Lecture 4

Genomes & Chromosomes

1
 Today...
• Lecture Outline:
1. Genomes
2
2. Bacterial DNA Packaging
3. Eukaryotic Chromosomes
4. Nucleosomes
5. C
Chromatin structure
Reading:
g MBoC,, 5th edition,, pages
p g 202-206;; 208-218
Sequenced
q Genomes
can sequence bacterial DNA in one day!

Poplar genome
First tree genome
Neanderthal Genome Sequence

•Approximately 65% of the

sequence obtained
•DNA recovered from bones
from a 38,000 year old site in
Croatia
•Modern humans with non-
African ancestral genomes
contain approximately 1 - 4 %
Neanderthal DNA
bone and skin are diff Hmmmm...
-no clothes, tougher?
Does that mean...?
-ribs wider and smaller
•Partial sequence analysis
shows only 78 amino acid
variants in protein coding
genes that MIGHT impact on
f
function
ti
http://www.sciencemag.org/content/328/5979/680.full
Human genome
g
3 billion base pairs per
genome
One maternal + one
paternal genome = you
~25,000
~25 000 genes spread
across 23
chromosomes
XX female, XY male
a genome is a set, 23 pairs from each parent
.: two genomes - one maternal, one paternal

Chromosome: an organized structure of DNA and protein

Alberts Fig 4-11

 But genomes can come in all sizes.........

BACTERIOPHAGE: a virus that infects bacteria

<- 48 kilobases

circular genome very common in prokaryotes

4600 kilobases

Figure 1-29 Molecular Biology of the Cell, Fifth Edition (© Garland Science 2008)

Figure 1-27a Molecular Biology of the Cell, Fifth Edition (© Garland Science 2008)
.......and contrast these sizes with organellar
genomes

loci associated with diseases

16.6 kb in mito-
chondria

160 kb in chloroplast genome

SO SMALL! How? ...
Proteins made by nuclear DNA move to mitochondria
DNA transfer between mitochondrial genomes and nuclear genomes
- in plants, between chloroplasts and nucleus
 Comparing
p gggenome sizes
Advances in automated sequencing have made possible the sequencing
of many genomes.
Prokaryotic genomes in hours, eukaryotic genomes in days.
prokaryotic genomes are generally smaller

single-celled
eukaryote

Amoeba dubia:
has more kb than
US; size does not
correlate to
complexity!!!

Alberts, Figure 1-37

 Brain-eating
g amoeba
Advances in automated sequencing have made possible the sequencing
of many genomes.
Most recent include IlluminaTM and Ion Torrent systemsTM

affects nasal epithilium,

then goes up your nose and
kills your neurons

Naegleria fowleri
 Comparing
p gggenome sizes
Advances in automated sequencing have made possible the sequencing
of many genomes.
An organism’s complexity
____________________________
An organism's complexity and size are not reflected in genome size
and size

Alberts, Figure 1-37

 The human genome
Only1.5% of your
1.5% of genome encodes genome
protein (a encodes
lot is non-coding or redundant) protein

50% of your
50% of genome genome
is repetitive DNA is repetitive DNA
LINE: Long interspersed nuclear elements
SINE: short " " " (<500 bps)
retroviruses: stick their genetic material into your genome

nothing to do with
"AG-AG-AG" making RNA or
proteins
large amounts of genome duplicated

29
Transposons cut them selves out of DNA and place themselves back in somewhere else!
Alberts, Figure 4-17
 PROKARYOTIC CELLS***

Packaging of DNA in the cell

In a non
non-packaged
packaged state
state, even the small prokaryotic genome
would occupy a considerable portion of the cell volume;
much more of a p
problem in eukaryotes.
y

In prokaryotes, the DNA is condensed through folding and

t i ti about
twisting b t 1000 fold.
f ld Bound
B d together,
t th DNA + proteint i fform
the nucleoid
nucleoid

Important components of this packaging are: (all help to package DNA down

• Positively charged polyamines (types of proteins)

• Numerous nucleoid-associated
nucleoid associated proteins (NAPs) such as
H-NS, the histone-like protein HU, IHF, FIS
• Supercoiling of DNA by the enzyme topoisomerase
topoisomerase

Topoisomerase: enzymes that wind and unwind the DNA 12

 Organization of the Prokaryotic nucleoid

ONE line is a strand of DNA

Nature Micro. Reviews, March 2010 13

 Getting eukaryotic genome packed into cells:
A BIG PROBLEM!

• Consider the size of the human genome

g
1. 6 billion base pairs per cell
2. 2 meters of DNA per cell
2 metres of DNA per cells

3
3. located in the nucleus which is about 6 μm in diameter
4. geometric equivalent of packing 40 km of fine thread into
geometric equivalent of packaging 40 km of fine thread into a tennis ball

a tennis
t i ball
b ll
5. number of cells in human body: 1013
6. total length of DNA in human body: 2 X 1010 km
total length of DNA in human body 2*10^10 km
 Getting the eukaryotic genome packed into cells:
The chromosome solution
Genome packaged into
chromosomes

Karyotype: artificial array of paired chromo-

Karyotype – artificial array of
somes in numerical order - diagnostic aid
paired chromosomes in
Figure 4-10 numerical order – diagnostic aid
 Hybridization (chromosome painting - how it makes
them coloured - a fluorescent DNA)

Courtesy: National Human Genome Research Institute

 Getting the eukaryotic genome packed into cells:
The chromosome solution

•Inhumans - 23 pairs
(denature and renatured with heat)

each chromosome
g , long
contains a single, g
linear DNA molecule &
associated proteins
p
called chromatin
•Chromatin is tightly
packaged, but the DNA
must remain accessible for
transcription, replication &
repair.
Figure 4.10
DYNAMIC!
 Nucleosomes: basic structural unit

Chromatin isolated from cell in interphase

more loosely bound with proteins cell not dividing, growing

30nm fiber

little 'beads' are proteins on a 'string' (DNA)

Nucleosome

• Experimentally
p y decondensed chromatin

Fig. 4.22
Experimental isolation of nucleosomes
~80 bp longs
red: DNA, yellow: proteins
wrapped DNA:
~147 bps long

nucleosome: includes DNA

between the protein, the protein,
and the DNA wrapped around the
bead
Experimentally added -> core histone + DNA wrap =
digests string DNA nucleosome core, or nucleosome

Fig. 4.23
(Part 1 of 2)
 Isolation of nucleosome (continued)

•Histones
Histones are small
proteins—rich in lysine and
arginine are +vely charged, stick well to DNA
Positive charge neutralizes
negative
g charge
g of DNA
(different)
•Four core histone proteins
(H2A H2B,
(H2A, H2B H3 & H4)
•Pair of each in octamer core
Each are histones!
Fig. 4.23 •One linker histone (H1)
(Part 2 of 2) **not in the octamer core, on the linking part of DNA
Structure of a nucleosome

Fig. 4.24
Packaging
g g of nucleosomes
Nucleosomes - eukaryotic
Nucleoid - prokaryotic

Figure 10.21 from Lodish et al. (2003) Molecular Cell

Biology. See Fig. 4.29 in Alberts
Packaging of nucleosomes

+vely
charged

-vely charged

histone H1

clips DNA in place on the bead

Fig. 4.34
 Chromatin
packing
The net result is that each
DNA molecule has been
packaged into a mitotic
chromosome that is 10,000
times shorter than its
extended length
Packaging and unpackaging requires ATP

Fig. 4.72
 Chromatin packing and re-modeling

•Heterochromatin exists during M PHASE (cell division)

Highly condensed chromatin

Mitotic & meiotic chromosomes
Centromeres and telomeric regions
centre of chromosomes near very end of DNA

one of X chromosome in human females (Barr body)

XX female - one X is inactivated (random)

“heterochromatic”
heterochromatic regions of interphase chromosomes
- regions where gene expression is suppressed
suppressed

no transcription!
 Chromatin packing and re-modeling

•Euchromatin - more loose, more access to DNA

Relatively non-condensed chromatin

“euchromatic” regions of interphase chromosomes -
regions where genes tend to be expressed
expressed

Covalent modification of histones,

histones the presence of
chromatin remodeling complexes, and RNA
polymerase (transcription) complexes modulate the
reversible switching from euchromatic to
g
heterochromatic regions
 Implications for gene expression ...

Fig 4.63
Interphase chromosomes in discrete regions of nucleus
 allows access to DNA for protein making
Re-orientation of expressing gene within the chromatin

Condensed
chromosomal
territory

nucleus ->
yellow dot is
a gene

unravelled to gain
access to needed
gene

gene off gene on

Figure 4-65 Molecular Biology of the Cell (© Garland Science 2008)
 Loops of chromatin

- proteins anchor DNA to the wall

Chromatin is remodelled to alter access to

DNA
The End