W5L1 Transposable element

Question 1

What is transposable element

Answer 1

• Able to move from one chromosomal location to another. Dispersed throughout genomes.
• self-replicating: encode activities to allow themselves to replicate.
• A class of “selfish” DNA. Generally display vertical transmission through generations (unlike viruses).
• Large contribution to many genomes e.g. ≤80% of maize genome is TE sequence. Does not imply functional.
• Some genomes are littered with TE’s & some hardly any. Genomes differ in relative abundance of TE classes.
• 27% human genome been generated directly or indirectly (e.g. SINEs) by LINE1 family.

Question 2

Classes of TEs

Answer 2

I. Retrotransposons: Transpose via an RNA intermediate ‘copy & paste’: original copy stays in tact & produces a transcript that is retrotransposed & integrated elsewhere in genome; (a) Long Terminal Repeats (b) Non-LTR.
II. DNA transposons: No RNA intermediate, typically ‘cut & paste’.

Question 3

Long terminal repeat indepth

Answer 3

LTRs ~250-600 bp long. Two LTRs are in the same direction. Overall: ~7-10 kb length.
* Within LTRs are genes that encode gag & pol proteins (not env = encodes retroviruses).
LTR repeats encode transcription start site (allows transcription of RNA): then processed mRNA + polyadenylated (a tail).
o mRNA into dsDNA (double strand) (via RT) & integrated into genome leaving a target site duplication of host genome.
o Ends of the retrotransposon may be left out of the transcript (or poly-A-tail).
o Repetitive structure enables replication mechanism to regenerate whole element again.
* Enables insert back to genomic DNA at new site: target site duplication.

Question 4

Non-LTR Autonomous TE

Answer 4

• General structure: 2 ORFs (open reading frame) encoding proteins: 2 (RT converting RNA to DNA) 1 (endonuclease to nick DNA).
• Both proteins bind transcript & endonuclease nicks DNA where there is RT activity, allowing RT incorporation.
• Ensures full TE is incorporated due to repeats (enables regeneration).

Question 5

Line 1 element in human

Answer 5

Vast majority of LINE1 elements in human are “dead on arrival” (no function/junk/neutral) or unable to mobilise sue to damages.
o Occasionally replication process does not work & RT doesn’t get to the end.
o Cannot regenerate as they are only partial length (incomplete) but can still be integrated into genome. * ~80-100/500,000 LINE1’s in a human’s genome are capable of moving.

Question 6

Non-autonomous TE’s:

Answer 6

Use RT of autonomous TE’s to excise/replicate/insert e.g. Short Interspersed Elements (SINES).
* MANY in the genome but cannot move around themselves (deletion or functionality that stops their movement).
* IF in genome with active RT that recognises them, can be mobilised & inserted into genome.

Question 7

DNA Transposons: ‘Cut & Paste’

Answer 7

DNA segment excised by transposase (DSB) at original site, cut & paste elsewhere in genome. Also has TSD Target Site Duplications.
* DSB is then repaired by the cell. Original element may remain due to repair mechanisms that regenerate it.
* [Unlike type I elements where progenitor element is retained in genome as it is the RNA that replicates it].

Question 8

Ovo element in Drosophila melanogaster

Answer 8

-in D, ovoD1 is a dominant female strike mutation that is X-linked
-if a male carrier mate with female, it lead to infertile female
* Ovo is a hotspot for the gypsyTransposable element
* Gypsy is an endogenous retrovirus/ LTR-retrotransposon that usually does not transpose much

Question 9

Variant in gypsy

Answer 9

Several Drosophila melanogaster stocks have >20 euchromatic copies of Gypsy and high mutability is observed in these stocks. These have a ‘permissive’ background
-if a female with these permissive Gypsy cross with ovoD1 male, it lead to fertile daughter
-an ovoD1 reversion array to map the localizing the gene responsible for gypsy permissiveness

Question 10

Result of ovoD1 gene mapping

Answer 10

-found Flamenco gene, a highly repetitive heterochromatin

Question 11

Horizontal Transfer of TEs Deep Evolutionary comparisons

Answer 11

• Distribution of TE families is often phylogenetically ‘patchy’ (though loss of TEs may be involved)
• Example of horizontal transfer between species SPACEINVADERS (DNAtransposons)
• SPIN was introduced into numerous vertebrate lineages within the last 50 million years - its origin is unknown

Question 12

TE in asexual situation

Answer 12

• TE can hop around in the genome, leading to deleterious mutation accumulation.
  -This lead to lower fitness aka Muller’s Ratchet
  -this might be the reason why sex evolved

Question 13

TE in sexual species

Answer 13

Sexenables TE’s to spread through population
But Recombination breaks the ratchet, individual TE insertions can be selected against, especially the more deleterious ones

Question 14

Bdelloid rotifers: evolution scandal

Answer 14

No sex in 40 million years!
Asexual lineages generally do not last for long periods of evolutionary time because of Muller’s Ratchet.
* Slightly Deleterious mutation accumulate (and are not lost – hence the ‘ratchet’)
* Eventually the genetic load will be so much that the asexual species will go extinct.
* This is a theory to why sex (genetic exchange) is prevalent among organisms

Question 15

Bdelloid Rotifers - Persisting Elements

Answer 15

• Members of five DNAtransposon families are found in rotifers (though only Mariner elements appear to be full-length)
• A variety of retrotransposons exist in Adineta vaga
• Low copy number of diverse TE types

Question 16

Spread and loss of TE

Answer 16

• Horizontal transfere from another host
  -germ line invasion
  -proliferation by transposition
  -spread in the population ( can spread horizontally)
  -inactivation and loss

Question 17

Horizontal Transfer of TEs Closely related species and population genetics

Answer 17

• Silent site divergence of transposable element families from different Drosophila species suggest more recent divergence than host species divergence

Question 18

P-elements in Drosophila melanogaster

Answer 18

• If P male x Naive female -> progeny with high mutagenic load in germ line
• If P female X naive male: nothing happen
  incompatibility given the term hybrid dysgenesis.

Question 19

Cause of hybrid dysgenesis

Answer 19

• Transposase is encoded by gene with 3 different introns in TE sequence & germ line (to be passed onto next gen).
• Protein product is full length & very active BUT in the soma the third intron is not spliced out to get smaller proteinproduct that represses TE activity in somatic tissues. .
  *.TE’s in genomes (KP-elements) with deletion that mimics repressor 2 that represses ability of TE to move in genome & soma. After evolutionary time, some mutations could arise & suppress population => burst with high activity THEN this.
• Gypsy is an endogenous retrovirus/LTR-retrotransposon that usually does not transpose much.
• Several stocks have >20 euchromatic copies of Gypsy & high mutability is observed in these stocks.
• Mapped gene responsible for high motility => Flamenco locus is a piRNA locus.

Question 20

P element transfer in drosophila

Answer 20

P-elements thought to have entered the species from Drosophila willistoni some where in South America before the 1950’s.Perhaps via a mite?
* In 2015 a paper reports finding P elements in Drosophila simulans!
* Sample dated 2006
* It seems to come from a single event (all D.simulans share a variant that is very rare in melanogaster, and almost all P’s in D. simulans are full length and show little divergence to each other)
* Spread quicker : it has less gonadal dysgenesis and demographics different
* Rare hybrid responsible for this species jump?

Question 21

Distribution of TE in the Drosophila genome

Answer 21

The sequenced genome of Drosophila has: 93 different TE families.1 to 143 copies of each family
total of 1,572 elements, or 3.86% of euchromatic sequence
However TE’s make up 50-60% of Drosophila heterochromatin
* Enriched around telomeres/centromeres
* Enriched in regions of low gene density
* Generally insert in non-coding regions rather than coding regions
* Hotspots are observed

Question 22

Activity and insertion frequency in Drosophila populations

Answer 22

• TEs cause 50% of spontaneous morphological mutations in flies!
• But the ‘Occupancy’ is low in Drosophila: same number of TE but in different area

Question 23

Transposable element frequency in human genome

Answer 23

-42% of euchromatic DNA
-100 family of TE
-most insertion are fixed and we have low spontaneous mutation rate

Question 24

Human TEs:Active ones

Answer 24

Of the 90 L1s in ‘freeze 1’ of the human genome that have full length ORF:
*44% are polymorphic for different people
*49% are active in cell culture assay
*Six ‘hot’ L1s account for most of the retrotransposition activity

Question 25

SVAs TE in human

Answer 25

-have the potential for expansion
-* A single SVA insertion into Fukutin gene responsible for 87%of Fukuyama-type muscular dystrophy
* Fewer than 1 in 500 novel(new) heritable mutations in humans caused by TEactivity
* TEsmore active in cancer cells and associated more speculatively with other conditions

Question 26

Human TEs:past activity

Answer 26

• Of the half a million L1 elements in the average human genome, 30-60 per person are active, and six are responsible for the majority of TEreplication
• Most endogenous retroviruses inserted over 25 million years ago, and present activity is minimal to non-existent
• Slowdown of L1 activity began about 25 million years; L2sand L3s (active in some other mammals) seem never to have proliferated in the human lineage
• DNAtransposons ceased activity in the human lineage about 37 million years ago

Question 27

How to measure the age of TE

Answer 27

-Human have any “dead in water” TE, using mutation rate to work out
-some TE can hop into “dead in water” corpse of previous TE, the hopper must be younger

Question 28

Selection removes insertions

Answer 28

-A TE can hop in, which could disrupt coding region-> deleterous mutation
- lead to purifying selection
-rare case which hoping in lead to higher fitness

Question 29

Hoping TE lead to better fitness

Answer 29

-Doc 1420 into ancestral transcript, lead to higher level of transcription
-related to insecticide resistance

Question 30

Lots of TEs increase the chance of ectopic
recombination

Answer 30

• large amount of TE can cause ectopic exchange/ illegal recombination causing gene loss
  -lower fitness

Question 31

Mevel-Ninio Genetics 2007 hypothesis

Answer 31

-within a gene of dip 1, the intron contain many TE
-Nearly all retro elements are oriented towards the telomere. In the intron region
-Transcription of the dip1 gene that is responsible for the follicular development function In a telomere to centromere direction, could give anti-sense retroelement sequences in the follicle cells.

Question 32

Flamenco is a piRNAcluster

Answer 32

• Loci that encode TE insertion seq. all transcribed into one “mega”-transcript. Flamenco is near this host gene.
• It is then recognised by piwi (protein) that chops the transcript into pieces.
• MANY piwi proteins do this, each holding a piece of RNA of a certain length that can then be maternally inherited.
• Loaded onto piwi proteins, bind RNA of transposon of corresponding seq. => cleave: molecular memory of TE’s.
  Maternal inheritance of loaded piwi proteins
• Ping-pong amplification (between different small RNA binding proteins -> effective control)
• Control of TE’s based on sequence based ‘memory’ mechanism .
• pi-RNA clusters provide a history of TE infection & presumably exhibit footprints of repeated positive selection.

Question 33

pi-RNA loci control T.E.’s: The trap Model

Answer 33

• Control of TE’s based on sequence based ‘memory’ mechanism!
• a new T.E. enters the genome – it runs rampant until a version integrates into a pi-RNA locus and then control can be exerted).
• Predict that pi-RNA clusters provide a history of TE infection and presumably exhibit footprints of repeated positive selection