Lec 5. HR and Transposition Flashcards
What are uses for HR?
Damage repair,Meiosis/Crossing over, and for rescuing stalled replication forks.
What are some implications for HR?
Heterozygosity, Linked genes and genomic integrity
What are the types of Transposons?
DNA only, Retroviral, Nonretroviral
Which is a more seamless way to resolve double stranded breaks? HR or NHEJ?
HR
Using HR causes crossing over in Meiosis resulting in
increase offspring diversity and helps link sister chromatids together.
What is one important characteristic about HR?
Maintains genome stablility
What does sister chromatids mean pertaining to templates?
A perfect template exists during replication. Occurs in late S phase or early G2.
What does a diploid genome mean?
Perfect or near perfect template always exists but may not be nearby
Pertaining to a diploid genomes near perfect template, why may it not be nearby?
Duplicate genes/elements dont have to be on the homologous chromosome.
What is the first step for HR to work?
Single-strand ends must be produced. Nuclease digests 5’ ends of broken strands.
What is the 2nd step for HR to work?
RAD51 helps the single strand invade a DNA duplex with an identical sequence (d-loop). This invasion mimics the RNA primer in DNA replication.
What is the 3rd step for HR to work?
DNA polymerse extends the invaded strand
During the 3rd step for HR, which pols are likely to be used to extend the invaded strand?
Pol δ (delta), Pol ζ (Zeta), and Pol η (eta)
During the 3rd step for HR, which pols are not likely to be used to extend the invaded strand?
Pol β, Pol ι (lota), Pol μ (mu). TDT
What is the 4th and final step for HR to work?
Disentanglement and ligation
How can you tell when a cell commits to HR versus NHEJ?
the creation of single stranded DNA overhangs.
During HR using sister chromatid as a template results in
Sealmess repair. Good copy.
During HR using a homolog as a template results in
Loss of heterozygosity.
What are the consequences of a loss of heterozygosity?
Exposes recessive traits and its a characteristic of cancer progression
During HR when does Crossing over occur?
During Meiosis I
During HR where does Crossing over tend to occur near?
Methylated CpG islands. H3K4me3 marked histones.
What is the first step for crossing over in HR?
Spo11 cleaves the DNA
What is Spo11?
Part of a Type 2 topo complex.
How many Spo11 copies are there and where are they located?
2 copies one for each strand
What is the 2nd step for crossing over in HR?
MRN nuclease complex processes and tethers the newly broken ends
What does the MRN nuclease complex contain?
Mre11, Nbs1/Nibrin,RAD50,WDCP
True or False? Mre11 nuclease has only endonuclease functions
False. Has endonuclease & exonucleasue functions
Is Mre11 sufficient?
No but it is necessary. Needs other proteins
What is the 3rd step for crossing over in HR?
RPA protects overhangs and RAD51 replaces RPA and assists in D-loop formation/ strand invasion
What is the 4th and final step for crossing over in HR?
Progression from D-loop structure proceeds as with repair
What are the two options during HR?
Extend one strand NO crossover, Extend both strands crossover.
What is a holliday junction?
a four-way DNA junction
What are some implications for crossing over?
Aids in proper chromosome sorting, increases genetic diversity
How does crossing over increase genetic diversity?
By uncoupling linked genes.
What crossing over implication reduces aneuploidy risk?
Proper chromosome sorting
What is one implication for stalled replication forks?
Maintains genome stability and integrity.
When is the CMG helicase unable to bind and what happens?
CMG helicase is unable to bind after G1, broken forks must restart by HR
What are the 3 steps for Fork-repair by BIR in S-phase?
- End resection RAD51 loading 2. D-loop formation. 3. BIR (break induced replication) by migrating D loop.
What are the 3 steps for DSB repair by BIR in G2-phase?
1.End-resection RAD51 loading. 2. D-loop formation. 3. BIR by migrating D-loop
What are the 4 steps for fork-repair in G2/M (MiDAS)?
1.Fork cleavage. 2.RAD52 recruitment. 3. D-loop formation by RAD52 dependent strand annealing. 4. BIR by migrating D-loop.
In HR what happens when synthesis takes too long?
Usually happens during S phase unless replication takes longer which goes into G2. We use the helicase to keep it going not the CMG helicase.
What happens when a replication fork stalls?
Replication fork reversal can occur
What happens during fork reversal?
BRCA1 and BRCA 2 aid in restarting reversed replication forks.
What does BRCA2 do?
Loads RAD51
What class are DNA-only transposons?
Class II
What circular intermediate on DNA-only Transposons mediates cut-and-paste jumps?
Transposase
What do DNA-only transposons contain at their ends?
Short inverted repeats
For DNA-only transposons, how are previous insertion sites known?
Residual duplication of host sequence
DNA-only transposons are less common in human genome than
Class I transposons
DNA-only transposons have similar mechanism to
V(D)J recombination in antibodies
What is an example of DNA-only transposons?
Antibiotic resistence genes
what class are Retroviral-like transposons?
Class 1
What two enzymes are required for Retroviral-like transposons?
RNA-dependent DNA Pol (reverse transcriptase) and Integrase (endocuclease)
Retroviral-like transposons contain what at their ends?
Long terminal repeats (LTR) contain promoter for RNA
What is an example for Retroviral-like transposons
HERVs (human endogenous retroviruses
True or False? HERVs are not silent
True
Where are HERV proteins expressed in?
Embryogenesis, Mothers placenta
In Embryogenesis expression of HERV genes does what?
Protect stem cells from viral infection
In the mother’s placenta, what HERV protein is necessary for placental development?
Syncytin-1
How could HERV elements play a role in causing cancer?
elicits an immune response that could be anti-tumorigenic
What class are Nonretroviral-like transposons?
Class I
What two enzymes are required for Nonretroviral-like transposons?
RNA-dependent DNA pol (reverse transcriptase) and Integrase (endonuclease)
What are two key features of Nonretroviral-like transposons?
No terminal repeats and has a poly A tail in DNA sequence
What are some examples of Nonretroviral-like transposons?
SINEs and LINEs
What are 3 implications of transposons?
Can insert into coding region of genes, deletions and inversions of significant portions of chromosomes and the insertion is random.
What is Conservative Site-Specific Recombination?
a process that enables genetic recombination between DNA molecules that contain short DNA sequences, which are bound by specific recombinase proteins
True or False? Conservative Site-Specific Recombination occurs in viruses, humans but not bacteria
False. Occurs in Viruses,Bacteria but not humans
What are three characteristics of Conservative Site-Specific Recombination?
Its a reversible temporary process, Site-specific/homologous, and recombinases act like topoisomerases in reverse (they put stuff together)
