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Lecture Comments (7)

0 answers

Post by Jonathan Aguero on December 13, 2012

as in steps

1 answer

Last reply by: Dr Carleen Eaton
Wed Jan 9, 2013 2:17 AM

Post by Jonathan Aguero on December 13, 2012

steps for gene regulation numbered 1-7?

0 answers

Post by Jonathan Aguero on December 13, 2012


2 answers

Last reply by: Armaghan Shahid
Sun Apr 21, 2013 7:43 PM

Post by Amina Tanko on October 8, 2012

We just covered this in Uni and I had no idea what was going on until now.

Thank you very much Dr. Eaton, you're a life-saver!

Eukaryotic Gene Regulation and Mobile Genetic Elements

    Coming soon

Eukaryotic Gene Regulation and Mobile Genetic Elements

Lecture Slides are screen-captured images of important points in the lecture. Students can download and print out these lecture slide images to do practice problems as well as take notes while watching the lecture.

  • Intro 0:00
  • Mechanism of Gene Regulation 0:11
    • Differential Gene Expression
    • Levels of Regulation
  • Chromatin Structure and Modification 4:35
    • Chromatin Structure
    • Levels of Packing
    • Euchromatin and Heterochromatin
    • Modification of Chromatin Structure
    • Epigenetic
  • Regulation of Transcription 14:20
    • Promoter Region, Exon, and Intron
    • Enhancers: Control Element
    • Enhancer & DNA-Bending Protein
    • Coordinate Control
    • Silencers
  • Post-Transcriptional Regulation 24:05
    • Post-Transcriptional Regulation
    • Alternative Splicing
    • Differences in mRNA Stability
    • Non-Coding RNA Molecules: micro RNA & siRNA
  • Regulation of Translation and Post-Translational Modifications 32:31
    • Regulation of Translation and Post-Translational Modifications
    • Ubiquitin
    • Proteosomes
  • Transposons 37:50
    • Mobile Genetic Elements
    • Barbara McClintock
    • Transposons & Retrotransposons
    • Insertion Sequences
    • Complex Transposons
  • Example 1: Four Mechanisms that Decrease Production of Protein 45:13
  • Example 2: Enhancers and Gene Expression 49:09
  • Example 3: Primary Transcript 50:41
  • Example 4: Retroviruses and Retrotransposons 52:11

Transcription: Eukaryotic Gene Regulation and Mobile Genetic Elements

Welcome to Educator.com.0000

Today we are going to be continuing our discussion with molecular genetics with the topics of eukaryotic gene regulation and mobile genetic elements.0002

Recall that in a previous lesson, we discussed the mechanisms of gene regulation in prokaryotic cells, and we have focused on operons.0013

Regulation in eukaryotic cells is a little bit different because genes are not organized in the operons with the single promoter.0024

However, there, of course, is gene regulation, and this occurs at multiple levels.0032

Gene regulation takes on new implications in a multicellular organism.0038

When we are looking at multicellular eukaryotic organisms like humans, cells are specialized.0043

A liver cell has a very different function and makes different products than a neuron.0052

And gene regulation allows a cell to be specialized, produce particular proteins at certain times and be differentiated from another cell type.0058

Gene regulation serves as a mechanism for specialization. We described this as differential gene expression.0068

All the cells in an organism have pretty much the same DNA in them, yet, different genes are expressed.0086

Before we even go on to talk about regulation of gene expression, I would like to define what we mean by gene expression.0092

Sometimes, you may think "OK, gene expression, the transcript gets made, the gene is transcribed".0100

However, the end product for a gene is sometimes a protein.0107

When we talk about a gene being expressed, we mean that the functional product is being made, and that allows for more levels of regulation.0112

Not only does the transcript needs to be produced, but translation must occur.0121

Modifications to the polypeptide may need to occur before you get a functional product.0126

Sometimes, the product of a gene is just RNA. They are non-coding RNAs such as tRNA, transfer RNA or rRNA, which is ribosomal RNA.0134

What we are going to focus on now is the full spectrum of gene regulation.0145

We are going to consider situations in which the product is a protein and talk about these different levels of regulation that can occur.0151

The first level of regulation would be through modification of the chromatin, so levels of regulation of gene expression.0160

One level would be at the level of the chromatin.0173

We are going to talk about modification of the DNA in histones.0177

Before the transcript is even produced, modifications can occur that can affect the level of gene expression.0182

The next level would be at the level of transcription.0191

And this is the most important level of regulation, controlling, whether or not transcription is initiated, and the rate of transcription.0195

That is an extremely important level of regulation of gene expression.0205

Post transcription is another point at which regulation can occur.0210

Recall that there are modifications such as splicing that occur on the pre-mRNA.0217

In addition, the stability of the mRNA molecule can differ from gene to gene. That is another point of regulation.0225

Once the transcript has been made, the next thing that has to happen is translation. Therefore, initiation of translation can be regulated.0240

Finally, post-translational modifications occur.0251

We are going to go through each of these, but just recall that there are multiple levels of regulation of gene expression0259

and that the most important one is the level of transcription- initiation or non-initiation of transcription.0265

Before we discuss how chromatin can be modified in order to regulate gene expression, we are going to discuss the chromatin structure.0278

In an earlier lecture, we talked about chromosomes.0286

The chromosome you see here is the DNA in the form that you could visualize under light microscope during metaphase of mitosis or meiosis.0291

And we talked about here would be the two sister chromatids, which are held together by a centromere in the long arms and short arms of the chromosome.0303

And we discussed that when we talked about mitosis and meiosis.0318

But now, let's just back up a step and recall the structure of DNA. Here, we have the DNA double helix.0322

In order for all the DNA that comprises the genome to fit inside the nucleus, it actually needs to be very tightly packed and, there is various levels of packing.0331

Looking here at now a smaller version of this DNA double helix, the first level of packing is sometimes described as beads on the string.0345

Chromatin can be looked at as beads on the string because what you see here are nucleosomes.0362

And what nucleosomes consist of are histone proteins with DNA wound around them.0374

Here, we have the nucleosomes are the beads, and the DNA itself would be the string.0391

A nucleosome here it is shown schematically as a sphere, but it is actually four histone proteins; and this gives us just how the DNA is going to be packed.0404

The next level is comprised of the association of the nucleosomes with each other.0421

And for this to occur, what has to happen is a fifth or an additional histone associates with the nucleosome.0430

And this is a slightly different type of histone, and it allows the nucleosomes to associate with each other.0440

And if you looked at this level of packing and these nucleosomes packed tightly together,0447

and you measure the width of this fiber, you would find that it is 30nm.0454

So, this is sometimes known as the 30nm fiber, and it results from nucleosomes associating with each other.0459

The next level of packing, it occurs when there is a looping of the chromatin.0480

And if you took this chromatin right here and formed loops from it and then, measure the width,0488

you would find that it is 300nm, so this is called the 300nm fiber.0496

These looped fibers are, then, further wound up, looped around, compressed,0502

packed, to give you this final form that we see when we are able to visualize DNA in the light microscope during mitosis or meiosis.0508

These various levels of packing allow a lot of DNA to fit in a small space.0523

Here, you can see that histones clearly have a structural function in chromatin, but they also have a regulatory function.0530

Before we go on, note that during interphase, this chromatin can exist in two general forms:0538

loosely packed euchromatin or heterochromatin, which is more tightly packed.0546

When the chromatin is more loosely packed, when it is in the euchromatin form, genes are accessible to be transcribed.0554

The RNA polymerase and the transcription factors need to be able to get to the promoter region.0562

And in order to do that, the DNA cannot be too tightly packed.0569

By contrast, heterochromatin is more tightly packed.0573

And therefore, the genes in DNA, when it is in the heterochromatin form, are not accessible for transcription.0577

Therefore, a mechanism by which gene expression can be regulated is chromatin structure0585

because the chromatin structure affects whether or not transcription will occur.0593

One type of modification of chromatin structure is acetylation of the tails of the histone protein.0600

One mechanism is acetylation, and that is the addition of an acetyl group which is COCH3 of histones.0610

When the histone proteins are acetylated, the nucleosomes cannot pack as tightly together.0623

I described how we have these beads on a string arrangement, and then, these nucleosomes can associate together to form the 30nm fiber.0631

Well, when the histones end up acetylated, these cannot pack as tightly together.0637

The result is chromatin is less tightly packed, and then, we get increase transcription because the DNA is more accessible to RNA polymerase.0646

There are other chemical modifications that can occur on histones, as well.0667

This is just one example, and these other modifications may act like this one to make the chromatin less tightly packed0671

so that there is increased transcription or more tightly packed so that transcription is decreased,0678

so less tightly packed, increased transcription, more tightly packed, decreased transcription.0687

Now, we are talking about chemical modification of the histones, but in addition to histones, obviously, a major part of the chromatin is the DNA itself.0694

And chemical modifications can occur on the DNA, and it has been observed that DNA can be methylated in this chromatin form.0703

We have acetylation of histones. That is one type of modification of chromatin structure.0715

The second is DNA methylation.0720

It has been observed that genes that are methylated or more heavily methylated are less frequently expressed than other genes.0727

DNA methylation decreases expression of a gene or genes.0737

Therefore, if a particular cell does not need certain genes to be expressed, perhaps those genes, that DNA region would be methylated.0749

And this type of inactivation appears to be long term, so a cell does not need a certain protein.0759

It can methylate that region of DNA. That will stay quiet.0765

Interestingly, when a cell divides, daughter cells carry the same methylation pattern.0770

This pattern is actually passed on from the parent cell to the daughter cell.0776

The same set of genes that are methylated in one cell will be methylated in the daughter cells.0783

What we are seeing is the regulation being passed on from cell to cell is called epigenetic.0793

and this is a word you may here in other context; and epigenetics is a very interesting area of study.0799

When we say epigenetic, we are talking about a change in the DNA structure that is heritable. It is passed along, but it is not a change in the DNA sequence.0806

It is an inherited change in the DNA, but it is not a change in the actual nucleotide sequence.0816

This is a type of epigenetic regulation because it is due to a change in the DNA structure. There has been a modification of the DNA.0837

It is passed along, but it is not an actual change in the nucleotide sequence.0845

Alright, this is the first level of regulation of gene expression at the level of the DNA in the histones- chromatin.0853

The second and extremely important level is the regulation of transcription.0861

Just reviewing what we talked about earlier on about how transcription occurs, recall that there is a promoter region.0868

And this is where the RNA polymerase plus transcription factors bind, and these two together can form a transcription initiation complex.0876

And this will get transcription going, and the promoter is usually upstream of the gene that is being expressed.0901

Here, it shows these different boxes, but this is all part of one gene.0908

This might be an exon though, and this is an intron, exon, intron.0913

But again, eukaryotic DNA is not organized into operons, so a promoter is not going to control various different genes.0919

We are just going to have this promoter controlling this particular gene.0927

For many genes, the base rate of transcription is not that high.0935

If you just looked at a gene, studied it and saw "OK, the transcription initiation complex does bind". It makes mRNA, but it is just not making that much.0940

Really, to get things truly activated into a high level of gene expression, what is often needed is additional factors.0953

And what we are going to talk about right now is something called enhancers.0962

Enhancers are one type of control element. Control elements are segments of DNA that can be bound by proteins and therefore, regulate transcription.0967

Control elements, in general, are segments of DNA that can be bound by proteins in order to regulate transcription.0986

And there are various types of control elements. An enhancer contains multiple control elements that bind to activator proteins.1010

Enhancers contain multiple control elements, and these control elements are bound to activators in order to increase the level of transcription.1022

So, there might be multiple segments within an enhancer, and these proteins can bind there.1040

In particular, enhancers are known as distal control elements.1046

And they may be located very distant, even thousands of base pairs away from the gene that they are regulating transcription for.1051

They could actually be located upstream of the gene. They could be downstream of the gene.1064

They could even be located within an intron, and that is why this line is shown here, to show that there is some1069

distance between the enhancer and the promoter, that enhancer does not need to be near the gene to regulate it.1076

How does it go about regulating it if it is a thousand base pairs away?1081

Well, what happens is a particular type of protein or group of proteins called DNA-binding proteins, bending - not binding, bending- DNA-bending proteins.1086

Here, we have an example of the DNA-bending protein.1100

Actually, can bend the DNA and bring the enhancer in close proximity with their promoter.1106

What happens is an activator protein, which is shown here in purple - I will use red for that one here - here we have activator protein.1111

The activator protein can bind to the enhancer, so they bind.1123

Then, the DNA-bending protein will bend this portion of the DNA, bring the enhancer close to the promoter.1129

The next thing that can happen is that the activator proteins can bind to what is called mediator proteins.1137

And these mediator proteins are going to facilitate the interaction between the activator protein and the RNA polymerase and its transcription factors.1149

What we have here is activator proteins, mediator proteins - those are shown in dark green - and then the other proteins could be other mediator proteins.1161

Or they could be transcription factors, and here, we have the RNA polymerase.1173

What the formation of this whole protein complex does is it facilitates the formation of the transcription initiation complex.1185

Thus, it is going to increase the rate of transcription.1193

Maybe, transcription could occur without this enhancer activity, but it is not going to occur at as higher rate as if we have1196

the enhancer with its activator proteins and then, the mediator proteins helping this transcription initiation complex to form.1205

In fact, a particular gene might be regulated or controlled by multiple enhancers.1213

We could have another enhancer maybe over here. There could be another one downstream, and these might bind to different activators.1218

Therefore, at certain times in the cell's life, this enhancer maybe working or maybe another one. There can multiple enhancers regulating a particular gene.1230

Repressors decrease the rate of transcription of a gene.1241

It is possible for certain repressors to bind and then, prevent the activator from binding.1247

Repressors can also act by other mechanisms. They can also affect chromatin structure.1258

They might change the level of acetylation or cause the - as we talked about -1262

chromatin to be more tightly packed so that transcription rates would not be as high.1270

Again, the enhancer is going to increase the level of transcription. This repressor could decrease the level of transcription.1275

The mechanism, then, for coordinately controlling sets of genes in eukaryotic organisms can involve specific combinations of control elements and activators.1286

In a bacterial cell, you might see that "OK, three genes are needed to be activated to break down lactose".1298

All of those are under the control of an operator and a single promoter and organizes an operon.1306

That does not happen here, but we still can get coordinate control of genes.1312

So,let's say the cell needs three genes to be activated at the same time.1318

Those genes do not even need to be clustered near one another because what can happen is, let's say I have a gene on one piece of DNA,1327

I have a gene on another piece of DNA or on another area of the chromosome and then, a third one, and these only need to be turned on at once.1337

Well, one mechanism that could work would be if these three genes all had enhancers that bound to the same type of activator.1344

Coordinate control can occur through combinations of control elements and activators.1355

If a particular activator is present, it might activate transcription from multiple genes even though those genes are not clustered near one another.1369

So, we still get coordinate control.1378

Another term you should be familiar with is silencers, so we talked about enhancers.1382

Silencers are also control elements, and like enhancers, they might be located far distant from the gene they control.1388

Silencers are control elements, and they bind repressors; and they decrease transcription.1397

Here, we see an enhancer binding to an activator and increasing the level of transcription. We have a repressor that could block that.1410

We also could have a separate segment of DNA that is a silencer segment that could bind to a repressor, thus, decreasing transcription.1416

This is an extremely important mechanism of regulation of gene expression.1426

So far, we have gone through regulation of the DNA level.1429

Now, we have gone through regulation at the level of initiating or regulating the rate of transcription.1433

Once transcription has occurred, what the cell ends up with is a primary transcript.1440

Recall that we have got here a segment of DNA and 5' to 3'-end, and then, it is transcribed. The initial product is going to be what we call pre-mRNA.1445

In order for this to actually form or be described as mRNA and function as mRNA for translation, it is going to have to go through some processing.1471

This processing allows for another level of control of gene expression because if the end product is a protein,1483

the gene is not truly expressed until a functional protein exists.1492

Recall some of the types of post-transcriptional modification that occur to convert this pre-mRNA to an mRNA.1497

One post-transcriptional modification is splicing.1507

Post-transcriptional modification, recall one is splicing. We also have addition of the 5' cap and 3' poly(A) tail.1514

We have a piece of DNA, and a lot of that DNA does not actually contain material or sequence that can be translated.1530

Those segments that are not translated are referred to as introns, and those need to be spliced out.1543

We have the DNA, and let's say this is an exon number one; and then, here we have an intron, an intron, exon number two and exon number three.1552

The primary transcript that forms the pre-mRNA is going to contain both exons and introns.1566

It is going to have all these same nucleotides. It is going to contain all of that information- exon and intron sequences.1578

We do not need all these extra interrupting sequences for when translation occurs, so what happens is splicing.1590

During splicing, these introns are cut out, and the exons end up right next to each other like this.1600

It is possible to make different but related proteins from a primary transcript like this. This is one way that splicing can occur.1616

Another way that splicing could occur, would be to actually clip out, let’s say, this middle exon and then you would end up with just exon one and exon two.1624

And this going to be a related polypeptide to this first one, yet, different.1634

Another way to regulate gene expression is through alternative splicing.1640

If the cell needs this protein but not this one, actually what happens is regulatory proteins1644

bind to the mRNA and determine which of the alternate splicing pathways will occur.1662

This is another level of regulation, and again, this is mediated through proteins that bind to the RNA.1671

Another mechanism of regulation post transcriptionally besides alternative splicing has to do with the stability and longetivity of the mRNA.1684

In prokaryotic cells, mRNA only last a few minutes. However, in eukaryotic cells, messenger RNA can last hours, days and even longer sometimes.1694

And if you think about it, if an mRNA transcript only lasts a few minutes,1708

not that much protein can be produced obviously compared with an mRNA transcript that last days.1713

Therefore, if the cell needs a lot of a particular protein, it could regulate that by having mRNA for those proteins lasting longer.1721

And it has been found that specific sequences near the 3'-end of an RNA molecule may determine the stability and longetivity of that molecule.1731

So, there are sequences near the 3'-end of RNA. It may determine the stability or half-life of the molecule.1743

A particular sequence may let the cell know "OK, degrade this mRNA pretty rapidly".1770

Well, it is known that the cap and the tail protect the ends of the RNA molecule.1784

And it is thought that shortening the poly(A) tail will trigger degradation of the mRNA.1789

There is sequences near that 3'-end that somehow can trigger this degradation to occur.1794

Finally, research in the past decade or so has shown that non-coding RNA molecules also play a role in the regulation of gene expression.1802

We have talked about non-coding RNA molecules like transfer RNA and ribosomal RNA that have important functions in the cell.1814

And relatively recent discoveries have shown other types of non-coding RNAs.1821

Two of these are microRNAs. These are known sometimes as miRNAs and siRNAs.1825

si stands for small interfering RNAs.1834

Looking first at microRNAs, miRNAs, miRNA molecules are single-stranded RNA molecules that can bind to complimentary sequences on messenger RNA.1843

They bind complementary sequences on mRNA, and what this can, then, cause is it can block translation,1857

which we are going to talk more about the translation step in a minute, but another possibility is that can trigger RNA degradation.1872

Rather than just regulating post transcription regulating gene expression through binding of regulatory proteins,1887

non-coding RNAs may also play a role in this regulation.1896

siRNAs function similarly although they are made from a different precursor molecule.1900

And they are also thought to play a role in modification of chromatin structure, as well.1907

Post-transcriptional regulation- multiple ways in which this can occur: alternative splicing to make different proteins from the same primary transcript;1913

differences in the stability of a messenger RNA molecule.1925

Some messenger RNA molecules are unstable of the short half-life, and they are rapidly degraded. Others can last much longer.1928

And finally, recall that non-coding RNA molecules can play a role in the stability of an RNA1935

molecule in allowing translation to occur or blocking it and in the modification of chromatin.1942

Now that transcription has occurred, presumably modification has occurred, splicing, the addition of that cap and tail, we have the messenger RNA.1952

And then, the messenger RNA is transported out of the nucleus into the cytoplasm where translation can occur.1961

Translation is another step where expression of a gene can be regulated.1970

Recall that translation begins at the start codon, and the start codon codes for the amino acid methionine; and the start codon is AUG.1976

Initiation of translation can actually be blocked so the ribosome would not be able to bind and move along.1988

and translation will not occur via the bonding of the regulatory proteins.2000

You have your messenger RNA molecule, and for translation to occur, the ribosomal complex will actually need to initiate translation.2005

However, regulatory proteins could bind and thereby block...let’s say we have the ribosome here.2021

This regulatory protein could block the ribosome from being able to initiate the translation.2034

It would not be able to actually translate this transcript into a polypeptide.2041

Just as we talked about with transcription, you get the RNA transcript, and modifications occur, capping in the poly(A) tail.2053

Well, recall that once the amino acid sequence has been translated, and we get a polypeptide that polypeptide also...so, we get translation.2062

We get a polypeptide, and then, we get modification of polypeptide. Some proteins are not functional without these modifications.2075

Modifications can include things like adding functional groups, so addition of functional groups.2084

With some proteins, for them to be active, there needs to be cleavage. Certain sequences can be removed or separated.2097

Again, this is another level at which regulation can occur.2107

Proteins might be activated or inactivated by a modification, so even though the protein exists, it could be inactivated or activated.2111

Longetivity of proteins varies as well. We talked about mRNA molecules.2122

Some last longer. Some last shorter, same thing with proteins.2128

Some proteins are more stable. Some are less stable.2131

There is a protein called ubiquitin, and when ubiquitin binds to a protein- ubiquitin is a protein.2134

And when it binds to another protein, it signals that the protein should be degraded.2146

Ubiquitin binds to a protein and signals protein should be degraded.2152

There are protein complexes in the cell called proteasomes, and what these proteasomes do is they degrade proteins.2166

They will actually unfold the protein, cleave it up in the polypeptides.2177

And then, those polypeptides get released into the cytoplasm where enzymes can break them down even further.2182

Again, regulation, once the mRNA has been made, it has been exported into the cytoplasm, the cell can still regulate the ultimate outcome.2189

It can regulate it through the binding of regulatory proteins that will block translation. There will be no translation occurring.2199

Regulation can also occur via the addition of functional groups, cleavage of certain sequences, thus, activating or inactivating the protein.2208

Finally, degradation of the protein can occur once ubiquitin has bound2218

and signals a proteasome to go ahead and unfold and break down that protein into peptides.2224

We have talked about various mechanisms of regulation of gene expression, which is obviously very important for the correct functioning of the cell.2232

One outcome if genes are not being properly regulated is malignancy.2239

Cancer can occur if a gene is not being expressed when it should or it is being overexpressed, and then, a tumor can form.2246

This is a very important area of research in the field of oncology.2254

We discuss now mechanisms of eukaryotic gene regulation, the second topic that we are going to discuss today briefly is that of mobile genetic elements.2260

We are going to focus on a particular type of mobile genetic element called a transposon.2271

First of all, what are mobile genetic elements? Mobile genetic elements, their name tells you what they are.2277

They are segments of DNA that can actually move to new locations in the genome.2284

This is the general name. There are multiple types of these, and one type is transposons, which are transposable genetic elements.2296

Sometimes these are known as jumping genes. Not completely accurate name, but it gives you the idea that they can move around.2305

The history of the discovery of transposons goes back to the 1940s when a scientist named Barbara McClintock was studying maize.2317

And she did a series of breeding experiments and genetic studies on maize.2328

Maize is sometimes known as Indian corn, and it is a type of corn you may have seen that produces different patterns of kernel color.2336

The kernels are not just all yellow. There is various patterns that can be produced.2346

And Barbara McClintock closely studied these patterns and bred corn and took note of what the patterns looked like with the variations were.2351

And she determined that the only way that particular patterns could occur is if there were genetic elements that were actually moving around the genome.2360

And she postulated that these segments of DNA that moved around the genome would2369

insert into other segments of the genome where the color of the corn kernel was controlled.2374

Thus, when these segments moved they would disrupt the genes for corn kernel color and change the color.2382

Initially, Barbara McClintock's work was not very well received.2391

At that time, a lot of people in the scientific community thought this could not happen. Genetic elements cannot move around.2396

Pieces of DNA cannot go and insert to other areas.2404

For many years, her work was not fully recognized, but in the early 1980s, she actually did receive a noble prize for this work.2407

There are couple of different ways in which these segments can insert into other areas of the genome.2417

First, when we just say transposons, we talked about one mechanism, and there are also retrotransposons which use a slightly different mechanism2424

Transposons can be thought of as having what is often described as a cut and paste mechanism.2440

These segments of DNA can be cut out of their original location and then, insert into a different location in the genome.2452

The second type of mechanism which occurs in retrotransposons can be thought of as a copy and paste mechanism.2463

This is slightly more complicated.2473

Let's say we have a piece of DNA, and this is my double-stranded DNA; and there is - within it - this transposon.2475

We have DNA and actually these retrotransposons are able to use an RNA intermediate to copy themselves.2495

This DNA on the genome would be reverse transcribed into an RNA molecule.2506

This RNA molecule is, then, used as a template to form DNA.2520

And once we have that single strand of DNA that can be used as the template for the second strand and then, this can go insert elsewhere in the genome.2530

Looking at this, this might sound familiar.2543

Back when we talked about retroviruses, we talked about this kind of reverse transcription2545

using an RNA intermediate to form DNA and this enzyme is also reverse transcriptase.2550

That is the enzyme that catalyzes this process of going from RNA to DNA.2560

It requires the enzyme reverse transcriptase, and in fact, scientists can find reverse transcriptase in cells that are not infected with retroviruses.2571

This is a process that does not just occur in viruses but that actually occurs in transposons.2588

Some transposons are more simple. They are just what is called insertion sequences.2595

The insertion sequences just encode gene for an enzyme called transposase.2605

We see the ase ending that tells us it is an enzyme, and this is the enzyme that allows the DNA sequence to insert elsewhere in the genome.2619

Insertion sequences- simple. They just have encoded transposase that allows them to insert elsewhere in the genome.2631

There are other transposons that are more complex like ones for corn kernel seed color would be an example.2638

Complex transposons not only would contain DNA coding for transposase, but they would include other genes.2646

Insertion sequences just contain the gene for transposase.2659

Complex transposons contain this gene. They also include other genes such as the one for corn kernel color.2667

As you can imagine, transposons are mutagens because if you have DNA moving around2675

and inserting into various sequences, that is causing a change in the DNA sequence.2683

And if this insertion happens to occur in an area of the genome that affects gene regulations, that could cause big problems.2688

And in fact, that is an area of study when we look at cancer- could transposons play role by disrupting regulation of gene expression.2696

OK, now we are going to go ahead and do some questions to review what we just discussed and example one.2708

If the cell does not need a particular protein, what are four mechanisms through which the cell can decrease production of the protein?2715

This is only asking for four however, there are many more mechanisms.2723

Starting at the beginning, thinking about chromatin, one thing that can occur is modification of chromatin.2728

In particular, if the DNA is methylated - you methylate the DNA - the genes in that segment of DNA will not be as frequently transcribed.2740

The first mechanism would be the modification of chromatin through either modifying the histone or the DNA.2756

The second level would be regulation of transcription. The cell could decrease the level of transcription, and we talked about ways that could occur.2765

This might be through a silencer that binds to a repressor and decreases the level of transcription.2778

It might be that a repressor protein blocks an activator from binding to an enhancer.2784

So, decrease level of transcription and this could be via a silencer or a repressor blocks - I will just say blocks - the enhancer.2790

It blocks binding of the protein to the activator enhancer.2808

Third mechanism following decrease in the level of transcription or blocking the initiation of transcription2813

would be regulation at the level of post-transcriptional modification.2819

Alternative splicing: if a cell does not need a particular protein, regulatory proteins might bind to that mRNA.2824

And the transcript could be spliced in a different way so that different protein is created, or another thought is decrease stability of the mRNA.2833

If a protein is not needed or not much of it is needed, there might be sequences near the 3'-end that causes that mRNA to be degraded more rapidly.2849

This gives us four but just to be complete, you might have chosen some other options for example regulation of translation.2858

Translation might be decreased, so decrease the initiation of translation.2870

Even after the mRNA has been translated, and we have got a polypeptide, regulation could occur post-translationally.2880

The polypeptide could be modified in such a way so as to inactivate the protein, cleaving off groups, adding groups to inactivate the protein.2894

If the cell needs to decrease production of a protein, it could start up at the DNA level to decrease the level of transcription at the RNA level,2906

at the post-transactional level and then, finally, at the level of translation, and finally, even the active protein, you can deactivate it so that it is not working2916

That actually would not decrease the production but because it has already been produced, but what it would do is decrease production of the active protein.2930

This one really is not decreasing production. These five are.2938

Here, the proteins have already been produced but just to note that you can inactivate the protein.2943

Enhancers can regulate transcription although they may be located thousands of nucleotides away from a gene's promoter.2951

How can enhancers affect gene expression form such a distance?2958

Recall that you could have an enhancer sequence, and then, let's say this is 5'end, the promoter might be here; and then, we have the gene.2963

This distance can be thousands of nucleotides.2981

Well, recall that activators bind to the enhancer, and DNA-bending protein brings the enhancer near the promoter.2984

The DNA-bending protein could bind somewhere in this region and cause the enhancer to be brought in proximity to the promoter.3014

Mediator proteins, deactivator protein, transcription factors in the RNA polymerase, all form a complex that allows the transcription rate to increase.3024

Example three: how can a cell produce multiple proteins from a single primary transcript of a gene?3042

Recall splicing. If I have a DNA sequence that consists of various exons, exon 1, intron, exon 2, intron, exon 3, there are multiple ways splicing can occur.3049

This DNA would be transcribed to form an RNA primary transcript that would contain all of these sequences.3076

And then, one possibility is to splice so that these introns are removed and we get E1, E2 and E3 all together, and a protein is made from that.3084

Another possibility might be to - as I described earlier - splice this one out, or if there is even more exons, there is more possibilities.3099

Or perhaps this could be cut out, and then, you could end up with maybe just E1 and E3 or this mRNA or E1 and E2 only.3106

A single primary transcript can produce multiple related proteins through alternative splicing.3125

Example four: it has been postulated that retroviruses evolved from retrotransposons.3133

What similarities between the two provide support for this theory?3140

Recall that retroviruses, if you think about their life cycle, they insert into the host cell's genome and that they also use an RNA intermediate to form DNA.3145

If you think about what retrotransposons do, it is pretty similar. Retrotransposons can insert into DNA.3164

This time, the host cell is, say, all the same genome.3173

But nonetheless, they are able to insert into a segment of DNA, and they use an RNA template to make DNA.3177

The two ways in which retroviruses and retrotransposons are similar is both can insert into the genome.3186

Retroviruses are inserting their viral DNA into this host genome.3199

Whereas, in a retrotransposon, the host cell DNA is just moving from one area of the genome to another. They are still inserting.3209

Both retroviruses and retrotransposons also use RNA as the template to make DNA, and this process requires reverse transcriptase.3219

I am going to say "using RT, which is the enzyme reverse transcriptase".3237

Both of those facts provide evidence for the theory that or support for the theory that retrotransposons and retroviruses may be related.3245

That concludes this lecture on eukaryotic gene regulation and mobile genetic elements.3258

Thanks for visiting Educator.com.3264