Eukaryotic chromosomes
Bacterial
DNA is in a nucleoid body
There is one large DNA molecule
Circular
Eukaryotic
DNA is in chromosomes
There are many molecules
Linear
The DNA in the diploid nucleus is ~2 meters long.
It is present in a nucleus that is a 1000 cubic microns.
Function of chromosomes
Packaging
Regulation
Total human DNA is 3x109 bp
Smallest human chromosome is 5x107 bp
The DNA in this chromosome is 14 mm long
The chromosome is 2um long
7000 fold packaging!
1
C-value
How do we account for the differences in DNA content/nucleus
No of genes
Gene size
Distance between genes
2
Junk DNA
Amount of DNA varies in eukaryotes
Salamander genomes are 20 times larger than human genomes
Barley genome is 10 times larger than the rice genome
Barley and rice are related.
Measurements of DNA length
Amount of DNA/nucleus = C value
Species
DNA content (pg or 10-12g)
haploid
Sponge
Drosophila
Human
Lungfish
Locust
Frog
Yeast
0.05
0.2
3.5
102
46
4.2
0.03
This is often called the C value paradox.
There is no phylogenetic relationship to DNA content
There are sibling amphibian species - they look morphologically
identical but have 4-fold difference in DNA content
3
Junk DNA
Does increase in DNA content = Increase in gene content?
1)
Number of genes could vary in these organisms
2) Size of genes could increase as genomes increase
4
Intergenic DNA
3
Amount of DNA between genes increases
5
Genome
Human Gene catalog
Vertebrates
46%
Eukaryote &
Prokaryote
21%
Human specific
<1%
Eukaryotes
32%
Human Genes are categorized according to their function, as
deduced from the protein domains specified by each gene.
6
Repetitive DNA
7
Chromatin
The single chromosome of the prokaryote Escherichia coli is
about 1.3 mm of DNA.
A human cell contains about 2 m of DNA (1 m per chromosome
set)
The human body consists of approximately 1013 cells and
therefore contains a total of about 2 × 1013 m of DNA.
Distance from the earth to the sun is 1.5 × 1011 m
The DNA in your body could stretch to the sun and back
about 50 times.
The diameter of the nucleus is 5x10-6 meters
How is the DNA packaged?
Chromatin=
DNA
+histones
+non-histones
1g
+1g
+1g
8
Chromatin
9
Nucleosomes
Four histone proteins
H2A
H2B
H3
H4
Very highly conserved
There are two copies of
each core histone
2 mol H2A
2 mol H2B
2 mol H3
2 mol H4
1 mol H1
~200 bp DNA
DNA is wrapped around
the outside of the histone
octamer
166 bp of DNA wraps
around the histones
Linker DNA connects
nucleosomes
1 mol of linker Histone H1
10
10 nm fiber folds into the 30 nm filament
[
10 nm
30 nm
[
11
30nm fiber folds into Chromatin Loop Domains
12
Nucleus
DNA needs to be compacted in chromosomes
200 nm fiber
700 nm fiber
13
xxxxx
14
Different types of chromatin
heterochromatin
Euchromatin
Constitutive heterochromatin:
• constitute ~ 10-20 % of nuclear DNA
• highly compacted, transcriptionally/Recombinationally inert
Euchromatin + facultative heterochromatin:
• constitute ~ 80% of nuclear DNA
• less condensed, rich in genes,
however,
• only small fraction of euchromatin is transcriptionally
active
• the rest is transcriptionally inactive/silenced (but can be
activated in certain tissues or developmental stages)
• these inactive regions are also known as “facultative
heterochromatin”
15
Gene Silencing and its importance
In any given cell, only a small percentage of all genes are
expressed
Vast majority of the genome has to be shut down or silenced
Knowing which genes to keep on and which ones to silence is
critical for a cell to survive and proliferate normally
Repetitive DNA tends to recombine expanding/contracting
repeats.
Preventing repetitive DNA from recombination is critical for cell
survival
16
Properties of active/inactive domains
17
Facultative heterochromatin
Regions of genome, rich in genes that are condensed in specific
cell types or during specific stages of development It includes
genes that are highly active at a particular stage of
development but then are stably repressed.
X-chromosome inactivation in mammals.
Dosage compensation
No. of transcripts are proportional to no. of gene copies
Diploid- 2 copies of a gene
XX
2
XY
1
Measuring transcript levels for genes on the X chromosome in
female and male show that they are equivalent.
Dosage imbalance is corrected!
In nematodes there is a decrease in transcription from both
X chromosomes- dpy27 binds the 2X chromosomes and causes
chromosome condensation which reduces transcription.
In Drosophila in the males there is an increase in transcription
from the single X chromosome. A inhibitor of transcription is
turned off in males allowing for full expression from the one X
chromosome
In mammals, X chromosome inactivation occurs in females by
formation of heterochromatin.
18
Dosage compensation
19
Mammalian X-chromosome inactivation (epigenetics)
20
X-inactivation
21
X-inactivation
The inactivation of one of the two X-chromosomes means that
males and females each have one active X chromosome per cell.
X-chromosome inactivation is random. For a given cell in the
developing organism there is an equal probability of the female or
the male derived X chromosome being inactivated.
22
Barr bodies
·
The inactive X-chromosome in normal females is called the
barr body
.
XXX individuals have 2 Barr Bodies leaving one active X
·
XXXX individuals have 3 Barr Bodies leaving one active X
·
XXY individual have one Barr Body leaving one active X
(Klinefelter's syndrome)
·
X0 individuals have no Barr Bodies leaving one active X
(Turner's syndrome)
Given X-chromosome inactivation functions normally why are they
phenotypically abnormal?
Part of the explanation for the abnormal phenotypes is that the
entire X is not inactivated during Barr-Body formation (Escape loci)
Consequently an X0 individual is not genetically equivalent to an XX
individual.
XX female
XXX female
XY male
XXY23male
Mosaic expression
24
Tortoise shell cats
The O gene changes black pigment into a reddish pigment
(orange). The O gene is carried on the X chromosome.
Female cats heterozygous for the O gene on the X- chromosome
have a particular pattern called Tortoise shell.
According to Mendel’s rules the cats should be either orange or
black. But the cats are neither! They are Tortoise shell.
25
Tortoiseshell cats
26
Tortoise shell cats
The O gene changes black pigment into a reddish pigment
(orange). The O gene is carried on the X chromosome.
Female cats heterozygous for the O gene on the X- chromosome
have a particular pattern called Tortoise shell.
According to Mendel’s rules these cats should be either orange or
black. But the cats are neither! They are Tortoise shell.
OO
x
oY
F1 females are Oo
27
Tortoise shell cats
The O gene changes black pigment into a reddish pigment
(orange). The O gene is carried on the X chromosome.
Female cats heterozygous for the O gene on the X- chromosome
have a particular pattern called Tortoise shell. According to
Mendel’s rules these cats should be either orange or black. But
the cats are neither! They are Tortoise shell.
Calliphyge
40% more muscle
7% less fat
20% increased profit
29
Calliphyge
30
31
32
Callipyge
Normal female
Normal female
Normal male
Mutant male mutant female
*
Normal male
*
33
Imprinting
Gamete
A=off
A=off
A=on
A=on
Somatic cell
34
Imprinted loci
35
War of the sexes
36