Transposable Elements Flashcards
Transposable element classifications?:
DNA transposons - “cut and paste” move via DNA (Class II)
retrotransposons - “copy and paste” elements move through RNA intermediates (ClassI)
how can proportion of TEs in genome change?
number can change quickly between closely related species due to:
-different transposition rates
-acquisition rates of new TEs
-efficiency of selection in removing TEs
rapid gain and loss of TEs
balance between these factors
TE selfish genes concept?
can copy themselves around genome
this allows them to increase in frequency until something stops them
because if they copy themselves in the germline - there will be more in the next generation than in previous one
if it copies itself onto EACH chromatid of EACH homologous chromosome - will end up in ALL the gametes
instead of if it was just on one allele - onlt 1/2 offspring inheriting
RNA retrotransposase number increase?
Class I - “copy and paste”
goes through RNA intermediate
in DNA
then transcribed as RNA
RNA expressed to produce reverse transcriptase protein
RNA intermediate reverse transcribed and inserted into new part of genome
copy themselves when RNA is transcribes then new DNA element is reverse transcribes - old one stays where it is
DNA transposon number increase?
Class II -“cut and paste”
mariner/P-element -like
Do not copy themselves so have other mechanisms for increasing in number in next gen
solution:
cut themselves out and wait for host to repair DNA
Missing DNA forms ds break in chromosome
if happens after chromsome replication then host can repair ds break using HR (RecBCD, RecA, RuvABC pathway)
transposon DNA is present in other chromosome so it is repaired back into genome
while one that was cut out is free to insert back somewhere else - increasing copy number by 1
can also increase by excising after replisome has passed and replicated it - then can insert ahead of replication - gets replicated again - increase
TE insertion consequences
-breaking reading frame or promoter of protein coding gene - protein either ceases to be expressed or loss of function
-TEs (unlike single base mutations) can carry coding sequences (their own promoters, enhancers) which can impact expression of neighbouring genes
host cell targets TEs with heterochromatin to reduce their expression (as they can cause deleterious effects) - which can end up spreading to and affecting expression of other nearby genes
So TEs usually deleterious when inserted in or near genes
TE insertion throughout genome consequences?
having TEs in genome can be deleterious even if they’re not near a gene
TEs move around the genome a lot
but don’t diverge in sequence very quickly
means that there can be many near-identical sequences througout the genome
TEs have head to tail target sites either side of them that (at least cut and paste elements) to excise and insert into genome
the near identical target sites between two different TEs in different parts of the genome allow recombination to happen between them
ECTOPIC RECOMBINATION
consequences of Ectopic recombination between different TEs
since sequences of TEs are nearly identical they can recombine with each other
if this occurs between two different chromosomes
causes them to pair incorrectly (because TEs on different parts of chromosomes line up)
causes them to bunch up and form loop s (see diagram)
recombination between these sites causes Duplication of region on one chromosome (neutral or bad) and deletion of same region on other chromosome (BAD)
costs of ectopic recombination
faster than linear rise in cost with increase in number of TEs
(as opposed to cost of TE insertion that just increases linearly with no. of TEs)
more TEs = increased opporunies for ectopic recombination for EVERY similar TE in genome - exponential rise in cost
Host parasite relationships with TEs?
insertion and hiding in genome is costly
hosts are selected to stop or suppress TE activity
so when should TEs jump?
if TE jumps and inserts in chicken Soma - can cause damage to that one host but this will not increase its number in next gen (just in soma so new number will not be inherited)
So won’t benefit the TE either
host and TE “interests” aligned - no benefit for either chicken or TE for TE to jump in soma
when TE jumps in the germline - can increase TE frequency in gametes - so will increase TE frequency
jumping in germline is beneficial for TE, even at cost to host as TE will cause harm if it spreads (interrupting genes etc)
expect to see host defence and escape from TE action
some TE benefits
TE mutagenesis can provide source of new genetic variety (even if most of time its neutral or bad)
can also provide complex mutations that include ORF and regulation changes - that are less common for point mutations to give
still more deleterious than helpful tho
TE “domestication” in drosophila
drosophila telomeres functionally equivalent to other animals
EXCEPT telomerase has been lost
the place of telomeric repeats has been taken by :
multiple adjacent insertions of Het-A, TART, amd TAHRE non-LTR elements
(see diagram)
take up part of telomere that would normally be taken up by telomere like sequences
reverse transcriptase for these copy and paste elements uses the 3’ OH at the end of the telomere to replicate the TE RNA transcript - so can only jump to end of chromosomes and replenish the telomeres protecting drosophila chromosomes from chromosome erosion
(instead of telomerase doing it)
detecting new TE insertions?
via sequencing
but TEs are longer than read length for some sequences
can be identified by multiple read pairs (reads next to each other that face each other) that cross the insertion site
map them to reference genome
ones that overlap the insertion site don’t map
can tell where new insertion has occurred
this only works in TE poor regions
as if a TE has inserted into TE derived sequence that won’t be on the reference genome then can’t do this as whole region around it won’t show up
where do the most TE insertions occur?
in highly expressed genes
more in eu- than heterochromatin
ACCESS is important for where insertion occurs
DNA cut and paste transposon structure
class II
include Mariner and P-elements
1-5kb
encode single protein - transposase
transposase mediates excision and insertion
inverted terminal repeats at either side needed for transposition
when inserted into genome TE is flanked by short direct repeats generated by target site duplications
