Chromosome biology lecture 7 Flashcards
Transpositional recombination overview
- Similar to SSR as involves protein DNA + protein-protein interactions
- Only 1 of the recombining partners is specifically recognised by the protein that catalyses transposition
3 general mechanisms for genetic mobility
- SSR
- Transposition - transposes binds inverted DNA at end of element, each transposes cleaves ends of elements + transfers to new molecule
- Target-primed reverse transcription - transposable element copied from its DNA by RNA pol + produces RNA copy of element → encodes reverse transcriptase that nicks target DNA + element copied in
Transposable elements
- Abundant, 12% of c elegans genome
- Most a silent, some are active
- Specific DNA/RNA elements can move
- Source of spontaneous mutation
- Can lead to gene rearrangements
Classification of eukaryotic transposable elements
- Class I = retrotransposons, transpose via RNA int, use reverse transcriptase, split into LTR, non-LTR or DIRS
- Class II - DNA transposons
LTR transposons
- Inc retroviruses like HIV
- Both use integrate
- Retroviruses can be distinguished from LTR transposons by presence of envelope gene located at 3’
Non-LTR transposons
- x have LTR
- Transposes via target-primed reverse transcriptase
- uses endonuclease to nick DNA (restriction-like or AP)
- e.g. = LINES/ SINES
DNA transposons
- Divided into autonomous elements + non-autonomous
Classification of prokaryotic transposable elements
- Simple insertion sequences (800-1500bp, inverted terminal repeats flanking gene for transposase)
- Compound transposons (have 2 insertion sequences which cooperate to transpose own DNA as well as DNA in btw)
- Complex transposon (terminal inverted repeat flanking range of genes)
Transposable element abundance + activity
- Most common = Tc1/Marnier family
- Only around 10 elements are active inc P elements in Drosphilia
Mechanism of transposition
- Liberation from donor DNA + insert/joining to target DNA
- Can either paste in or copy w/ reverse transcriptase
Transposition types
Conservative vs replicative
Both use endonucleolytic cleavage of phosphodiester bonds, transfer ends into target DNA
Conservative (cut + paste) transposition
- Tc1/Marnier family
- Typically these transposes = DBD, CT catalytic domain,
- Asp + Glu coordinate 2 Mg2+
- 2 transposes recognise inverted repeats, bind w/ HTH → ‘single end’ complex
- Cleave 5’ of inverted repeat → ‘paired end complex’
- 3’ end cleaved + release 3’OH termini
- Bind target DNA
- 2 strand cleavages liberate from end of donor DNA
- Fill in w/ DAN pol
- Transposon footprint
Coordination of transposition w/ DNA replication
- Conservative = wasteful
- Overcome by coordinate
- Excision of transposon ensures ds break is repaired by HR
Replicative transposition
- Only 1 strand cleaved at each transposon end
- Strand transfer of cut 3’ end into target DNA → Shapiro int.
- 2 3’ ends → replication of transposon
- Intermolecular replication transposition → co-integrate structures where donor + target replicon are joined but separated by directly repeated copy of element
- Resolution
Life cycle of DNA transposon
- Retrotransposons are transcribed
- Assoc. w/ mRNA
- In retroviruses, envelope gene means mRNA + proteins → infectious particles by bonding off
- In virus-like particles, pol derived protease cleaves protein
- RNA reverse transcribed to comp. DNA
Reverse transcription of retroviral DNA
- 3’ end of host tRNA binds 5’ of viral RNA
- Reverse transcriptase makes short segment of RNA
- RNase H exposes 3’ end of - DNA
- tRNA mostly degraded
- Short stretches of RNA persist, primes synthesis of + DNA which proceeds to 5’
- 2nd template switch
Integrase integration
- Integrates into cDNA of host
- Generates 2 base recessed 3’ ends in LTR + staggered ends in target DNA
Strand cleavage
- Transposition requires assembly of synaptic complex
- Precise cleavage to liberate 3’OH
- Cleavage of compl strand sometimes occurs
- Hairpins hydrolysed → 3’OH
- 3’ ends transferred into target DNA
Disadv of transposition
- Insertion near genes can Δ gene expression (can carry gene promoter)
- Indirectly harm by acting as sites for non-allelic HR
Transposable elements targeting specific sites
- E.g. in some yeast specifically target promoter regions or genes transcribed by RNA pol III
- E.g. TyI integrase in yeast has LTR that interacts w/ subunit of RNA Pol III
Regulation of transposable elements
- small RNAs silence
- KRAB domain (>400 genes), bind transposable elements in a sequence-specific manner + recruit KAP1 → H3 lys 9 methyl transferase recruited → epigenetic silencing
- De-reg = hallmark of cancer
Adv of transposition
- Antibiotic resistance
- VDJ recomb = antigen receptor diversification (relies on transposition-like reaction + NHEJ, RSS bound by VDJ recombinase which initiates recombination
Transposon as genetic tool
- Typical gene transfer = 2 plasmids
- ↑ efficiency of transposons in catalysing genomic insertion
