Lecture 16: Transposable Elements

Question 1

define transposition

Answer 1

movement of small segments of DNA called transposable elements from one position to another in the genome

Question 2

who discovered transposition?

Answer 2

Barbara McClintock in the late 1940s, awarded Nobel prize in 1983

Question 3

define a transposable element (TE)

Answer 3

any segment of DNA that evolves the ability to move within a genome

Question 4

how did Rhoades and McClintock infer the existence of TEs?

Answer 4

from genetic studies of corn

Question 5

where are TEs found?

Answer 5

in all organisms

Question 6

how has our understanding of the impact of TEs varied over the years?

Answer 6

• previously considered to be selfish DNA carrying no genetic information useful to the host
• now it is known that some TEs have evolved functions that are beneficial to the host sometimes

Question 7

TE length ranges from

Answer 7

50bp to 10kb

Question 8

how many copies of TEs can be present in genomes?

Answer 8

TEs can be present in hundreds of thousands of copies per genome

Question 9

how did McClintock realise the presence of TEs in corn?

Answer 9

• some kernels showed a mottled coloration, rather than a uniform color
• the mutant phenotype was colourless, whereas the wild type phenotype was red
• this pattern could not be explained by standard Mendelian inheritance, since all cells in a kernel should theoretically have the same genotype and produce the same pigment.
• this suggested that gene expression was being turned on and off during development, pointing to the movement of genetic elements within the genome.

Question 10

What is the C mutable (c-m) element in maize?

Answer 10

an unstable version of the C gene responsible for kernel pigmentation. It causes mottled color due to the insertion of a transposable element that disrupts gene function.

Question 11

What phenotype does the C mutable element cause and why?

Answer 11

It causes colorless kernels with red spots, because the pigment gene is inactivated by an inserted Ds element. If Ac is present, it enables Ds to jump out, restoring gene function in some cells and producing spots of pigment.

Question 12

What role does the Ac (Activator) element play in C mutable pigmentation?

Answer 12

Ac is required for Ds to transpose. If Ac is present, it allows the Ds element to move out of the C gene, restoring pigment production in some cells.

Question 13

What is the difference between Ac and Ds elements?

Answer 13

Ac (Activator) is autonomous and can transpose on its own. Ds (Dissociator) is non-autonomous and needs Ac to move.

Question 14

If Ac can move, why doesn’t kernel color keep changing throughout the kernel’s life?

Answer 14

Kernel color is set early in development, when cells are still dividing. Ac must be present in the same cell as Ds during this time to make Ds jump out of the C gene and restore pigment. Once the kernel matures, cells stop dividing and pigment production is fixed, so even if Ac moves later, it can’t change the color anymore.

Question 15

TEs in bacteria

Answer 15

several types, inserted several times

Question 16

TEs in drosophila

Answer 16

approximately 12.5% of the genome

Question 17

TEs in humans

Answer 17

44% of the genome

Question 18

two main classes of TEs in eukaryotes

Answer 18

DNA transposons
Retrotransposons

Question 19

DNA transposons

Answer 19

move directly without being transcribed into RNA (eg TEs studied by McClintock in corn, P elements in Drosophila)

Question 20

Retrotransposons

Answer 20

move via reverse transcription of an RNA intermediate (eg copra elements in Drosophila, L1 and Alu in humans)

Question 21

further classification of retrotransposons

Answer 21

LINEs, SINEs, HERVs

Question 22

LINEs

Answer 22

encode their own reverse transcriptase and endonuclease, allowing them to copy and insert themselves into new genomic locations.

Question 23

SINEs

Answer 23

non-autonomous retrotransposons that rely on LINE enzymes to move - they do not encode any proteins

Question 24

HERVs

Answer 24

ancient LTR retrotransposons that originally encoded enzymatic components but are mostly now inactive due to mutations

Question 25

what do DNA transposons encode?

Answer 25

an enzyme called transposase that helps them cut and move to different places in the DNA.

Question 26

how was it experimentally demonstrated that retrotransposons move through an RNA intermediate?

Answer 26

An intron was added to a yeast Ty1 retrotransposon (located on a plasmid and flanked by LTRs). After splicing and reverse transcription, the DNA inserted into the yeast's genomic DNA lacked the intron, proving the RNA (not DNA) was the template.

Question 27

How do LTR retrotransposons move within the genome?

Answer 27

Target-site duplication: - they are transcribed into RNA, which is reverse-transcribed into cDNA by reverse transcriptase. This cDNA is inserted into a new genomic site via endonuclease cleavage, generating target-site duplications flanking the new insertion.

Question 28

transposon structure

Answer 28

most transposons contain two components: - inverted repeats (IRs) of 10-200 bp long at each end - gene encoding transposase, which catalyses the transposition through recognition of the IRs (cuts at border between the IR and genomic DNA)

Question 29

how do P element transposons move?

Answer 29

P element excised from its original location and is transposed to new location by transposase enzyme

Question 30

what are the two ways in which the original location where the P element was is repaired?

Answer 30

in both cases, exonucleases first widen the gap. Then there is: - repair of gap using a sister chromatid or homologous chromosome containing a P element, resulting in the transposon remaining in its original position OR - repair of gap using a homologous chromosome lacking a P element, resulting in the transposon no longer being at the original position

Question 31

how do animals and plants survive with so many mobile elements?

Answer 31

- these are usually inserted into introns - often defective and unable to transpose again due to mutations (ie lack of repeats or active transposase) - epigenetic changes from heterochromatin, resulting in no transcription/transposition - inserted into safe havens (non-essential/repetitive regions)

Question 32

cellular mechanisms that inhibit TE activity

Answer 32

- production of transposon repressors through alternate splicing - piRNAs (kiwi-interacting RNAs) that block TE transcription and translation (both DNA transposons and retrotransposons)

Question 33

consequences of transposable elements on organisation and function of genes and chromosomes

Answer 33

- unequal crossing over can occur between TEs found in slightly different locations on homologous chromosomes due to misalignment - recombination between them can lead to duplications, deletions, or inversions of the DNA between them.

Question 34

Bar eye

Answer 34

- bar gene product limits eye growth - its enhancers increase transcription of the gene Bar (one duplication of gene + enhancer): reduced expression leading to bar eye Double Bar (two duplications of gene + enhancer): even more reduced expression

Question 35

how can transposition relocate genes?

Answer 35

- two transposons can form a large, composite transposon - composite transposon can move to new location - the level of expression of the gene between them may be altered

Question 36

3 types of transposons

Answer 36

1. insertion sequence (IS) element: IR - transposase - IR 2. complex transposon (IS + genes): IR - transposase - gene - IR 3. composite transposon (two transposons) - IR - transposase - IR - gene A - gene B - IR - transposase - IR

Question 37

give examples of gene mutations caused by TEs

Answer 37

- wrinkled pea mutation likely resulted from insertion of a TE near the sbe1 gene (starch branching enzyme) - ~100 human genetic diseases i.e. forms of Hemophilia A, Hemophilia B, cystic fibrosis, neurifibromatosis, muscular dystrophy - many spontaneous mutations in the white eye gene (Drosophila)