Lecture 35 Flashcards
1
Q
Transposable elements:
A
- Jumping genes
- Able to move from one chromosomal location to another
- Achetypes are self replicating, so they encode activities to allow themselves to replicate
- A class of ‘selfish’ DNA
- Dispersed throughout genomes
- Generally display vertical transmission through generations (germline parasites)
2
Q
Retrotransposons:
A
- Transpose via an RNA interments
- Use a reverse transcriptase, with long terminal repeats
3
Q
DNA transposons:
A
- cut and paste method of transcription
4
Q
Long terminal repeat retrotransposons:
A
- Like retroviruses but lack env, have a target site duplication and encode a number of genes
- Have long terminal direct repeats, the whole unit is 7 - 10 kb long
- eg) gypsy virus like particles, it forms viral like particles, even though it may not transfer horizontally
5
Q
How to LTR’s work?
A
- Transcribed from DNA
- Processed via poly-adenylation, which cuts off the outer ends, but these are repeated so all the material is still there
- This can be translated to give retrotransposition function
- This is processed into dsDNA
- Integration into dsDNA occurs
6
Q
RNA to dsDNA and maintenance of LTRs:
A
- A tRNA is used as a primer to generate the other strand, using reverse transcriptase
- Slippage occurs, and tRNA jumps due to homology with the RNA sequence.
7
Q
LTR retrotransposons genes:
A
- Have a polymerase gene, protease domains, RNase domains, integration domains
- Gag gene which assembles RNA into retrotransposon particules
8
Q
Non-LTR retrotransposons:
A
- Don’t have long terminal repeats, but have short repeats at the 5’ and 3’ end.
- A transcript is produced which gives a reverse transcriptase, which takes the transcript and makes it DNA
- The repeat structure means it is possible to regenerate the ends
- They don’t replicate after they have replicated once, so have no selective constraint on them at all
9
Q
Non-automomous TE’s:
A
- Use the enzymes of autonomous TE’s to excise/replicate/insert
- eg) short interspersed elements (SINES)
- Can still replicate but they rely on the proteins of other elements
10
Q
All of these elements have the RT (reverse transcriptase) gene:
A
- These are conserved and homologous
- So we can align them and draw phylogenetic trees
11
Q
Cut and paste transposons:
A
- eg) P-elements
1. Target sit is cut and digested
2. Transposon integrated with ITR’s on either end (inverted terminal repeats
3. The transposon is fully integrated
4. DNA segment is directly excised from surrounding DNA by transposase
5. dsDNA break gets repaired by the cell with direct depeats
12
Q
Some genomes are littered with TE’s:
A
- Human’s have around 40%
13
Q
Genomes differ in relative abundance of TE classes:
A
- Retrotransposons but no DNA transposons
- Humans are mostly retrotransposons but not many DNA transposons
14
Q
Density of TE varies throughout the genome:
A
- Heterochromatin regions tend to have many TEs
- Enriched around telomeres/centromeres
- Enrich in regions of low gene density
- Generally insert in non-coding regions rather than coding regions
- Hotspots are observed
15
Q
In drosophila there at 93 different TE families:
A
- with 1 - 43 copies of each family
- Occupancy is low in drosophila: among individuals, there is high variation in where he TE are found, but they will have equal amounts of TEs