the same enzyme downother cell types don’t respond at all

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The patterns of mRNA abundance, characteristic of a cell type can be determined using DNA microarrays

It reflects the pattern of gene expression

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The radical differences in gene expression between cell types can be appreciated by two-dimensional gel electrophoresis protein levels are directly measured some of the most common posttranslational

modifications can be displayed

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Gene expression can be regulated at Gene expression can be regulated at many of the steps in the pathway from many of the steps in the pathway from DNA to RNA to proteinDNA to RNA to protein

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How does a cell determine which How does a cell determine which of its thousands of genes to of its thousands of genes to

transcribe? transcribe?

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The transcription of each gene is The transcription of each gene is controlled by two types of fundamental controlled by two types of fundamental components:components:1.1. Regulatory regions:Regulatory regions: short stretches of DNA of

defined sequence Some are simple and act as switchesswitches

Respond to a single signal especially in bacteria Many others are complex and act as tiny

microprocessorsmicroprocessors Respond, interpret and integrate a variety of signals to

switch the neighboring gene on or off

2.2. Gene regulatory proteinsGene regulatory proteins (Transcription factors) that recognize and bind to regulatory regions

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Gene regulatory proteins must recognize Gene regulatory proteins must recognize specific nucleotide sequences embedded specific nucleotide sequences embedded within the DNA double helix within the DNA double helix

The edge of each base pair is exposed at the surface of the double helix

The surface of protein must fit tightly against the special surface features of the double helix

Features on the DNA surface vary with nucleotide sequence

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A gene regulatory protein interacts with DNA by:hydrogen bonds ionic bondshydrophobic interactions

Typically ~20 contacts combine to ensure that the interaction is both highly specific and very strong

Protein-DNA interactions are among the tightest and most specific molecular interactions known in biology!

Most DNA/protein interactions are on Most DNA/protein interactions are on the major groovethe major groove

Proteins usually insert into the major groove of DNA helix and make molecular contacts with its base pairsDNA binding proteins don’t

have to open the double helix.

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A distinctive pattern of hydrogen bond donors, and acceptors, and hydrophobic patches are available in both grooves

Only in the major groove are the patterns markedly different for each of the four base-pair arrangements

For this reason, gene regulatory proteins generally bind to the major groove

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The Geometry of the DNA Double Helix The Geometry of the DNA Double Helix Depends on the Nucleotide SequenceDepends on the Nucleotide Sequence

The normal DNA conformation must be distorted to maximize the fit between DNA and proteinThe extent to which the

double helix is deformable is variable

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Some sequences (for ex. AAAANNNAAAANNN) form a double helix with a slight bend.

If this sequence is repeated at 10-bp intervals in a long DNA molecule, the small bends add together so that the DNA molecule appears unusually curved when viewed in the electron microscope

A few gene regulatory proteins induce a striking bend in the DNA when they bind to it

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Short DNA Sequences Are Fundamental Short DNA Sequences Are Fundamental Components of Genetic Switches Components of Genetic Switches

Nucleotide sequences typically < 20 bp function as fundamental components of genetic switches

They serve as recognition sites for the binding of specific gene regulatory proteins

Each is recognized by a different gene regulatory protein (or by a set of related gene regulatory proteins).

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Gene Regulatory Proteins Contain Gene Regulatory Proteins Contain Structural Motifs That Can Read DNA Structural Motifs That Can Read DNA SequencesSequencesCertain aa structures

make precise contacts with one or more bases in the major groove.

This is not sufficient and the right structure has to be in the right position.

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Many of the proteins contain one or Many of the proteins contain one or another of a small set of another of a small set of DNA-binding DNA-binding structural motifsstructural motifsThe DNA binding motifs generally use

either helices or sheets to bind the major groove of DNA

The major groove, contains sufficient distinctive information to distinguish one DNA sequence from any other.

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A few examples of DNA A few examples of DNA binding motifsbinding motifs

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The Helix-Turn-Helix Motif (The Helix-Turn-Helix Motif (HTHHTH))

The first DNA-binding motif to be recognized in bacterial proteins

The two helices are held at a fixed angle, primarily through interactions between them

The more C-terminal helix is called the recognition recognition helixhelix because it fits into the major groove of DNA

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Three important features about HTH Three important features about HTH proteins:proteins:

1. The actual amino acids within the recognition helix can vary from one transcription factor to another This variation allows proteins with similar global

structures to recognize very different DNA sequences.

2. Amino acid composition and structure outside the HTHHTH region of the protein can vary tremendously. Amino acids outside the HTHHTH region can also

make important contacts with the DNA.

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3. Many HTHHTH proteins function as dimers Dimers are complexes of two protein molecules that

come together and function as a unit Dimerization allows/requires the complex to have twice

the number of contacts with the DNA

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HomeodomainHomeodomain Proteins: a Special Proteins: a Special Class of Class of HTHHTH Proteins Proteins HomeodomainHomeodomain an almost identical stretch of 60 aa that

defines a class of proteins termed homeotic selectorhomeotic selector The homeotic selector geneshomeotic selector genes, play a critical part in

orchestrating the Drosophila fly development. Homeodomain Homeodomain contains a HTHHTH motif related to that of

the bacterial gene regulatory proteins. Thus the principles of gene regulation established in

bacteria are relevant to higher organisms as well. HomeodomainHomeodomain proteins have been identified in virtually

all eucaryotic organisms that have been studied, from yeasts to plants to humans.

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The structure of a The structure of a homeodomain bound to homeodomain bound to its specific DNA its specific DNA sequencesequenceThe HTHHTH motif of

homeodomains is always surrounded by the same structure (which forms the rest of the homeodomain)

Structural studies have shown:A yeast homeodomain

protein and a Drosophila homeodomain protein have very similar conformations

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DNA-binding DNA-binding Zinc Finger MotifsZinc Finger Motifs

A zinc-coordinated DNA-binding motif.

Two major structurally distinct types of zinc finger that: both use zinc as a structural element, both use an helix to recognize the

major groove of the DNA.

1. The first type: Discovered in the protein that activates the transcription of a eukaryotic ribosomal RNA gene. Consists of an helixhelix and a sheetsheet held

together by the zinc

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A strong and specific DNA-protein interaction is built up through a repeating basic structural unitzinc fingers, are arranged one after the otherThe helix of each can contact the major groove of

the DNA, forming a nearly continuous stretch of helices along the groove

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2. The second type: is found in the large family of intracellular receptor intracellular receptor proteinsproteins:

It forms a different type of structure (similar in some respects to the HTHHTH motif) in which two helices are packed together with zinc atoms

Like the HTHHTH proteins, these proteins usually form dimers that allow one of the two helices of each subunit to interact with the major groove of the DNA

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sheets DNA binding motifsheets DNA binding motif

In this case the information on the surface of the major groove is read by a two-stranded sheet

The exact DNA sequence recognized depends on the sequence of amino acids that make up the sheet.

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The Leucine ZipperThe Leucine Zipper Motif Motif

Unlike other proteins, the leucine zipper motif dimerizes and binds DNA using the same domain.Two helices, one from each

monomer, are joined together to form a short coiled-coil

The helices are held together by interactions between hydrophobic amino acid side chains (often on leucines)

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The Helix-Loop-Helix Motif The Helix-Loop-Helix Motif HLHHLH

HLHHLH motif should not be confused with the HTHHTH Consists of a short helix

connected by a loop to a second, longer helix.

Also Mediates dimerization and DNA bindingHLHHLH proteins can create a

homodimer or a heterodimer.

Example of DNA binding proteins: DNA recognition by the P53

The most important DNA contacts are made by arginine 248 and lysine 120

They extend from the protruding loops entering the minor and major grooves.

The folding of the p53 protein requires a zinc atom (shown as a sphere)

but the way in which the zinc is grasped by the protein is completely different from that of the zinc finger proteins, described previously.

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The gene regulatory proteins can The gene regulatory proteins can bind DNA asbind DNA as dimersdimers

1.1. Homo-dimersHomo-dimers: dimers made up of two identical subunits.

2.2. Heterodimers:Heterodimers: composed of two different subunits

heterodimers typically form from two proteins with distinct DNA-binding specificities

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There are tremendous advantages to There are tremendous advantages to dimerizationdimerization

1. Doubles the number of contacts with DNA, i.e. stronger binding affinity

2. Can turn two weak binders into one moderate or strong binder

3. Adds specificity to the system

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Let’s consider a fictional protein binding site of one bpThere are four possible bp possibilities at this site.The likelihood of this site occurring is one in every 41

Let’s consider a fictional protein binding site of 4 bpThe binding site has 4 positions but at any given

one position there are 4 possible bpThe likelyhood of this site occuring is one in every

44=256 bp

How can dimerization contribute to How can dimerization contribute to specificity??specificity??

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How can dimerization contribute to How can dimerization contribute to specificity??specificity??

Consider that the human genome is 3.2x109 bp, and most of it is not genesthen by random chance we would find

3.2x109/256=1.25x107 (12.5 million12.5 million) sites for this protein.

However,there are only ~30,000 genes in the whole genome and very few are regulated by the same specific transcription factor!!

In this case the cell would have to make a lot of this protein to ensure that it would actually get to the few binding sites where it is really needed or have another solution.

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How can dimerization contribute to How can dimerization contribute to specificity??specificity??

If the binding site is 8 bpthen this sequence will randomly, be found once every

48 (1/65,536) bp (roughly 48,82848,828 (3.2x109/48) sites in the human genome)

If the protein requires two of these sites (in dimer)then this sequence will, randomly be found once every

(48)x(48) = 1/4,294,967,296 or 1/4.29x109 bproughly 0.750.75 times in the human genome

(3.2x109/4.29x109)

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How can dimerization contribute to How can dimerization contribute to specificity??specificity??

If number of 8 bp sites is 48,82848,828 times in the human genome

And number of two adjacent 8 bp sites is 0.750.75 times in the human genome (less than one)

then it is far less likely that a protein requiring two half-sites will find a random place in the genome that it can bind to, when compared to a protein that requires only one half site.

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HeterodimerizationHeterodimerization Expands the Expands the Repertoire of DNA Sequences Recognized Repertoire of DNA Sequences Recognized by Gene Regulatory Proteinsby Gene Regulatory Proteins Heterodimerization is an example of combinatorial combinatorial

control:control:combinations of different proteins, rather than individual

proteins, control a cellular process. Heterodimerization occurs in a wide variety of different

types of gene regulatory proteins

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Heterodimerization greatly expands the Heterodimerization greatly expands the DNA-binding specificitiesDNA-binding specificities

ExampleExample: Three distinct DNA-binding specificities could, in principle, be generated from two types of leucine zipper monomer

Heterodimerization depends on the exact amino acid sequences of the two zipper regions.Thus each leucine zipper protein in the cell can form

dimers with only a small set of other leucine zipper proteins

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Is There a DNA Sequences Is There a DNA Sequences Recognized by All Gene Regulatory Recognized by All Gene Regulatory Proteins?Proteins?

For example, is a G-C base pair always contacted by a particular amino acid side chain?

The answer appears to be NONOHowever, certain types of aa-base

interactions appear much more frequently than others

HomeworkHomework

Briefly discuss at least 2 methods that are used to experimentally determine the DNA sequence recognized by a gene regulatory protein (DNA binding protein)

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How a Genetic Switch How a Genetic Switch WorksWorks

Bacterial Genes

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Regulatory proteins and specific Regulatory proteins and specific DNA sequences control the switch.DNA sequences control the switch.

How?How?

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Negative control by transcriptional Negative control by transcriptional repressorsrepressors Tryptophan operon:Tryptophan operon:

5 E. coli genes code for enzymes that manufacture the aa tryptophan, arranged in a single transcriptional unit.

Promoter: Promoter: the 5 genes are transcribed into a single long mRNA molecule.

Operator: Operator: a short sequence of regulatory DNA within the promoter that directs transcription of the tryptophan biosynthetic genes

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Cells need tryptophan to liveCells need tryptophan to liveCells need tryptophan to liveCells need tryptophan to live

Get it from environmentGet it from environmentGet it from environmentGet it from environment Synthesized inside the cells Synthesized inside the cells Synthesized inside the cells Synthesized inside the cells

The The operon operon is onis on

The The operon operon is onis on

The The operooperon is offn is off

The The operooperon is offn is off

On/off switchOn/off switch

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Three essential features of this Three essential features of this on/off switchon/off switch

1. The cell needs to know whether it has tryptophan or not.

2. Accordingly, the cell then turns the operon ONON or OFFOFF.

3. ON or OFF, the cell needs to continuously monitor tryptophan levels.

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Tryp & Tryp & tryptophan repressortryptophan repressor will will do the jobdo the jobThe tryptophan repressortryptophan repressor is a member of the

HTHHTH family that recognizes the operator

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Three essential features of this Three essential features of this on/off switchon/off switch

1. The cell needs to know whether it has tryptophan or not.The repressor binding to tryp is the sensor.

2. Accordingly, the cell then turns the operon ONON or OFFOFF.The activity of the repressor dependent on the

presence/absence of tryp.

3. ON or OFF, the cell needs to continuously monitor tryptophan levels.The repressor can be turned on/off by the simple presence

or absence of tryp.

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This is an example of a feedback This is an example of a feedback looploop

Tryp that is being synthesized by the gene products can directly feedback information to the switch and dictate whether more or less gene products should be made.

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How does tryptophan activate the How does tryptophan activate the repressor?repressor? Two molecules of tryp can bind to the repressor Tryp binding causes a conformational change

the DNA binding domains of the repressor swings into a different position

This is a very good DNA binding state thus can exclude RNA pol from biniding.

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Negative regulationNegative regulation can be controlled can be controlled by ligandsby ligands

1. The repressor is originally active A ligand inhibit its

activity

2. The repressor needs the ligand for being activated

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Positive Control by Transcriptional Positive Control by Transcriptional ActivatorsActivatorsPoorly functioning bacterial promoters can be

rescued by gene regulatory proteins (transcriptional activators or gene activator transcriptional activators or gene activator proteins)proteins):They bind to a nearby site on the DNAThey may strengthen the RNA pol binding to the

promoter by providing an additional contact surface for it.

They may facilitate the polymerase transition from the initial DNA-bound conformation to the actively transcribing form

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Positive regulationPositive regulation can also be can also be controlled by ligandscontrolled by ligands

1. Ligands can serve to remove positive regulators form DNA.

2. Ligands can also serve to allow positive regulators to bind DNA.

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Repressors and Activators are Repressors and Activators are similar to one another.similar to one another.

1. They may bind DNA in very similar ways using similar helical structures.

2. They may be controlled by similar or identical ligands or be independent of ligands.

3. Some transcriptional regulator proteins can act as both repressors and activators

depending on the exact placement of their DNA recognition sequence in relation to the promoter

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The lambda repressor can both: The lambda repressor can both: activate and repress.activate and repress.

when bound in the right position, relative to the RNA pol binding site on the promoter, the lambda repressor can activate transcription.

A shift of even one basepair, in another promoter, of the repressor binding site relative to the RNA pol binding site inhibits RNA pol binding to the promoter, thus repressing transcription.

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The lac operonThe lac operon, uses both negative , uses both negative and positive regulation to controland positive regulation to control The lac operon codes for proteins required to transport

the disaccharide lactose into the cell and to break it down.

The operon is highly expressed only when two conditions are met:1. lactose must be present2. glucose must be absent

CAP:CAP: enables bacteria to use alternative carbon sources such as lactose in the absence of glucose. It needs the presence of lactose to induce expression of the lac

operon The lac repressorThe lac repressor ensures that the lac operon is shut

off in the absence of lactose.

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How a Genetic Switch How a Genetic Switch WorksWorks

Eucaryotic Genes

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1. A single promoter can be controlled by an almost unlimited number of regulatory sequences Regulatory proteins can act even when they are bound to DNA

thousands of bps away from the promoter

2. Eucaryotic RNA pol II, which transcribes all protein-coding genes, cannot initiate transcription on its own. It requires general transcription factorsgeneral transcription factors The rate of there assembly and thus the rate of transcription

initiation can be controled in response to regulatory signals

3. The packaging of eucaryotic DNA into chromatin provides opportunities for regulation not available to bacteria.

Transcription regulation in eucaryotes Transcription regulation in eucaryotes differs in three important ways from that differs in three important ways from that in bacteria.in bacteria.

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A Eucaryotic Gene Control RegionA Eucaryotic Gene Control Region

Refers to the whole region of DNA involved in regulating transcription of a gene, including:The promoterThe promoter: site of the general TFs and the RNA

Pol II assemblyThe regulatory sequences:The regulatory sequences: to which gene regulatory

proteins bind and control the rate of assembly at the promoterRegulatory sequencesRegulatory sequences of a gene can be found over

distances as great as 50,000 bp of "spacerspacer" sequenceSpacer DNASpacer DNA may facilitate transcription by providing the

flexibilityMuch of the DNA in gene control regions is packaged into

nucleosomes and higher-order forms of chromatin, thereby compacting its length.

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EnhancersEnhancers

The DNA sites to which the eucaryotic gene activatorsgene activators boundThey could be thousands of bp away from the

promoter.They could be located either upstream or

downstream from it.

How do enhancer sequences and the How do enhancer sequences and the proteins bound to them communicate with proteins bound to them communicate with the promoter the promoter over these long distancesover these long distances?

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A model for action at a distanceA model for action at a distance

The DNA between the enhancer and the promoter loops out to allow the activator proteins bound to the enhancer to come into contact with proteins bound to the promoter (RNA polymerase, one of the general transcription factors, or other proteins)

DNA Looping Occurs During DNA Looping Occurs During Bacterial Gene RegulationBacterial Gene Regulation

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If this were a random or passive interaction then one would predict that the further away the enhancer from the promoter the less likely it is to be able to control transcription.

Note that being too close also presents a problem.

Eukaryotic enhancers can be spaced out over a 50,000 basepair region, relative to the promoter.

Thus, the interaction between enhancers and promoter complexes cannot be random or passive since this great distance would predict a very low likelyhood of chance interaction.

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We have reason to believe that looping occurs in both prokaryotes and in eukaryoteswe can see something that looks like looping in EM

pictures from bacteria.

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There are thousands of different There are thousands of different gene regulatory proteins.gene regulatory proteins. About 5-10% of the roughly 30,000 human genes,

encode gene regulatory proteins. Each regulatory protein is usually present in very small

amounts in a cell, often less than 0.01% of the total protein.

Most of them directly recognize their specific DNA sequences using one of the DNA-binding motifs

Some do not recognize DNA directly but instead assemble on other DNA-bound proteins.

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Eucaryotic Gene Activator ProteinsEucaryotic Gene Activator Proteins

Consist of at least two distinct domains:A DNA binding domainA DNA binding domain usually contains one

of the structural motifs that recognizes a specific regulatory DNA sequence.

An activation domainactivation domain accelerates the rate of transcription initiation.

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The yeast GAL4GAL4 TF needs its DNA binding domain to recognize its target.

It is the activation or repressor domain of a TF that influences the activity of RNA pol and trans-cription initiation.

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In general activators work on the level of In general activators work on the level of initiation of transcriptioninitiation of transcription

Once bound to DNA, eucaryotic gene activator proteins increase the rate of transcription initiation

They attractattract, positionposition, and modifymodify the general TFs and RNA pol II at the promoter so that transcription can begin.

1.1. They can act directly on the transcription They can act directly on the transcription machinery itself machinery itself

2.2. They can change the chromatin structure around They can change the chromatin structure around the promoter.the promoter.

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1.1.Activators act directly on the Activators act directly on the transcription machinery itself transcription machinery itself

General TFsTFs and RNA pol IIRNA pol II assemble in a stepwise, prescribed order in vitro

In living cells some TFs and RNA pol II are brought to the promoter as a large pre-assembled complex (RNA pol II RNA pol II holoenzyme)holoenzyme).

The holoenzyme typically also contains a 20-subunit protein complex called mediatormediator required for activators to stimulate

transcription initiation.

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Eucaryotic activators help to Eucaryotic activators help to attractattract and and positionposition

RNA pol on specific sites on DNARNA pol on specific sites on DNA Activator proteins interact

with the holoenzyme complex and thereby make it more energetically favorable for it to assemble on a promoter

Most forms of the holoenzyme complex lacks some of the general transcription factors (notably TFIIDTFIID and TFIIATFIIA) these must be assembled

on the promoter separately

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Experimental support: “Activator bypass”Experimental support: “Activator bypass”

A sequence-specific DNA-binding domain is experimentally fused directly to a component of the mediatorThe hybrid protein lacks an activation domain

It strongly stimulates transcription initiation when the DNA sequence to which it binds is placed in proximity to a promoter

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Many activators have been shown to interact with one or more of the general transcription factors

Several have been shown to directly accelerate their assembly at the promoter

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2.2.Activators change the chromatin Activators change the chromatin structure around the promoter.structure around the promoter.

Two most important ways of locally altering chromatin structure are:Covalent histone modificationsChromatin remodeling

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Many gene activator proteins bind to and recruit:Histone acetyl transferases (HATs).Histone acetyl transferases (HATs).ATP-dependent chromatin remodeling complexesATP-dependent chromatin remodeling complexes

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A. Activator proteins bind to enhancers and recruit HATs. Acetylation then allows other

activator proteins to bind to DNA and/or acetylated histones and enhances RNA pol activity.

B. The bromodomain of TFIID specifically binds to Acetylated Lysine 8 & 16 on the terminal tail of histone H4.

Covalent histone modificationsCovalent histone modifications

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An example of how events are ordered on a An example of how events are ordered on a particular yeast gene.particular yeast gene.

Note that the order of events can be slightly or even dramatically different at another gene.

The order of events during transcription activation can vary from one gene to another.

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Eucaryotic Gene Repressor Proteins Can Eucaryotic Gene Repressor Proteins Can Inhibit Transcription in Various WaysInhibit Transcription in Various Ways

A. A repressor physically blocks activator binding site on DNA

B. The repressor has a distinct DNA binding site, but it interacts with and inhibits the activator activity

C.The repressor binds directly TFIID and inhibits activation by the activator.

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Eucaryotic Gene Repressor Proteins Can Eucaryotic Gene Repressor Proteins Can Inhibit Transcription in Various WaysInhibit Transcription in Various Ways

D. Repressors recruit remodeling enzymes that make DNA inaccessible

E. Repressors can also recruit histone modifying enzymes (like histon histon deacetylasedeacetylase) they covalently modify

histones in a pattern that is not favorable for activation and thus inhibits transcription

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Gene Activator Proteins Work Gene Activator Proteins Work SynergisticallySynergistically

Gene activator proteins often exhibit what is called transcriptional synergytranscriptional synergythe transcription rate produced by several activator

proteins working together is much higher than that produced by any of the activators working alone

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Gene Activator Proteins Work Gene Activator Proteins Work SynergisticallySynergisticallyTranscriptional synergy is observed both:

Between different gene activator proteins bound upstream of a gene

between multiple DNA-bound molecules of the same activator.

Synergistic effects turn a simple genetic on/off switch into a “dimmer” switchThe quantity of transcript being made can also be

regulatedSynergy allows cells to respond to conditions that

require production of small amounts as opposed to large amounts of gene products.

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Eucaryotic Gene Regulatory Proteins Eucaryotic Gene Regulatory Proteins Often Assemble into Complexes on DNAOften Assemble into Complexes on DNA

Two gene regulatory proteins with a weak affinity for each other cooperate to bind to a DNA sequenceneither protein having a sufficient affinity for DNA

to efficiently bind to the DNA site on its own.Once bound to DNA, the protein dimer creates a

distinct surface that is recognized by a third protein that carries an activator domain that stimulates transcription

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An important general point:An important general point: protein-protein interactions that are too weak to cause

proteins to assemble in solution can cause the proteins to assemble on DNA the DNA sequence acts as a "crystallization" site or seed

for the assembly of a protein complex.

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An individual gene regulatory protein can often participate in more than one type of regulatory complex.

A protein might function, in one case as part of a complex that activates transcription and in another case as part of a complex that represses transcription

Thus individual eucaryotic gene regulatory proteins function as regulatory units that are used to generate complexes Their function depends on the final assembly of all of the

individual components. This final assembly, in turn, depends both on:

the arrangement of control region DNA sequenceswhich gene regulatory proteins are present in the cell.

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Coactivators or Coactivators or corepressors:corepressors:Gene regulatory proteins that:

do not themselves bind DNAThey assemble on DNA-bound gene regulatory proteins

Coactivators and corepressors typically can interact with:chromatin remodeling complexeshistone modifying enzymesthe RNA polymerase holoenzymeseveral of the general transcription factors

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The DNA sequence directly bound by a The DNA sequence directly bound by a regulatory protein can influence its regulatory protein can influence its subsequent transcriptional activitysubsequent transcriptional activityFore example: a steroid hormone receptor

interacts with a corepressorcorepressor at one type of sequence and turns off transcription.

it assumes a different conformation and interacts with a coactivatorcoactivator, at a slightly different DNA sequence, thereby stimulating transcription.

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In some cases, a protein-DNA structure, In some cases, a protein-DNA structure, termed an termed an enhancesomeenhancesome, is formed, is formed

A hallmark of enhancesomes is the participation of architectural proteinsarchitectural proteins that bend the DNA by a defined angle and thereby promote the assembly of the other enhancesome proteins.The formation of the enhancesome requires the presence of

many gene regulatory proteinsThis ensures that a gene is expressed only when the correct

combination of these proteins is present in the cell.