Week 11 Flashcards
Major genome sequence variation
indels
translocaton
iversion
Duplication
a special subtype of insertions
they increase the copy number of genes
Large scale genome changes
Cytogenetics
PCR
DNA sequencing
Cytogenetics
What you can see down a microscope:
Karyotype
salivary gland giant chromosomes
Autosomes are organized based on size
Karytope chromosome types
depends on the location of the centromere
metacentric (middle centromere)
submetacentric (slightly before center)
acrocentric (closer to the one side)
telocentric (end of the chromosome)
human chromosome
no telocentric chromosomes
Drosophila giant polytene chromosomes
during salivary gland development cell division stops
DNA keeps replicating
homologs are aligned
protein associate differentially along the chromosomes creating a specific banding pattern when stained
PCR detection of genome variation
microsatellites or short tandem repeat
there can be variation at these loci due to slippage and translocation
use reverse PCR primers (2 on each strand) to detect the STRs
allows you to tell if an individual is heterozygous or homozygous for tandem repeats
Chromosomal deletions
multiple genes affected
effect on recombination frequency
complementation analysis
cytogenetics and PCR
If the deletion is large enough we can detect it in the karyotype
lethal when homozygous
Chromosomal deletion: effect on recombination frequency
decreases recombination frequency
if deletion is 10mu the map distance between two genes will decrease
Chromosomal deletion: effect on recombination frequency
decreases recombination frequency
if deletion is 10mu the map distance between two genes will decrease
Polytene chromosome deletions
because the homolohues align you get a bubble wt info not present on the chromosome forms a bulb
PCR analysis of chromosomal deletions
we get product from the deletion (primers designed for the deleted chromosome)
wt would be to long to detect
Chromosome duplications
Duplication are copy number variation that you can see through a microscope
Tandem duplication
Displaced duplication
Reverse duplication
Polytene chromosome duplication
duplicated homolog forms a bulge on the wt homolog
Use of duplication
allows us to test for haploinsufficiency
if the addition of the functional duplicated gene resues the phenotype we are dealing with haploinsufficient
Duplication of genes
increases gene dosage
Copy number variants in humans
estimated that between 5-10% of the human genomic sequence are copy number variants
smaller duplication
Copy number variants in humans
estimated that between 5-10% of the human genomic sequence are copy number variants
smaller duplication
origin of deletions and duplications
generally associated with recombination between repeated DNA sequence
transposons and other repeated sequences
genetic variation can be due to repetitive dna sequence recombining
Types of inversions
paracentric: around the centromere
pericentric inversion: inversions containing the centromere
Genes at breakpoints will be affected
genes can be split in half resulting in a null loss of function
genes can be linked to a new regulatory sequence resulting in gain-of-function
Effect of inversion on recombination frequency
any recombination within the inverted region results in non-viable gametes
only viable recombinants are going to occur just outside the inverted region
shrinks map distance between genes flanking the inversion
Non-reciprocal translocation
portion of the chromosome is duplicated into another chromosome
a displaced duplication
Reciprocal translocation
exchange beween chromosome arms
Effects of translocation
splitting of genes at breakpoints (lf)
gene is next to a new DNA sequence (gf)
Oncogenes as a gain of function
Bcl-2 gain of function, the gene is translocated to another chromosome arm containing a Igg heavy chain promoter
lots of Bcl2 is produced leading to cell survival and reducing apoptosis
Adjacent 1 segregation
horizontal between chromosomes
translocated genes are missing from either gamete
Adjacent 2 segregation
vertical segregation results in missing genes on the untranslocated arm in the gametes
inviable gametes
rare
Alternate segregation
normal chromosomes move to one side
translocated chromosomes move to the other side
viable gametes
Aneuploidy Types
Nullisomy: 2n-2
Monosomy: 2n-1
Trisomy: 2n+1
Tetrasomy: 2n+2
Nullisomy
loss of a pair of chromosomes
Monosomy
loss of a single chromosome
Trisomy
addition of an extra chromosome
Tetrasomy
addition of a pair of chromosomes
Mitotic nondisjunction
both sister chromatids are pulled to one pole resulting in the cells with different number of chromosomes
Gynandromorph
one side has male tissue the other side has female tissue
non-disjunction of x chromosomes during female development
Meiotic Nondisjunction
Nondisjuction at Meiosis I
Nondisjunction at Meiosis II
Nondisjunction at Meiosis
Homologoues chromosomes move to the same pole during meiosis
2 gametes are missing chromosomes
fertilization results in trisomy and monosomy
Nondisjunction at Meiosis
Homologoues chromosomes move to the same pole during meiosis
2 gametes are missing chromosomes
fertilization results in trisomy and monosomy
Non disjunction at Meiosis II
Sister chromatids are pulled to the same pole
1 gamete is missing chromosomes, fertilization results in two viable gametes, trisomy and monosomy
Trisonomy 21
progeny can survive with an extra chromosome 21 because it doens’t contain that much info and it is not lethal
92% of down’s
75% are maternal in origin
majority arise at meiosis I
Inheritance of recessive cystic fibrosis
not always mendelian
uniparental disomy
non-disjunction at meiosis II
fertilization of the gamete containing the two CF+ alleles resulting in trisonomy
If the cell divides normally the progeny will not survive, if non-disjunction occurs during cell division of the embryo, it will be viable and have cystic fibrosis
Polyploidy
Change in the number of sets of chromosomes (all chromosomes)
2n to 3n to 4n
2n to 4n is a whole genome duplication
Whole genome duplication durgin vertebrate evolution
genomes have duplicatede so that all genes have a copy number of 4
Occurs in the hox2 genes (important for determining which body part develops where)
Four copies of each Hox gene, some have been lost during vertebrate evolution.
Autopolyploidy (Mitotic)
Mitotic
no division of the nucleus, stimulate non-division by treating cells with colchicine (microtubules can’t breakdown)
Autopolyploidy (Meiotic)
All homologous chromosomes go to one pole
gametes contain two copies of each homologous chromosomes (2n instead of n) fertilization results in 3n cells
segregation of 3n or odd n chromosomes
this is the origin of seedless fruits
the gametes are so unbalanced and inviable that no seeds form
results in problems at meiosis
random number of each one of these chromosome
more chromosomes result in more unbalanced gametes
Allopolyploidy
fusion of gametes from two distinct species
inviable gametes, each chromosome is different from one another, random segregation of the chromosomes
