Lecture 35

Question 1

Transposable elements:

Answer 1

• Jumping genes
• Able to move from one chromosomal location to another
• Achetypes are self replicating, so they encode activities to allow themselves to replicate
• A class of ‘selfish’ DNA
• Dispersed throughout genomes
• Generally display vertical transmission through generations (germline parasites)

Question 2

Retrotransposons:

Answer 2

• Transpose via an RNA interments

- Use a reverse transcriptase, with long terminal repeats

Question 3

DNA transposons:

Answer 3

• cut and paste method of transcription

Question 4

Long terminal repeat retrotransposons:

Answer 4

• Like retroviruses but lack env, have a target site duplication and encode a number of genes
• Have long terminal direct repeats, the whole unit is 7 - 10 kb long
• eg) gypsy virus like particles, it forms viral like particles, even though it may not transfer horizontally

Question 5

How to LTR’s work?

Answer 5

• Transcribed from DNA
• Processed via poly-adenylation, which cuts off the outer ends, but these are repeated so all the material is still there
• This can be translated to give retrotransposition function
• This is processed into dsDNA
• Integration into dsDNA occurs

Question 6

RNA to dsDNA and maintenance of LTRs:

Answer 6

• A tRNA is used as a primer to generate the other strand, using reverse transcriptase
• Slippage occurs, and tRNA jumps due to homology with the RNA sequence.

Question 7

LTR retrotransposons genes:

Answer 7

• Have a polymerase gene, protease domains, RNase domains, integration domains
• Gag gene which assembles RNA into retrotransposon particules

Question 8

Non-LTR retrotransposons:

Answer 8

• Don’t have long terminal repeats, but have short repeats at the 5’ and 3’ end.
• A transcript is produced which gives a reverse transcriptase, which takes the transcript and makes it DNA
• The repeat structure means it is possible to regenerate the ends
• They don’t replicate after they have replicated once, so have no selective constraint on them at all

Question 9

Non-automomous TE’s:

Answer 9

• Use the enzymes of autonomous TE’s to excise/replicate/insert
• eg) short interspersed elements (SINES)
• Can still replicate but they rely on the proteins of other elements

Question 10

All of these elements have the RT (reverse transcriptase) gene:

Answer 10

• These are conserved and homologous

- So we can align them and draw phylogenetic trees

Question 11

Cut and paste transposons:

Answer 11

• eg) P-elements
  1. Target sit is cut and digested
  2. Transposon integrated with ITR’s on either end (inverted terminal repeats
  3. The transposon is fully integrated
  4. DNA segment is directly excised from surrounding DNA by transposase
  5. dsDNA break gets repaired by the cell with direct depeats

Question 12

Some genomes are littered with TE’s:

Answer 12

• Human’s have around 40%

Question 13

Genomes differ in relative abundance of TE classes:

Answer 13

• Retrotransposons but no DNA transposons

- Humans are mostly retrotransposons but not many DNA transposons

Question 14

Density of TE varies throughout the genome:

Answer 14

• Heterochromatin regions tend to have many TEs
• Enriched around telomeres/centromeres
• Enrich in regions of low gene density
• Generally insert in non-coding regions rather than coding regions
• Hotspots are observed

Question 15

In drosophila there at 93 different TE families:

Answer 15

• with 1 - 43 copies of each family
• Occupancy is low in drosophila: among individuals, there is high variation in where he TE are found, but they will have equal amounts of TEs

Question 16

Spontaneous morphological mutations:

Answer 16

• TE’s cause 50% of spontaneous morphological mutations in flies
• In humans s

Question 17

The spread and loss of TE’s:

Answer 17

• Horizontal transfer from another host resulted in a germ line invasion and then proliferation by transposition
• Most TE’s retain the original copy (ie, they are replicative)
• They proliferate and spread throughout the population in the same way as gene flow does (recombination and drift)
• Over time vertical inactivation may occur, further horizontal transmission may occur and stochastic loss may occur.

Question 18

Selection remove insertions deleterious to host fitness:

Answer 18

• TE insertion could disrupt coding region
• TE insertion could disrupt regulation of a gene
• TE could have no effect
• Gene inactivation
• Disrupt genome function
• Recombination facilitates ectopic exchange

Question 19

Lots of TE’s increase the chance of ectopic recombination:

Answer 19

• Ectopic exchange/illegitimate recombination may occur
• Deletions and duplications will increase in frequency
• They will reach a threshold and they can’t increase in frequency by much

Question 20

Evidence that TE’s become tamed:

Answer 20

• They replicate less over time
• Analysis of the human genome indicates different LINE families have been active at different points in evolutionary time (before gorillas and before old world monkeys diverged)
• Pairwise divergence and number of elements can be used to study this

Question 21

Other ways to age TE insertions:

Answer 21

• Seeing how nested the families of TE’s are (which TE is inside another TE)
• Degree of divergence in LTR’s

Question 22

Hybrid dysgenesis:

Answer 22

• Male that has crontrolled the TE x naive female (never seen the TE) -> progeny with high mutagenic load due to TE activity, doesn’t occur in the reciprocal cross
• P-element

Question 23

KP element:

Answer 23

• A truncated form of the P-element, which results in repression of internally deleted P-elements
• Active in the germ line but not in the soma, due to an inactive shorter protein, germ line specific splicing!

Question 24

Gypsy:

Answer 24

• An endogenous retrovirus/LTF-retrotransposon that usually does not transpose much
• Several drosophila stocks have high Gypsy mutagen
• Flamenco gene causes the Gypsy allele to move around the genome

Question 25

Mapping of flamenco locus:

Answer 25

• Mapped to the chromocenter which is a heterochromatin region, which is highly repetitive
• IT is very hard to reach this region as it is so dense
• The PIWI locus has various dead TE’s, when the PIWI locus is transcribed it is taken to a complex which is loaded into an argonaut protein which destroys similar to RNAi gene silencing

Question 26

TE domestication:

Answer 26

• Het-A and TART of drosophila: are non-LTR types, and are found in tandem repeats at telomeres but never in the other regions