Transposable Elements Flashcards
What are transposable elements?
‘Mobile DNA’ capable of copying themselves around the genome
As they move around they change/block expression from nearby genes
What are the 2 kinds of TE?
DNA transposons, ‘cut & paste’ DNA (Class II)
Retrotransposons, ‘copy & paste’ through RNA (Class I)
Why is there so much TE in the genome and why does it vary?
Different transposition rates
Acquisition of new TEs
Efficiency of removing TEs
Why are there TEs?
TEs are ‘selfish’ genes, a sequence that can copy itself around genome will increase in frequency until stopped - if you copy from 1 parent will be passed to over half offspring
Even if causes harm, as long as reduction in fitness less than benefit of spreading
(Arguably most abundant parasites)
How do ‘copy & paste’ RNA retrotransposons work?
Copy themselves via RNA intermediate
Transcribed as RNA, reverse transcriptase expressed
Reverse transcribed to another part of the genome
How do ‘cut & paste’ DNA transposons work?
2 methods:
- Repair using sister chromatid
- excised during replication
- repair excision using homologous part of genome, which is the same as the transposable element
- leaves 3 copies - Move ahead of replication
- jumps ahead of replication fork so host will produce 2 copies
What consequences can TE insertions have?
Reading frame/promoter of protein can be broken and expression stopped
TEs can carry functional coding sequences which can be broken & expression stopped
Can lead to targeting of heterochromatin which can spread to nearby sequences
What are the consequences of HK2?
HK2 is retro-transposing element
Polymorphic insertion polymorphism in intron 17 of gene in 5% alleles
Inserting HK2 alters expression of gene that’s associated with dopaminergic signalling
Carrying allele doubles chance of being chronic injection drug user
How can TEs cause rearrangements?
Movement of TEs mean there are near-identical sequences everywhere
Allows ectopic recombination which can delete and duplicate large chunks of genome
Likelihood increases exponentially as number TEs increase
When should TEs jump?
Transposition bad for host
No reason to transpose in somatic cells, could harm host with no benefit to TE so could have self regulation
In germline may be bad for host but increases frequency of TE in next generation, expect defence and escape
What do we know about ‘cut & paste’ DNA transposons (Class II)?
Generally 1-5k kbp long & encode single protein - a transposase that mediates excision & insertion
Inverted terminal repeats at each end, required for transposition
When inserted flanked by short direct repeats generated by target site duplications
What are P-elements?
‘Cut & paste’ transposon - contain single transposase gene with 3 intron & 4 exons
Cause hybrid disgenesis: if maternal line carries P-element but paternal doesn’t offspring fertile, opposite then offspring infertile
What is the mechanism of P-element action?
DNA cleavage of both strands by transposase encoded by TE
Excised transposon finds DNA with appropriate target site
Makes staggered cut & inserts
DNA copied using target site as template & ligated - results in target site duplication
How does Mariner transposition happen?
Cut 2 nucleotides inside transposon at right end
Dimerisation of transposase and second nick 2 nucleotides in on other stand at 5’ end of TE
Then second cut is made on both uncut strand at end of TE
The hydroxyl ends mediate integration at TA site
What are some recently discovered DNA transposons?
Helitrons, Polintons, Cryptons
How do Helitrons transpose?
Nick TE plus strand at the LTS and replicate
Leading strand synthesis reconstitutes donor TE
Lagging strand synthesis results in dsDNA circle
Circle may serve as transposon donor
Can start replicating in rolling-circle replication or insert into the genome
What do we know about RNA retrotransposons?
‘Copy & paste’ elements
Encode a reverse transcriptase
2 informal subclasses: LTRs and non-LTRs incl. LINE
What are non-LTRs?
LINE-like elements
Have 1 or more ORFs and express a mRNA-like product encoding reverse transcriptase, usually transcribed by host RNA pol II
Most truncated in genome at 5’ end due to incomplete transcription
How are non-LTRs transcribed?
Following transcription & nuclear export, transcripts translated & proteins form ribonucleoprotein particle (RNP)
RNP imported into the nucleus & non-LTR reverse transcribes from mRNA into another location in the genome
If there’s a polyA tail, cuts near a polyT motif so polyA tail can bind - BUT depends on TE-encoded nuclease, can be sequence-specific
1. Top strand cleavage - upstream or downstream
2. Template jump from mRNA to top strand of target site
3. Plus strand synthesis using cleaved top strand as primer, either:
- completion of synthesis and fill in leads to target site duplication
- completion of synthesis and degradation of non-homologous ends leads to target site deletion
What are LTRs?
Generally 5-7 kbp long, encode 2/3 ORFs
Characterised by long terminal direct repeats at each end
pol gene encodes integrase (IN), reverse transcriptase (RT), & RNAse H domains
Protease which processes primary protein product containing gag & pol can be encoded by either
How are LTRs transcribed?
tRNA binds at a priming site near 5’ end
This primes the start of reverse-transcription, which proceeds through a unique sequence & then repeat to 5’ end on RNA template
Repeat sequence of new DNA can now bind 3’ end of RNA
Primes continued reverse transcription through whole TE transcript
RNA template degraded by RNAse H leaving a fragment that primes 2nd strand DNA synthesis
Synthesis moves through 3’ unique sequence, the repeat and 5’ unique sequence
This fragment primes from 5’ end
Synthesis completes in both directions
Resulting dsDNA enters nucleus with viral integrase allows 3’ OH of each strand to attack target at sites a few bps apart - short target site duplication
What else do LTRs encode?
Gag protein, associates with LTR element transcripts to form virus-like particles
Env if gene present contributes to forming virus-like particles - may contribute to cross-species transmission
How are LTRs and retroviruses similar?
Same genes in same order
Replicate in same way
Difference is that LTRs aren’t horizontally transmitted, at least probably not often
What are ERVs?
Endogenous retroviruses
Retroviruses that cannot transmit horizontally
