L12 Transposable Elements

Question 1

Transposable Elements

Answer 1

• mobile elements, “Jumping genes”
• able to move from one chromosomal location to another
• archetypes are self-replicating; encode activities to allow themselves to replicate
• class of “selfish” DNA
• dispersed throughout genomes
• generally display vertical transmission throughout generations

Many TEs retain the original copy, are replicative

Question 2

Classes of transposable elements

Answer 2

1. Retrotransposon: transpose via RNA intermediate “copy and paste”
   1a. Long terminal repeats
   1b. Non-LTR
2. DNA transposons: no RNA intermediate, “cut and paste”

Question 3

LTR Transposons

Answer 3

See OneNote diagram

• encode 2-3 genes including gag and pol, sometimes has a 3rd ORF
• similar to retroviruses but lack env genes

LTR

• important for replication process of retrotransposons
• have different parts

Question 4

pol gene

Answer 4

many different functions e.g. reverse transcriptase

Question 5

gag

Answer 5

assembly of RNA into a retrotransposon particle

Question 6

Non-LTR Transposon

Answer 6

See OneNote
- line elements belong to this class, vast majority of LINE1 elements in human are d.o.a. or otherwise unable to mobilise

Question 7

Non-autonomous TE

Answer 7

Use the enzymes of autonomous TE’s to excise/replicate/insert e.g. SINEs

Question 8

SINES

Answer 8

See OneNote

Derived from LINES and an RNA made by RNA-POL3
e.g. Alu element

Alu element

• Occurred in the early primates, now present in all primate genomes
• Rare event that create it and allowed it to proliferate

Question 9

DNA transposons

Answer 9

See OneNote

1. DNA segment excised by transposase
2. Original site has a DNA break which gets repaired by the cell

“cut and paste”

Don’t go through RNA intermediate, replicate at the DNA level

Different transposons leaves different footprints behind once they have been excised. Have inverted terminal repeats.

Question 10

Genomes differ in relative abundance of TE classes

Answer 10

See OneNote

TEs are almost everywhere

Question 11

Bdelloid rotifers

Answer 11

See OneNote

- Muller’s Ratchet

Question 12

TE spread in asexual organisms

Answer 12

See OneNote

First lineage not mixing with other lineages as there is no sex

Question 13

TE spread in sexual organisms

Answer 13

See OneNote

Recombination will occur, TE elements put in different genetic backgrounds and spread throughout the population => sexual populations tend to have lots of TE

Question 14

The sequenced genome of Drosophila

Answer 14

See OneNote

Where the different TE elements are in the reference genome

Heterochromatin tend to be repeat rich, sequencing requires long reads. Heterochromatin richer in TE than in euchromatin.

Near telomeres and centromeres, more TE

Question 15

The unequal genome distribution of TEs

Answer 15

• dense distribution in heterochromatin
• enriched around centromere/telomere
• enriched in regions of low gene density
• generally insert in non-coding regions rather than coding regions
• hotspots are observed e.g. in singed genes

Question 16

Occupancy

Answer 16

“occupancy” = look at one particular insertion, unlikely that a different fly will have a TE at that exact site

Most flies would have a particular TE at a particular site, selected for or in LD with something nearby that is selected for e.g. Doc1420 infers resistance to insecticide

High occupancy in humans but low in flies

Question 17

Spontaneous morphological mutations

Answer 17

• TEs cause 50% spontaneous morphological mutations in flies
• TEs cause 10% spontaneous morphological mutations in mice
• <0.2% human mutations are TE based: only non-LTR currently active, 96 disease causing mutations known

Question 18

P-elements crossing species barriers

Answer 18

See OneNote
Can age TE by looking at silent sites and using the molecular clock, if silent sites is much older then transfer must be due to horizontal transfer?

Question 19

The spread and loss of TEs

Answer 19

See OneNote diagram

• active genome defense?
• horizontal transfer
• vertical inactivation: mutations accumulate or excision
• stochastic loss by genetic drift

Question 20

Selection removes TEs because they are deleterious to host fitness

Answer 20

deleterious because:

1. gene inactivation
2. transcripts and proteins nick genome and disrupt genome function
3. facilitates ectopic exchange

Question 21

Selection removes insertions deleterious to host fitness

Answer 21

See OneNote

Question 22

Lot of TEs increase the chance of ectopic recombination

Answer 22

See OneNote

Question 23

Analysis of human genome indicates different LINE families have been active at different points in evolutionary time

Answer 23

See OneNote

Evidence of inactivation over time

Question 24

Aging TE insertions

Answer 24

See OneNote

1. Nested nature
2. LTR mutation accumulation

Question 25

Hybrid Dysgenesis

Answer 25

See OneNote

KP-element: P-element repressed by an internally deleted P-element

Question 26

Gypsy

Answer 26

See OneNote

Mapped LINE with a high rate of gypsy elements jumping around

• Endogenous retrovirus/LTR-retrotransposon that usually does not transpose much

Question 27

PiWi

Answer 27

Pi-RNA loci controls TEs

Molecular memory of transposable elements that have happened in the past
Immunity evolved over time
Transcript recognised by PiWi, chopped them up into little bits
Different sequences loaded
PiWi loaded with RNA are inherited
PiWi recognises TE and degrades it

Question 28

TE’s domesticated

Answer 28

See OneNote