L12 Transposable Elements Flashcards
Transposable Elements
- 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
Classes of transposable elements
- Retrotransposon: transpose via RNA intermediate “copy and paste”
1a. Long terminal repeats
1b. Non-LTR - DNA transposons: no RNA intermediate, “cut and paste”
LTR Transposons
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
pol gene
many different functions e.g. reverse transcriptase
gag
assembly of RNA into a retrotransposon particle
Non-LTR Transposon
See OneNote
- line elements belong to this class, vast majority of LINE1 elements in human are d.o.a. or otherwise unable to mobilise
Non-autonomous TE
Use the enzymes of autonomous TE’s to excise/replicate/insert e.g. SINEs
SINES
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
DNA transposons
See OneNote
- DNA segment excised by transposase
- 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.
Genomes differ in relative abundance of TE classes
See OneNote
TEs are almost everywhere
Bdelloid rotifers
See OneNote
- Muller’s Ratchet
TE spread in asexual organisms
See OneNote
First lineage not mixing with other lineages as there is no sex
TE spread in sexual organisms
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
The sequenced genome of Drosophila
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
The unequal genome distribution of TEs
- 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
Occupancy
“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
Spontaneous morphological mutations
- 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
P-elements crossing species barriers
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?
The spread and loss of TEs
See OneNote diagram
- active genome defense?
- horizontal transfer
- vertical inactivation: mutations accumulate or excision
- stochastic loss by genetic drift
Selection removes TEs because they are deleterious to host fitness
deleterious because:
- gene inactivation
- transcripts and proteins nick genome and disrupt genome function
- facilitates ectopic exchange
Selection removes insertions deleterious to host fitness
See OneNote
Lot of TEs increase the chance of ectopic recombination
See OneNote
Analysis of human genome indicates different LINE families have been active at different points in evolutionary time
See OneNote
Evidence of inactivation over time
Aging TE insertions
See OneNote
- Nested nature
- LTR mutation accumulation
Hybrid Dysgenesis
See OneNote
KP-element: P-element repressed by an internally deleted P-element
Gypsy
See OneNote
Mapped LINE with a high rate of gypsy elements jumping around
- Endogenous retrovirus/LTR-retrotransposon that usually does not transpose much
PiWi
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
TE’s domesticated
See OneNote
