Lecture 20

Question 1

Transposable elements: class 1 and 2

Answer 1

Class 2: DNA transposons, has flanking DNA repeats (from staggered insertion), requires transposase for transposition, cut and paste
Class 1: retro-transposons, have flanking LTR regions, similar to retro viruses, contains the genes required for self-transposition, just cant leave the cell
- has regions encoding for pol, a reverse transcriptase and gag, another protein

Question 2

How do retrotransposons move

Answer 2

Initially transcribed by the cells own transcription machinery (not its encoded RT), exported from nucleus, gets translated, at this point the pol ORF with be synthesized into the reverse transcriptase, this RT will transcribe DNA from the RNA template, that DNA will then be taken back to nucleus and inserted into another chromosome, randomly

Question 3

ORF 1 and ORF 2

Answer 3

Found on retrotransposons, translated once that initial transcript is taken to cyto, ORF2 encodes the reverse transcriptase and ORF1 will bind to the RNA/DNA hybrid and take it back to the nucleus

Question 4

Retrotransposons jump around, will these changes be inherited

Answer 4

Not necessarily, they could be in they’re in the germline but if its in a random skin cell likely not

Question 5

LINEs vs SINEs

Answer 5

LINEs can transpose independently/autonomously, SINEs cannot (they dont have ORF1 or 2), also make up different proportions of the genome
LINEs approx 21% and SINEs approx 13%

Question 6

Where are transposable elements generally found/inserted

Answer 6

Either in introns or intergenic regions, not disrupting genes
(Makes sense cuz evolutionarily in a transposable element inserts itself and ruins a gene that would not be selected for)
LTR retrotransposons also like to insert themselves into safe havens

Question 7

Safe havens

Answer 7

Places in the genome that already have retrotransposons present, LTR retrotransposons are more likely to insert tehre than other places in the genome

Question 8

What led to loss of function in the chardonnay grape pigment gene

Answer 8

An insertion of a retrotransposon right in the regulatory region, clearly affecting transcription of the pigment, thus rendering it dead, loss of function

Question 9

Why does the ruby okuyama still produce some pigment

Answer 9

Some produced but not wild-type levels, the insertion it has is small, small enough to only be an issue some of the time, survived cuz its about pigment and not something important

Question 10

Why can we say that the ruby is likely decent from the chardonnay

Answer 10

Because the only thing intervening with pigment function is a small flanking region that wouldve been found on both side of the retrotransposon, so it looks like at some point there was a crossing over gone wrong cuz different flanking regions got paired and it got cropped out, leaving only 1 LTR aka flanking sequence, only a small disruption

Question 11

Cancer and transposons

Answer 11

Studies have shown association between increased retrotransposon activity and cancer (not in all cancer obviously, could just be a potential cause), like in the colon cancer where all cancerous masses in an individual had a certain LINE repeated a bunch of times, like above average, and the non-cancerous tissue didn’t
This destabilization of the genome is what can possibly lead to mutations and such, cell failures, etc

Question 12

Why dont we all have cancer if retrotransposons be jumping around pretty simply

Answer 12

Cell has mechanisms to limit the transposition of these transposable elements, a regulation almost