Download Chromosome structure and mutations

The nucleosome: the fundamental unit of
chromosomal packaging of DNA with histones



Fig. 12.3 b
DNA does not coil
smoothly
Base sequences dictate
preferred nucleosome
positions along DNA
Spacing and structure
affect gene function
Models of higher level compaction seek to explain
extreme compaction of chromosomes at mitosis

Fig. 12.4 a
Formation of 300 A
fiber through
supercoiling
Models of higher level compaction seek to
explain extreme compaction of chromosomes
at mitosis
 Radial loop-scaffold
model for higher
levels of compaction

Fig. 12.4 b
Each loop contains
60-100 kb of DNA
tethered by
nonhistone scaffold
proteins
Radial loop-scaffold model
continued
Fig. 12.4 c
A closer look at karyotypes: fully compacted
metaphase chromosomes have unique,
reproducible banding patterns


Fig. 12.6 a
Banding
patterns are
highly
reproducible
Not known
what they
represent
A closer look at karyotypes

Banding
patterns help
locate genes
Fig. 12.6 b
Polytene chromosomes are an
invaluable tool for geneticists

Fig. 12.15 c
in situ hybridization
of white gene to a
single band (3C2)
near the tip of the
Drosophila X
chromosome
Polytene chromosomes are an
invaluable tool for geneticists
A closer look at karyotypes


Banding patterns can
be used to analyze
chromosomal
differences between
species
Can also be used to
reveal cause of
genetic disease

Fig. 12.6 c
e.g., Downs
syndrome – 3 copies
of chromosome 21
Specialized chromosomal elements ensure accurate
replication and segregation of chromosomes

There are many origins of replication





Replication occurs in about 8 hours during S phase in
actively dividing human cells
DNA polymerase can assemble new DNA at a rate of
about 50 nucleotides per second
Many origins of replication are required to complete the
task of copying the DNA in a genome
In mammals, there are 10,000 origins of replication
Origins of replication are scattered throughout the
chromatin, 30 – 300 kb apart
Structure of yeast origin of
replication


Autonomously replicating sequences (ARSs) in
yeast consist of an A – T rich region
ARSs permit replication of plasmids in yeast cells
Fig. 12.11 b
Telomeres preserve the integrity of
linear chromosomes

Telomeres are
protective caps on
eukaryotic
chromosomes



Fig. 12.8
Prevent fusion with
other chromosomes
Protect tips from
degradation
Solve the endreplication problem

DNA
polymerase
cannot
reconstruct 5’
end of a DNA
strand
Fig. 12.9

Fig. 12.10
Binding of
telomerase to
TTAGGG and
addition of
RNA extends
the ends
Segregation of condensed chromosomes
depends on centromeres

Centromeres appear as constrictions on
chromosomes



Contained within blocks of repetitive, noncoding
sequences called satellite DNA
Satellite DNA consists of short sequences 5-300 bases in
length
Centromeres have two functions


Hold sister chromatids together
Kinetochore – structure composed of DNA and protein
that help power chromosome movement
Centromere structure and function
Fig. 12.11 a
Structure of yeast centromere
Fig. 12.11 b
Studies using DNase identify
decompacted regions
Fig. 12.12 a
Position effect variegation in Drosophila: moving a
gene near heterochromatin prevents it expression

Facultative
heterochromatin

Fig. 12.14 a
Moving a gene
near
heterochromatin
silences its
activity in some
cells and not
others
Comparing the mouse and
human genomes
The loss or gain of one or more
chromosomes results in aneuploidy
Autosomal aneuploidy is harmful to the organism


Monosomy usually lethal
Trisomies – highly deleterious
Trisomy 18 – Edwards syndrome
 Trisomy 13 – Patau syndrome
 Trisomy 21 – Down syndrome

Humans tolerate X chromosome aneuploidy
because X inactivation compensates for dosage
Fig. 13.27

Meiotic nondisjunction



Failure of two sister chromatids to separate during meiotic
anaphase
Generates reciprocal trisomic and monosomic daughter cells
Chromosome loss

Produces one monosomic and one diploid daughter cell
Fig. 13.28
a

Mosaics – aneuploid and normal tissues that lie
side-by-side

Fig. 13.28 b
Aneuploids give rise to aneuploid clones
Gynandromorph in Drosophila results from female
losing one X chromosome during first mitotic
division after fertilization
Fig. 13.29
Euploid individuals contain only
complete sets of chromosomes
Monoploid organisms contain a single copy of
each chromosome and are usually infertile

Monoploid plants have many uses
Visualize recessive traits directly
 Introduction of mutations into individual cells
 Select for desirable phenotpyes (herbicide
resistance)
 Hormone treatment to grow selected cells

Fig. 13.30
Treatment with colchicine converts back to diploid
plants that express desired phenotypes
Fig. 13.30 c
Polyploidy has accompanied the
evolution of many cultivated plants



1 out of 3 flowering plants are polyploid
Polyploid often increases size and vigor
Often selected for agricultural cultivation
Tetraploids - alfalfa, coffee, peanuts
 Octaploid - strawberries

Fig. 13.31



Fig. 13.32
Triploids are almost
always sterile
Result from union of
monoploid and
diploid gametes
Meiosis produces
unbalanced gametes



Tetraploids are often source of new species
Failure of chromosomes to separate into two
daughter cells during mitosis in diploid
Cross between tetraploid and diploid creates
triploids – new species, autopolyploids
13.33 a


Fig. 13.33 b
Maintenance of tetraploid
species depends on the
production of gametes with
balanced sets of
chromosomes
Bivalents- pairs of
synapsed homologous
chromosomes that ensure
balanced gametes
Fig. 13.33 c
Some polyploids have agriculturally desirable traits
derived from two species


Amphidiploids created by
chromosome doubling in
germ cells
e.g., wheat – cross
between tetraploid wheat
and diploid rye produce
hybrids with desirable
traits
Fig. 13.34
Deletions
remove
genetic
material
from
genome
Fig. 13.2
Phenotypic consequences of
heterozygosity


Homozygosity
for deletion is
often but not
always lethal
Heterozygosity
for deletion is
often
detrimental
Fig. 13.3
Mapping distances affected in
deletion heterozygotes



Recombination between homologues can only occur if both
carry copies of the gene
Deletion loop formed if heterozygous for deletion
Genes within the loop cannot be separated by
recombination
Fig. 13.4 a
Deletion loops in polytene
chromosomes
Fig. 13.4 b
Deletions in heterozygotes can
uncover genes

Pseudodominance shows a deletion has
removed a particular gene
Fig. 13.5
Deletions can be used to locate genes



Fig. 13.6
Deletions to assign
genes to bands on
Drosophila
polytene
chromosomes
Complementation
tests
Deletion
heterozygote
reveals
chromosomal
location of mutant
gene
Deletions to locate genes at the
molecular level

Fig. 13.7 a
Labeled probe hybridizes to wild-type
chromosome but not to deletion
chromosome
Molecular mapping of deletion
breakpoints by Southern blotting
Fig. 13.7 b, c
Duplications add material to the
genome
Fig. 13.8 a,b
Duplication loops form when chromosomes pair in
duplication heterozygotes

In prophase I, the duplication loop can
assume different configurations that
maximize the pairing of related regions
Fig. 13.8 c
Duplications can affect phenotype

Novel phenotypes
More gene copies
 Genes next to
duplication
displaced to new
environment
altering expression

Fig. 13.9
Unequal crossing over between duplications
increases or decreases gene copy number
Fig. 13.10
The effects of duplications and
deletions on phenotpye



Heterozygosity creates imbalance in gene
product altering phenotypes (some lethal)
Genes may be placed in new location that
modify expression
Deletions and duplications drive evolution
of the genome
Inversions reorganize the DNA
sequence of a chromosome


180° rotation of
chromosomal
regions after
double-stranded
break
Rare crossover
between related
genes on a
chromosome
Fig. 13.11a,b
An inversion can affect phenotype if
it disrupts a gene
Fig. 13.11 c
Inversion heterozygotes reduce the
number of recombinant progeny

Inversion loop in
heterozygote forms
alignment of
homologous regions
Fig. 13.12
Gametes produced from pericentric and
paracentric inversions are imbalanced
Fig. 13.13
Pericentric inversion
(cont’d)
Paracentric inversion
(cont’d)
Fig. 13.13
cont’d
Balancer chromosomes help
preserve linkage



Fig. D.6
Balancers carry
multiple, overlapping
inversions
Most contain a
dominant marker and
recessive lethal
mutation that
prevents survival of
homozygotes
Useful in genetic
manipulations and
mutant screens
Translocations attach one part of a
chromosome to another
Translocation – part
of one chromosome
becomes attached to
nonhomologous
chromosome


Reciprocal
translocationexchange between
nonhomologous
chromosomes
Robertsonian translocations can
reshape genomes

Reciprocal exchange between acrocentric
chromosomes generate large metacentric
chromosome and small chromosome

Tiny chromosome may be lost from organism
Fig. 13.16
A closer look at karyotypes


Banding patterns can
be used to analyze
chromosomal
differences between
species
Can also be used to
reveal cause of
genetic disease

Fig. 12.6 c
e.g., Downs
syndrome – 3 copies
of chromosome 21
Chronic myelogenous leukemia
Fig. 13.17
Heterozygosity for translocations diminishes
fertility and results in pseudolinkage
Fig. 13.18 a.b
Three possible segregation patterns in a translocation
heterozygote from the cruciform configuration
Fig. 13.18 c
Pseudolinkage –genes near breakpoints act as if linked

Semisterility
results from
translocation
heterozygotes

< 50% of gametes
arise from
alternate
segregation and
are viable
Fig. 13.18 d
Translocation Down syndrome
translocation of chromosome 21 is small and thus produces
viable gamete, but with phenotypic consequence
Fig. 13.19
Transposable elements move from
place to place in the genome

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
Any segment of DNA that evolves ability to move
from one place to another in genome
Selfish DNA carrying only information to selfperpetuate
Most are 50 – 10,000 bp in length
Present hundreds of thousands of times in a
genome
~ 7% of human genome are transposable
elements
Retroposons generate an RNA that encodes a
reverse transciptase-like enzyme

Two types
Poly-A tail at 3’
end of RNA-like
DNA strand
 Long terminal
repeat (LTRs)
oriented in same
direction on either
end of element

Fig. 13.23 a
Fig. 13.23 b
The process of LTR transposition
Fig. 13.23
LINEs and SINEs in humans

LINEs- Long INterspersed Elements

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
Likely source of retroviruses
L1 family in humans, 6-7 kb in length
Encode reverse transcriptase-like enzyme
>20,000 copies in human genome
SINEs-Short INterspersed Elements




appear to have evolved from cellular RNA species,
usually tRNAs
Depend on availability of reverse transcriptase
produced elsewhere
Alu family in humans, 300 bp in length
>500,000 copies in human genome
Creation of LINE and SINE families
Fig. 21.18
Transposons encode transposase enzymes that
catalyze events of transposition
Fig. 13.24 a
TEs can generate chromosomal rearrangements and
relocate genes
Fig. 13.26
TEs can generate mutations in adjacent genes
spontaneous mutations in white gene of Drosophila
Fig. 13.25
Genomes often contain defective
copies of transposable elements





Many TEs sustain deletions during
transposition or repair
If promoter needed for transcription is
deleted, TE can not transpose again
Nonautonomous elements – need activity of
intact copies of same TE for movement
Autonomous elements – move by themselves
Most SINEs and LINEs in human genome
are defective
P elements in Drosophila



M strains of Drosophila have no P elements (most
lab strains)
P strains have many copies of P elements
Hybrid dysgenesis – defects including sterility,
mutation, and chromosomal breakage from
crosses between P males and M females

Promotes movement of P elements to new positions
P-element transposons are critical
tools in molecular genetics

Hybrid dysgenesis

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


Males from Drosophila strains carrying P elements crossed to
females that lack P elements
P element becomes highly mobile in germ line of F1 hybrids
Chromosome breakage reduces fertility in hybrids
Progeny of F1 flies carry many new mutations induced by P
element insertion
Eggs produced by P female have repressor protein that
prevents transposition
Repressor coded for by alternatively spliced P element mRNA
Fig. D.7
Transformation: the introduction of
cloned DNA into flies




P-elements used as
vectors
Insert fly DNA into
intact P element and
then into plasmid
Inject into embryos
from M strain mothers
Cross to P males
Fig. D.8a
Figure D.9
Transformation in plants by T-DNA

Bacterium Agrobacterium
tumefaciens is agent of
transformation



Fig. B.10 a
Transfer of T-DNA into
genome of wounded plant
Antibiotic resistance
markers engineered into
plasmids provide selection
Cells expressing the GUS
reporter gene stain blue
Transformation by Transposon
Tagging



Transposon tagging using transposable
elements from Corn and Arabidobsis
Insertional mutagenesis allows generation of
mutants
Transposon or T-DNA sequence can be used
to identify and clone gene of interest
PCR can be
used to find
plants
carrying a
mutated gene
of interest
Fig. B.11 a-c
Fig. B.11 d,e
PCR can be used to find worms
carrying a mutated gene of interest
Fig. C.10