Mobile Genetic Elements

Question 1

What are conservative (cut-and-paste) transposons?

Answer 1

Elements that are cut away from their original sites and invade elsewhere in the cell genome.

Question 2

What are replicative (copy-and-paste) transposons?

Answer 2

They make a copy of themselves to move elsewhere in the genome.

Question 3

Describe features of IS sequences.

Answer 3

High simplicity
Very short genetic sequence.
Found in circular DNA of bacterial cells.
Can move from 1 site to another.

Question 4

Describe the conservative (cut-and-paste) mechanism.

Answer 4

The acceptor region is cleaved at different sites to produce protruding ends (as the cleavage isn’t blunt).

Then the IS is inserted.

The genome will need to repair single strand regions by DNA polymerase, which will copy the single strand remaining of the cleavage, producing a direct duplication of the target site.

Question 5

Describe composite transposons?

Answer 5

A central region representing 1 or more genes, often coding for antibiotic resistance.

They are flanked by direct repeats or IS sequences, owning their own inverted repeated sequences.

They move by conservative transposition.

Question 6

Describe how transposase is involved in conservative transposition.

Answer 6

The enzyme responsible is transposase. They bind at ends of transposon and mediate integration into the new genomic location.

Gene coding for transposase is present in the IS composite transposition.

Question 7

What are non-composite transposons?

Answer 7

They are longer than composite transposons. They are mostly important in bacteria also for antibiotic resistant genes.

Though they don’t include IS and move in a different modality of replicative instead of cut and paste.

Therefore everytime it moves, the number of copies in the genome increases.

Question 8

How do transposons in eukaryotes move?

Answer 8

Uses a DNA intermediate.

Uses a copy and paste mechanism (replicative). They replicate themselves, these additional copies move and invade elsewhere in the genome.

Question 9

How do retrotransposons in eukaryotes move?

Answer 9

Also found in retroviruses.

Formation of a RNA copy that encodes for reverse transcriptase. This enzyme can synthesise DNA from RNA.

Retrotransposon can’t move by simple replication. This new DNA copy will be inserted elsewhere on the genome.

Question 10

Describe the frequency of transposable elements and its main family in primates.

Answer 10

Transposable elements, particularly retrotransposable elements are frequent in the eukaryotic genome.

A large part of transposable elements consist of a family called Alu elements. They are highly present and transcribed, but their function is unknown.

Question 11

What are LINE 1 sequences?

Answer 11

A type of retrotransposon contained in human sequences.

They are larger and have lower rate of transposition, they may be very important in regulating gene expression.

Question 12

How much of human genome are made up of potential mobile elements?

Answer 12

45% of the human genome is made of repeated sequences which are potentially mobile elements.

Question 13

Describe the differences between LINE and SINE.

Answer 13

LINE codes for proteins while SINE doesn’t code for anything. Their proteins are probably derived from mutagenesis.

SINE are remnants of LINE. Therefore they are small parts of longer LINEs.

LINES are larger with lower rate of transposition.

Question 14

Which class of retrotranposons are Alu elements found?

Answer 14

Alu elements are a part of SINE.

Question 15

How does SINE move?

Answer 15

They are non-autonomous in movement and can only move when the products of SINE acts on them.

Question 16

Describe DNA transposons in humans.

Answer 16

Some can move through conservative transposition (cut-and-paste).

3% in the human genome, e.g. MER1 and MER2.

Now inactive (molecular fossils).

Evidence that they have been important for gene movements during evolution.

Question 17

Describe retrotransposons in humans.

Answer 17

20% of human genome.

LINE enzymes can move SINEs, which are non-autonomous, e.g. Alu.

Moves via replicative transposition through a RNA intermediate.

Question 18

Describe the Barbara McClintock study in corn kernels.

Answer 18

Barbara McClintock made breeding experiments with Indian corn.

She discovered changes in colour that made sense only by postulating that genetic elements move from other genome locations into the genes for kernel colour.

Question 19

Describe the findings of the Barbara McClintock study in corn kernels.

Answer 19

In violet corn kernels, an inact C gene promotes normal pigment production.

In uncoloured kernels, the C gene is disrupted by the Ds gene, which has moved into the C gene.

In spotted kernels, Ds gene transpositions out of C gene during kernel development.

Although Dc (dissociator) is not autonomous, and needs to be activated by Ac (activator).

Question 20

Describe how L1 element cause exon shuffling?

Answer 20

Transduction is when L1 elements carry sequences flanking the element from their source location to a new location. This can be on either the 3’ or 5’ end.

When this is transcribed, either the 3’ or 5’ end will be included with the L1 element into mRNA and then cDNA.

cDNA will be inserted elsewhere, representing a new region. This results in exon shuffling, or insertion of regulatory sequences such as transcription factor binding sites at the new genomic location.

Question 21

How can L1 elements affect mRNA transcripts?

Answer 21

Inside L1 elements, there are splice sites. If transposon integrates inside the intron of the gene, the slicing of the gene will be completely changed.

The gene will use splicing signals present in the L1 element instead of its normal one resulting in alternative mRNA transcripts that are very likely not active.

L1 elements contain polyadenylation sites. If the L1 elements are inserted before another polyadenylation site, transcripts will use this premature polyadenylation site, which means mRNA will be interrupted and be a premature one.

L1 elements contain promoter regions. If promoters are recognised, there will not only be transcription of L1, but another transcript will be started that spreads into 3’ regions. Or if used in thr 5’ direction, the transcription of an unexpected non-coding RNA.

Question 22

How can L1 elements affect nearby genome?

Answer 22

L1 elements can undergo epigenetic modifications. Their modifications can be spread across the gene.

This could lead to activation or silencing of neighbouring genome that shouldn’t be.

Question 23

Describe the HIV replication cycle.

Answer 23

HIV is a lengthy virus made of a core where there is RNA and a protein called reverse transcriptase. They have a membranous envelope included in an external envelope. On the external side is the protein GP120 in order to recognise the receptor on lymphocytes.

Once the GP120 is bound to the CD4 receptor, these 2 membranes fuse (viral and cellular membrane) so that the external part remains outside and the core of the virus enters into the cell.

RNA and reverse transcriptase is released from the viral core. Reverse transcriptase can copy viral RNA into DNA copies. This viral DNA can enter the nucleus and integrate into the genomic DNA of cells via integrase.

From now on this DNA is transcribed into viral RNA. Parts of this viral RNA are used to reproduce new viral particles while other parts are translated to produce all the proteins needed for the virus.

Question 24

How do retrotransposon cDNAs insert into a new DNA sequence?

Answer 24

The L1 elment is translated into RNA, which is polyadenylated.

mRNA moves into the cytoplasm, where its translated to produce polypeptides ORF1 and ORF2.

They remain bounded to the mRNA as it’s imported back into the nucleus.

1 polypeptide starts knicks the chromosomal DNA. Whilst RNA remains there to be used as a primer for the synthesis of the cDNA copy.

cDNA is inserted into a new site in the genome.

Question 25

How can retrotransposons lead to crossing over?

Answer 25

The production of new transposable elements by replicative ways means production of new copies which invade new sites in the genome.

This can be the substrate for new recombination events.

If there are 2 copies of the same kind of transposons on different chromosomes, this may lead to crossing over between chromosomes that shouldn’t cross over because they are not homologous, but they do have homologous sequences.

Question 26

How can transposons lead to crossing over?

Answer 26

The production of new transposable elements by replicative ways means production of new copies which invade new sites in the genome.

This can be the substrate for new recombination events.

If there are 2 copies of the same kind of transposons on different chromosomes, this may lead to crossing over between chromosomes that shouldn’t cross over because they are not homologous, but they do have homologous sequences.

Question 27

Describe how crossing over between homologous transposons can lead to duplication/deletion.

Answer 27

Chromosomes with 2 or more transposons line up to cross over, but may cross over incorrectly to result in a chromosome with deleted regions and one with duplicated regions.

Consequently the sister chromatids pair unequally, thus produces a chromosome with a deletion and one with a duplication.