Click here for the Eukaryotic Gene Expression student learning guide

1. Introduction: Transcription, the Big Picture

In  previous tutorials on this website, we covered the basics of transcription, and how transcription is regulated in prokaryotes.

Here’s a quick review of the basics. RNA polymerase (3, below) is the enzyme that can transcribe DNA into RNA. To do so, it starts by binding at a promoter (1). The promoter is a sequence of DNA that signals to RNA polymerase that this is where transcription should start.  Once joined to the promoter, RNA polymerase transcribes the template DNA (at 5) into RNA (at 2). Transcription continues until the RNA polymerase reaches a terminator sequence (which is not shown below).

In eukaryotes, this system has several additional features.

 

The promoter (1) usually begins with a DNA sequence that consists of many A-T (adenine-thymine) pairs. It’s called a TATA box (2). Number 3 indicates the point where transcription starts (the first DNA base that will be transcribed into RNA). Following the promoter is the the template DNA (4).

Before RNA polymerase can bind with the promoter, a team of general transcription factors (5) has to bind with it. General transcription factors bind to most promoters, as opposed to other transcription factors that have more specific regulatory roles.

Once these general transcription factors are in place, RNA polymerase (6) binds. But transcription won’t begin until additional transcription factors (7) bind. Once in place, RNA polymerase will begin to transcribe RNA (8).

Let’s quickly check to see if you understand the two diagrams above.

2. Checking Understanding: Transcription and the Transcription Initiation Complex

[qwiz random = “true” qrecord_id=”sciencemusicvideosMeister1961-M24_transcription initiation complex”] [h]

Transcription and the transcription initiation complex

[i]

[q] In the diagram below, number 1 is the [hangman]

[c] promoter

[f] Great!

[q] In the diagram below, number 3 is RNA [hangman]

[c] polymerase

[f] Great!

[q] In the diagram below, the TATA box is at

[textentry single_char=”true”]

[c*] 2

[f] Excellent. The A-T rich region at the start of the promoter is known as the TATA box.

[c] Enter word

[f] No, that’s not correct.

[c] *

[f] No. The TATA box is rich in adenine and thymine base pairs.

[q] In the diagram below, the template DNA is at

[textentry single_char=”true”]

[c*] 4

[f] Nice job. “4” is the template DNA.

[c] Enter word

[f] No, that’s not correct.

[c] *

[f] No. The template DNA is the strand of DNA that’s transcribed into RNA. If 8 is RNA, then what has to be the template strand of DNA?

[q] In the diagram below, a general transcription factor is shown at

[textentry single_char=”true”]

[c*] 5

[f] Way to go. “5” is a general transcription factor.

[c] 7

[f] No, but you’re on the right track. “7” is a transcription factor, but it’s binding fairly late in the process. Find a transcription factor that shown binding before RNA polymerase arrives.

[c] *

[f] No. Find something that binds to the DNA before RNA polymerase (and makes that binding possible). 

[q] In the diagram below, RNA polymerase is shown at

[textentry single_char=”true”]

[c*] 6

[f] Nice. “6” is RNA polymerase.

[c] *

[f] No. Find something that binds to the DNA before RNA polymerase (and makes that binding possible). 

[q] In the diagram below, newly transcribed RNA is shown at

[textentry single_char=”true”]

[c*] 8

[f] Good job. “8” is newly transcribed RNA.

[c] *

[f] No. Find something RNA polymerase (6) is synthesizing from the DNA template. 

[c] Enter letter

[/qwiz]

 

3. Eukaryotic Transcription Factors and Control of Gene Expression

MyoD, a transcription factor

Many of the transcription factors referred to above have common features in their structures that enable them to specifically bind with both DNA sequences and with the many other proteins involved in regulating transcription. You can see this at left in the model of MyoD, a transcription factor involved in the development of muscle tissue in vertebrates. Like other transcription factors, MyoD can bind to DNA (1, above) through DNA-binding domains (at “2”). The protein-binding domain shown at “3,” called an activation domain, gives this molecule the ability to bind with proteins.

In addition to binding at the transcription initiation complex, transcription factors can also bind with DNA that’s at some distance away from the genes that they regulate. Look at the diagram below, which shows some of these control elements in relationship to the RNA that RNA polymerase will transcribe.

Number “1” in the diagram above is DNA. “Letter “c” indicates the promoter region. The segments labeled with letter “d” (d1, d2, d3) represent exon DNA, which will be translated into protein. The segments labeled as “e” represent intron DNA, which will be spliced out of the primary RNA transcript (shown at 2).

Upstream of the gene and its promoter are control elements. Those closer to the promoter are called proximal control elements, and are indicated by letter “b.” Further away from the promoter, up to thousands of base pairs upstream, are distal control elements (shown at “a”). Together, a group of distal control elements are called enhancers. These enhancers bind with activator proteins which, in turn, interact with the transcription initiation complex.

The rest of what’s shown above depicts what happens after transcription. Catalytic RNAs organized into teams called spliceosomes (not shown) remove the introns in RNA (f1 and f2), and splice together exons, creating messenger RNA (3). Further modification by other enzymes gives the mRNA a G3P (guanine triphosphate) cap on the 5′ end (indicated by letter “g”) and a poly-A tail (at “j”) at the 3′ end of the RNA. Both the cap and tail help the mRNA to resist enzymatic degradation while in the cytoplasm. Finally, letters “h” and “i” indicate the start and stop codons, respectively.

So, how do all these regulatory elements come into play when eukaryotic genes are transcribed? Here’s a model of the role of enhancers and transcription elements in eukaryotic gene expression.

The basic idea is this: signals, generated outside or inside a cell, cause DNA to bend in a way that enables a specific transcription initiation complex to form. Which gene is activated is determined by which activators (“b,” above) bind with which control elements (“c”). Let’s walk through this step by step.

In diagram 1 above, you can see activators (at “b”) binding with a group of distal control elements (“c”) which together make up an enhancer (“a”). Far away is the promoter (“d”) with its TATA box (“e”).

Now look at diagram 2. With these activators in place, the enhancer can bind with general transcription factors (at “h”) and mediator proteins (at “g”). If you look carefully at “g” and “h” you can see binding the binding sites that connect these elements with the activator proteins. On another region of the DNA, a DNA bending protein (at “f”) bends the DNA in a way that causes the enhancer to approach the promoter.

In diagram 3 the transcription initiation complex (j) has been fully assembled, allowing RNA polymerase (i) to bind with the promoter, enabling transcription (“k”).

Note that transcription factors can also act as repressors. Some of these repressors block activators from binding with the enhancer DNA (which, in the context of enzymes, would be analogous to competitive inhibition). Others bind with the activator itself. Activators and repressors can also modify chromatin structure, promoting acetylation (which would increase the rate of transcription) or by working with enzymes that remove acetyl groups (decreasing the rate of transcription).

Let’s pause for a moment to make sure we understand the diagrams and concepts above.

4. Quiz: Eukaryotic Gene Structure and Transcriptional Control

[qwiz random = “true” qrecord_id=”sciencemusicvideosMeister1961-M24_Eukaryotic Gene structure and transcriptional contol” style=”width: 650px !important; min-height: 400px !important;”]

[h]

Transcription and the transcription initiation complex

[i]

[q] In the diagram below, which number indicates the part that would interact with a protein?
[textentry single_char=”true”]

[c*] 3

[f] Excellent. Number “3” is a protein binding domain.

[c] Enter word

[f] No, that’s not correct.

[c] *

[f] No. Just use a process of elimination. Which part isn’t binding with DNA?

[q] In the diagram below, which letter indicates distal control elements?

[textentry single_char=”true”]

[c*] a

[f] Excellent. Distal control elements are at “a.”

[c] Enter word

[f] No, that’s not correct.

[c] *

[f] No. Here’s a hint. When you see “distal,” think “distant.”

[q] In the diagram below, which letter indicates intron DNA?

[textentry single_char=”true”]

[c*] e

[f] Nice job. The intron DNA (at “e”) is DNA that gets cut out of the pre-RNA before it gets made into mRNA.

[c] Enter word

[f] No, that’s not correct.

[c] *

[f] No. The intron DNA is DNA that gets cut out of the pre-RNA before it gets made into mRNA. “F” represents two RNA segments that have been cut out…so just work up from there and you’ll have the answer. 

[q] In the diagram below, pre-mRNA (still with introns) is represented by number

[textentry single_char=”true”]

[c*] 2

[f] Awesome. “2” is pre-mRNA.

[c] Enter word

[f] No, that’s not correct.

[c] *

[f] No. Spliced out RNA introns can be seen at “f.” Look for RNA that still contains introns.  

[q] In the diagram below, messenger RNA is represented by number

[textentry single_char=”true”]

[c*] 3

[f] Good work. “3” is messenger RNA.

[c] Enter word

[f] No, that’s not correct.

[c] *

[f] No. RNA introns can be seen in number  “2.” Look for RNA in which the introns have been spliced out.

[q] In the diagram below, the protective, 5′ G3P cap is at

[textentry single_char=”true”]

[c*] g

[f] Excellent. “G” is the 5′ G3P cap.

[c] Enter word

[f] No, that’s not correct.

[c] *

[f] No. Here’s a hint. G3P is attached to mRNA, and it has 3 phosphate groups. 

[q] In the diagram below, which letter indicates an enhancer?

[textentry single_char=”true”]

[c*] a

[f] Nice job! Letter “a” indicates an enhancer.

[c] Enter word

[c] *

[f] No. The enhancer is a control region located way upstream from the gene, and it consists of multiple control elements.

[q] In the diagram below, which letter indicates an activator?

[textentry single_char=”true”]

[c*] b

[f] Nice job. Letter “b” is an activator.

[c] Enter word

[c] *

[f] No. Activators are transcription factors that bind with the enhancer region.

[q] In the diagram below, which letter indicates a distal control element?

[textentry single_char=”true”]

[c*] c

[f] Awesome. Letter “c” is a distal control element.

[c] Enter word

[c] *

[f] No. Distal control elements are parts of enhancers.

[q] In the diagram below, which letter indicates the promoter?

[textentry single_char=”true”]

[c*] d

[f] Good work. Letter “d” indicates the promoter.

[c] Enter word

[c] *

[f] No. The promoter is just upstream of the gene.

[q] In the diagram below, if letter “g” indicates mediator proteins. which letter indicates general transcription factors?

[textentry single_char=”true”]

[c*] h

[f] Terrific. Letter “h” indicates general transcription factors.

[c] Enter word

[c] *

[f] No. First of all, the question tells you that the answer is not “g.” Second, look at diagram  number 3, where you can see the general transcription factors interacting with both the promoter and with RNA polymerase. If it’s not “g,” then what must it be?

[q] In the diagram below, if letter “h” indicates general transcription factors, then what letter has to be mediator proteins?

[textentry single_char=”true”]

[c*] g

[f] Terrific. Letter “g” indicates mediator proteins.

[c] Enter word

[c] *

[f] No. Mediator proteins interact with activators and with general transcription factors. What part above is doing both?

[q] In the diagram below, DNA bending proteins are shown at

[textentry single_char=”true”]

[c*] f

[f] Nice. Letter “f” indicates a DNA bending protein.

[c] Enter word

[c] *

[f] No. Look carefully at the diagram. What part seems to be associated with bending the DNA so that the enhancer comes close to the promoter?

[q] In the diagram below, RNA polymerase is shown at

[textentry single_char=”true”]

[c*] i

[f] Good work. Letter “i” indicates RNA polymerase.

[c] Enter word

[c] *

[f] No. Look for something that sits squarely on the promoter (and it looks a bit like a guitar pick).

[q] In the diagram below, a transcription initiation complex is shown at

[textentry single_char=”true”]

[c*] j

[f] Awesome. Letter “j” indicates the transcription initiation complex.

[c] Enter word

[c] *

[f] No. The transcription initiation complex consists of activators, mediators, general transcription factors, and RNA polymerase, ready for transcription.

[x]

[restart]

[/qwiz]

5. Activators, Cell Specialization, and Coordinated Control of Cells

5a. Combinatorial Control of Gene Expression

At the start of the last tutorial, I suggested that one of the key takeaways from this module was the idea of genomic equivalence: that all cells have the same DNA, and that their differences result from differential gene expression. One aspect of that differentiation involves DNA packaging and modification through acetylation and methylation (described in the previous tutorial). Now let’s use what we learned above to explore another aspect of differential gene expression.

In the diagram above, we have two protein-coding genes: one codes for dopamine, a protein produced in certain nerve cells. The second codes for keratin, a protein that comes in several forms: the one we’ll consider here makes up the outer layer of the skin. All cells in humans (and many other animals) have both of these genes. In certain nerve cells, the dopamine gene is turned on, and the keratin gene is turned off. In skin cells, the keratin gene is turned on, and the dopamine gene is turned off.

How do cells know which genes to turn on and off? In short, cells know because of the presence or absence of activators that interact with the DNA sequences that make up these genes’ control elements. In the image above (inspired by a description in Campbell Biology, 11th edition, page 374), the dopamine gene is associated with an upstream enhancer (at “2”). This enhancer has 3 control elements (1), represented by the colors yellow, gray, and red. Downstream of the enhancer is the dopamine gene’s promoter (at 3), followed by the gene itself. The keratine gene’s enhancer is shown at 4, and its promoter is at 5. Note that the combination of control elements for the keratin gene (represented by the colors orange, grey, and pink) is different from the combination of control elements for the dopamine gene.

In the nucleus of the nerve cell (diagram “a”), three activator molecules are shown (yellow, red, and gray). These activators bind with the dopamine gene’s enhancer, enabling a transcription initiation complex to form for the dopamine gene, allowing the dopamine gene to be expressed. Note that the nerve cells have the gene for keratin, but that because the nerve cells don’t receive the required activator molecules for the keratin gene,  no transcription initiation complex is formed, and no keratin RNA is transcribed.

In the skin cell, different activators are present (orange, grey, and pink). These activators bind with their corresponding enhancers upstream of the keratin gene, resulting in the formation of a transcription initiation complex for the keratin gene, resulting in that gene’s transcription. Because the required activators for the dopamine gene are not present, the dopamine gene is not expressed.

This system for controlling gene expression is called combinatorial control. In actual eukaryotic genes, the number of control elements is about 10, with each element able to bind with one or two transcription factors. “It is the particular combination of control elements in an enhancer associated with a gene…that is important in regulating transcription.” (Campbell, Biology in Focus, 2nd edition, p 312). Note that differences in activators don’t only explain the differences between cells: it also explains differences in cells over time, as cells change during the course of development.

5b. Coordinated Control of Gene Expression

Over the course of the life of a eukaryotic organism, there are many occasions where genes need to be turned on and off together. Unlike prokaryotic cells, these genes are not clustered together in operons. They may be on different chromosomes altogether. In a multicellular eukaryote, these genes might need to be activated in different cells.  The mechanism for turning these separate genes on at once involves shared regulatory sequences that respond to the same transcription factors.

One example of coordinated gene expression involves how plants respond to stress induced by drought. To survive, plants must produce a variety of proteins simultaneously. To do this, inactive transcription factors (shown at “a”) have to respond to stress by changing to an activated form (at “b”). This activation may involve a phosphorylation, or another type of conformational change.

Once activated, these transcription factors will bind with any promoter that has, as part of its structure, a matching regulatory sequence. In the diagram to the right, you can see three genes, each of which has a promoter (d) containing what’s called a “dehydration response element” (indicated by letter “c”). Binding of the transcription factor with this element allows RNA polymerase (g) to bind, producing each gene’s RNA (at “e”). This mRNA then gets translated into a variety of proteins (at “f”).

Estrogen

In our own bodies (and the bodies of related animals), a similar mechanism explains how one hormone can activate a variety of genes in a variety of cells. An example is the steroid hormone estrogen. Estrogen is known as the feminizing hormone, and in females it’s involved in development of secondary sexual characteristics, ovulation, changes in the uterine lining during the menstrual cycle, and sexual receptivity.

Estrogen is produced primarily by ovaries (but also by the placenta during pregnancy). From the ovaries, it diffuses into the bloodstream, and then goes everywhere in the body.

An estrogen receptor, bound to two estrogen molecules. Click to see a larger image in a new tab.

As a steroid hormone, estrogen can diffuse through the cell’s phospholipid bilayer. In the cytoplasm, estrogen binds with an estrogen receptor (see the image on right: two molecules of estrogen are circled with a dotted red line).

The estrogen receptor, once bound to estrogen, becomes a transcription factor. It diffuses into the cell’s nucleus, where it binds with estrogen response elements. These control elements combine with other transcription factors to create a transcription initiation complex, resulting in transcription of estrogen-related genes.

The diagram at left shows a generalized version of this process. “F” represents estrogen. “G” is the estrogen receptor. Once the receptor binds to estrogen, it becomes a transcription factor. Letter “H” shows this transcription complex: a cytoplasmic receptor bound to estrogen. This transcription factor can cross the nuclear membrane (“D”). Letter “I” shows this transcription factor interacting with DNA (“J”), producing RNA that can (after RNA processing) be translated by ribosomes (“L”) into protein (“M”).

 

6. Quiz: Activators, Cell Specialization, and Coordinated Control of Cells (and everything else on this page)

[qwiz random = “true” qrecord_id=”sciencemusicvideosMeister1961-M24_activators, cell specialization, coordinated control” style=”width: 650px !important; min-height: 400px !important;”] [h]

Control of Eukaryotic Transcription

[i]

[q] In the diagram below, the distal control elements are indicated by number

[textentry single_char=”true”]

[c*] 1

[f] Nice job. The distal control elements are indicated by number “1.”

[c] Enter word

[f] Sorry, that’s not correct.

[c] *

[f] No. Here’s a hint. “Distal” means distant. Find something that represents a DNA sequence that’s far upstream from the genes or their promoters.

[q] In the diagram below, the promoter for the keratin gene is indicated by number

[textentry single_char=”true”]

[c*] 5

[f] Nice job. Number 5 represents the promoter for the keratin gene.

[c] Enter word

[f] Sorry, that’s not correct.

[c] *

[f] No. First find the keratin gene. Now find a binding site just upstream from the gene.

[q] In the diagram below, the enhancer for the dopamine gene is indicated by number

[textentry single_char=”true”]

[c*] 2

[f] Excellent. Number 2 represents the enhancer for the albumin gene.

[c] Enter word

[f] Sorry, that’s not correct.

[c] *

[f] No. First find the dopamine gene. Now find a combination of regulatory elements way upstream from the gene.

[q] In the diagram below, the stress is drought. The drought response element  is indicated by


[textentry single_char=”true”]

[c*] c

[f] Nice job. The drought response element is indicated by letter “c.”

[c] Enter word

[f] No, that’s not correct.

[c] *

[f] No. Here’s a hint. It’s part of the promoter region of the genes. 

[q] In the diagram below, an activated transcription factor is represented by letter


[textentry single_char=”true”]

[c*] b

[f] Nice job! Letter “b” indicates an activated transcription factor.

[c] Enter word

[f] No, that’s not correct.

[c] *

[f] No. Here’s a hint. The activated transcription factor can bind with (or near) the promoter region.

[q] In the diagram below, RNA polymerase is represented by

[textentry single_char=”true”]

[c*] g

[f] Excellent! RNA polymerase is represented by “g.”

[c] Enter word

[f] Sorry, that’s not correct.

[c] *

[f] No. Here’s a hint. The activated transcription factor can bind with (or near) the promoter region.

[q] In the diagram below, messenger RNA is represented by


[textentry single_char=”true”]

[c*] e

[f] Excellent! Messenger RNA is represented by “e.”

[c] Enter word

[f] No.

[c] *

[f] No. Here’s a hint. Letter “g” represents RNA polymerase’s role. It transcribes DNA into RNA. If “g” is RNA polymerase, then mRNA must be …

[q] In the diagram below, estrogen would be letter


[textentry single_char=”true”]

[c*] F

[f] Correct! “F” represents estrogen.

[c] Enter word

[f] No, that’s not correct.

[c] *

[f] No. Look for a hormone that’s coming from outside the cell, then diffusing into the cytoplasm through the cell membrane.

[q] In the diagram below, a mobile estrogen receptor before it has bound to estrogen would be represented by

[textentry single_char=”true”]

[c*] G

[f] Correct! “G” represents a mobile estrogen receptor before it binds with estrogen.

[c] Enter word

[f] No, that’s not correct.

[c] *

[f] No. Look for a receptor that can bind with estrogen (which is represented by letter “F.”)

[q] In the diagram below, which letter represents the estrogen-receptor complex acting as a transcription factor?

[textentry single_char=”true”]

[c*] i

[f] Correct! Letter “I” shows an estrogen/receptor complex interacting with DNA, acting as a transcription factor.

[c] Enter word

[f] Sorry, that’s not correct.

[c] *

[f] No. Look for a receptor bound to estrogen, interacting with DNA.

[q] In the diagram below, which letter represents the part that’s translating the transcription product into protein?


[textentry single_char=”true”]

[c*] L

[f] Correct! Letter “L” shows a ribosome. the ribosome is translating RNA (the transcription product) into protein

[c] Enter word

[f] Sorry, that’s not correct.

[c] *

[f] No. Here’s a hint. The transcription product is RNA (first shown at “K”). What’s translating the RNA into protein?

[q] In the diagram below, number 5 is a general [hangman] factor.


[c] transcription

[f] Great!

[q] In the diagram below, number 2 is a [hangman] box.


[c] TATA

[f] Great!

[q] In the diagram below, number 1 is the [hangman].


[c] promoter

[f] Good!

[q] In the diagram below, numbers 5, 6, and 7, arrayed at a gene’s promoter, is called a [hangman]initiation complex.


[c] transcription

[f] Excellent!

[q] In the diagram below, the three DNA elements indicated by letter “a” together make up an [hangman]. Each one of the colored boxes represents a  [hangman] control element.


[c] enhancer

[f] Excellent!

[c] distal

[f] Great!

[q] In the diagram below, the two deleted RNA segments labeled as f1 and f2 must be  [hangman]. Once these are removed (and a few other modifications are made), the result (shown at “3”) is [hangman] RNA.


[c] introns

[f] Excellent!

[c] messenger

[f] Excellent!

[q] In the diagram below, “c” is a [hangman] control element. Letter “a” is an [hangman]. The molecule that’s binding with “c” is an [hangman]

[c] distal

[f] Excellent!

[c] enhancer

[f] Excellent!

[c] activator

[f] Excellent!

[q] In the diagram below, “d” is the [hangman]. Letter “f” is a DNA [hangman] protein. Letter “g” is a group of [hangman] proteins, and “h” is a group of general [hangman]  factors. When all of these assemble on the promoter, RNA [hangman] can finally bind and transcribe the gene.


[c] promoter

[f] Correct!

[c] bending

[f] Correct!

[c] mediator

[f] Excellent!

[c] transcription

[f] Good!

[c] polymerase

[f] Great!

[q] The main idea of the diagram below is that genes are transcribed only when the right [hangman] of activators is present.


[c] combination

[q] In the diagram below, the presence of the activators represented by the colors yellow, red, and gray result in the [hangman] of the dopamine gene.


[c] transcription

[q] A key idea represented by the diagram below is that all cells are genomically [hangman]. They express different [hangman]  in response to the presence or absence of specific [hangman].

[c] equivalent

[c] genes

[c] activators

[q] A key idea represented below is that the action of genes can be [hangman] if these genes share common [hangman] sequences.


[c] coordinated

[c] regulatory

[q labels = “top”]

 

[l]Activators

[fx] No. Please try again.

[f*] Good!

[l]Distal Control Elements

[fx] No. Please try again.

[f*] Good!

[l]DNA Bending protein

[fx] No. Please try again.

[f*] Correct!

[l]Enhancer

[fx] No, that’s not correct. Please try again.

[f*] Correct!

[l]Mediator Proteins and Transcription Factors

[fx] No. Please try again.

[f*] Great!

[l]Promoter

[fx] No. Please try again.

[f*] Good!

[l]RNA polymerase

[fx] No, that’s not correct. Please try again.

[f*] Great!

[x][restart]

[/qwiz]

7. Links