what does homology dependent DNA repair fix? what does it require?
fixes break in double stranded DNA
requires another chromatid and 2 double stranded DNAs
what might might cause DNA to come out of its linear sequence?
homology-based generalized recombination of chromosomes
what is generalized recombination?
what catalyzes it?
recombination between 2 homologous (similar sequences in the same orientation) chromosomes
Rad proteins (i.e. Rad 51) catalyze it
what does homolgous mean?
share a high percentage of similartiy
in context of chromosomes, have similar sequences in the same orientations
basis for recombination
why aren't children of the same parents identical?
when do processes causing this occur?
because there is random assortment of chromosomes AND because of recombination between pairs of chromomes
recombination occurs before formation of gametes
what is recombitant DNA?
when some paternal DNA is linked to maternal DNA and vice versa
product of homologous recombination between 2 double stranded DNA molecules
what is holiday junction?
1 model of recombination btwn 4 strands of DNA
what are all possible outcomes of recombination?
1) equal crossing over
2) unequal crossing over
3) inverted repeats on the same chromosome
4) exogenous DNA recombining w/ host chromsome
what is equal crossing over?
what is the outcome?
homologous recombination btwn similar sequenecs on 2 chromosomes
occurs b/c maternal and paternal have copies of same gene to contribute
result: diversity in sequences of the 2 chromosomes, no change in function overall although may have some ntd changes
results in 2 chromsomes
why does unequal crossing over occur? what is it?
what is the result?
2 or more copies of the same gene can be be present on a chromsome
happens if homolgous copies of gene align out of register and undergo recombination
result: unequal distribution of gene copies (i.e. 3 gene copies on 1 chromosome, 1 on the other); may cause disease
what is alpha-thalassemia? what causes it?
alpha-thalassemia = chromic anemic condition, manageable, but not good!
unequal crossing over of chromsomes w/ alpha globin genes
result is 1 chromosome w/ 3 alpha genes, 1 with 1 alpha gene
what does homologous recombination between 2 chromosomes yield?
what is the breakdown of chromosomal DNA between repeated sequences and unique sequenecs?
40% repetitive sequences
10% simple repeat sequences
where does homologous crossing over within a chromsome occur?
between regions of repeated sequences
what causes hemophilia A?
crossing over between inverted repeats on the same chromosome
what does Factor VIII gene do?
how does homologous recombination occur w/ the Factor VIII gene?
X-linked gene involved in blood clotting that, if deficient, results in hemophilia
end of X chromsome has 123 sequence, 4000 bp away is Factor VIII gene, and in middle of INTRON 22, repeated 123 DNA sequence
DNA of chromosome can loop around so that the 2 homolgous 123 sequences are near each other, and in same orientation
result is 1 nonfunctional Factor VIII gene, b/c exons 23-26, needed for function, are disconnected from the other exons
how does exogenous DNA recombining w/ a host chromsome work? when does it work, when does it fail?
if have mutate (beta globin, for ex.) gene, can introduce a wild type copy into a plasmid DNA, get homology between wild type B-globin and the nonfunctional version on chromosome
via homologous recomination, should get double crossing over from host chromosome into exogenous DNA, and vice versa
now should have recombinant molecule w/ wild type beta-globin which replaces mutant beta-globin
works in bacterial cell, not human cell, b/c get illegitimate recombination where our inserted DNA sequence ends up in another chromsome
why doesnt exogenous DNA recombination into a host chromosome work in some cases?
beta globin example
does not work when do it in human cell
b/c introduced gene does not express when out of its normal context
i.e. if introduce functional, wild type B-globin into human DNA, no expression continues after several weeks
what are 2 methods of gene therapy whereby can have wildtype gene insertion in chromosome?
1) direct delivery
2) cell based delivery
how does direct delivery method of gene therapy work?
take your cDNA of interest mRNA
put into a viral vector, usually lenti virus
directly introduce this into tissue target - i.e. liver
how does cell-based delivery of gene therapy work?
take bone marrow cells out of body
do genetic modifications to cells out of body
then put genetically modfiied cells back into body
what are the problems w/ doing gene therapy by direct delivery and cell-based delivery?
1) locus size of gene to insert may be too large for packaging into a viral vector
2) position effect: cannot guarantee that homologous recombination occurs - illegitamate recombination may - gene can go somewhere heterochromatic, therefore won't be expressed
3) insertional mutagenesis: b/c we don't control where exogenous DNA inserts into chromosome, can get effects that turn off a gene we need or inappropriately turn on a gene (i.e. turn on an oncogenic gene and cause cancer as side effect)
what is gene addition gene therapy?
stem cells w/ a genetic mutation are pre-stimulated to prepare them for manipulation;
insert a functional copy of the gene into a retroviral vector;
do semi-random integration into cells;
express that vector in a person;
get normal gene product in person
what is gene repair gene therapy?
treat cells w/ a nuclease engineered to cut around mutated site
DNA template for functional sequences is added to pre-stimulated cells via a viral vector
mutated sequence is replaced w/ wildtype via homologous recombination
so try to replace the mutant gene w/ a wildtype copy of the gene, and this in turn expresses normal gene product
works if you treat cells w/ factors that prevent early differentiation (dmPGE2 and SR1) & treat with signalling molecules, cytokines, that decrease the cells' sensitivity to the toxic effects of the nuclease
result: turn on normal gene expression
what is transposition?
where and when does it occur?
what catalyzes it?
movement of a unit of DNA, a "transposon," from 1 site to a new target site
occurs in absence of homology, at random sites
transposaze enzyme catalyze transposition
what encodes for transposaze?
a gene located on the transposon itself
what does uncontrolled transposition cause?
havoc on genome structure!
thus it is highly controlled process
describe process of cut-and-paste, non-replicative bacterial transposition
ends of transposon unit in donor DNA are recognized by transposase
transposase makes cuts at both ends of donor DNA & staggered cuts in a target DNA site
transposon DNA is inserted in target site
target may be same DNA molecule as donor or different DNA molecule
what is complex transposition of a bacterial transposase?
carrying more genes than just the transposase gene into the target
i.e. antibiotic resistance gene can be carried, jump into plasmid DNA, and then recipient cell can receive antibiotic resistance gene which is not good
what is a simple "insertion sequence" versus "complex transposon"
bacteiral transposon can be
1) IS: insertion sequence; just the transposase coding sequence is carried, i.e. IS3
2) complex transposon: carries transposase coding sequence AND gene for antibiotic resistance, for ex. (i.e. Tn3 ampicillin resistance gene, Tn10 tetracycline resistance gene)- accounts for multiple drug-resistant strains in hospitals!
what is mechanism of bacterial versus eukaryotic transposon movement?
bacterial: DNA only
eukaryotic: RNA intermediate!
how does eukaryotic retrotransposon integration work?
transposon DNA sequence is transcribed by RNA polymerase
this creates an RNA copy of transposon sequence
then reverse transcriptase converts RNA intermediate to double-stranded DNA
double-stranded DNA integrates into target DNA via activity of an integrase protein
retroposon sequence includes coding sequence for reverse transcriptase & gene for txn of DNA into target
what kinds of sequences are found in the genome? examples of each?
1) unique sequences (may occur 2x since we are diploid)
2) repetitive sequences (i.e. rRNA genes, histone protein genes)
3) HIGHLY repetitive sequences (LINES, SINES, VNTR)
what kind of sequences encode for rRNA genes and histone protein genes? why, re: function?
need more than 1 18S rRNA gene so we can make enough RNA for all our ribosomes
need more than 1 H2A gene, for ex., or would never have enough protein for entire nucleosome
thus have dozens of copies of each rRNA gene
what are LINES?
long interspersed elements; a type of highly repetitive sequence
6000 bp long element
L1 is a LINE
what is L1 an example of?
what is L1?
a long interspersed element (LINE) that codes for retrotransposon, which can undergo retrotransposition itself:
makes an RNA copy of itself, makes that into DNA via reverse transcriptase, and jumps elsewhere in the chromosome
have 500,000 L1 elements in our genome, but only 50 are active
2) provides region of homology where recombination can take place
they are highly repressed via hyper methylation b/c can cause disease
what are SINES? how are they transposed? what is a major example?
short interspersed sequences
transposition depends on assistance of an L1 element
major type: AluI; 1 million copies (!) in genome; contains no coding sequence
what is a VNTR?
variable number of tandem repeats
small DNA sequence (9-80 bps) present in multiple contiguous copies in same orientation
diff individuals may have diff number of a certain tandem repeat at a particular locus
PCR takes advantage of VNTR for forensics
how do forensic studies use VNTRs?
can differentiate between 2 people based on the VNTR:
diff ppl have different number of repeats of the same sequence
thus can use primer to garget unique sequence outside the repeat region; size of PCR product will depend on number of repeats; if do this for several repeat regions simultaneously, unique personal pattern is generated; basis of forensic ID
is an AluI sequence going to be an intron or exon?
intron, b/c doesn't code for anything
Explain why crossing-over events in meiosis generally have no consequence or generate diversity without affecting human health.
Because equal crossing over involves homologous recombination between similar sequences on 2 chromosomes, and the result is 2 chromosomes that have genes of the same function. You do not get loss of function through this kind of homologous recombination, you just get diversity because maternal and paternal genes are mixed into resultant recombinant chromosomes.
There are multiple copies of ribosomal RNA genes in the chromosome. Why would unequal crossing over between these genes probably not result in serious consequences?
Multiple copies means redundancy!
We have so many copies of rRNA genes precisely because losing one would be devastating to that cell otherwise.
The sections of chromosomes with these genes generally have many copies in a row; unequal crossing over leaves many functional copies within that stretch of repeats (e.g. 40 repeats -> 30 or 50 repeats on the resulting chromosomes).
Reverse transcriptase activity is required for transposition in eukaryotes but not in prokaryotes. Explain.
Transposition in eukaryotes occurs via an RNA intermediate; transposition in prokaryotes occurs directly from the DNA w/ the transposase gene to the target DNA
Overuse of antibiotics has led to widespread antibiotic resistance. How do transposons play a role in this phenomenon?
Complex transposons present the transposon gene AND another gene into the target
They often carry antibiotic resistance genes