Chromosome organization

A K A Mandal

A K A Mandal 1
 Key Concepts
1. Prokaryotic and eukaryotic cells both contain
double-stranded DNA, but their genomes are
organized differently
2. Eukaryotic chromosomes contain an enormous
amount of DNA, which requires an elaborate
system of DNA packing to fit all of the cell’s
DNA into the nucleus
3. Changes in the physical arrangement of DNA,
such as level of DNA packing, affect gene
expression
4. Gene make up only a tiny portion of the
genomes of most multicellular eukaryotes 2
A K A Mandal
 LEVEL OF ORGANIZATION FOR
DNA
• DNA
• histones
• nucleosomes
• coils
• supercoils
• chromosome
A K A Mandal 3
 Why packaging?
• DNA is associated with proteins and each DNA and its
associated protein is called chromosome
• This organization is true for for both – prokaryotic and
eukaryotic cells and even for viruses
• Packaging of DNA into chromosomes serves several
important functions:
– First, chromosome is a compact form of DNA that readily fits inside
the cell. A human cell contains 3x109 bp per haploid set of
chromosomes. If thickness of each bp is 3.4 Å and the DNA
molecules of a haploid set of chromosomes were laid out end-to-end,
the total length of DNA would be approx. 1010 Å or 1 meter! In
diploid cell, it is 2 meters. Since diameter of a typical human cell
nucleus is only 10-15 µm, DNA must be compacted by several
order of magnitude to fit in such a small space

A K A Mandal 4
 Why packaging?
– Second, it serves to protect the DNA from damage.
Completely naked DNA molecules are relatively unstable
in cells. In contrast, chromosomal DNA is extremely
stable, allowing the information encoded by the DNA to
be reliably passed on
– Third, only DNA packaged into a chromosome can be
transmitted efficiently to both daughter cells each time
a cell divides
– Finally, the chromosome confers an overall
organization to each molecule of DNA. This organization
facilitates gene expression and recombination between
parental chromosomes that generates the diversity
observed among different individuals of any organism
A K A Mandal 5
 Eukaryotic chromosomal organization
• Nucleosome are the building block of chromosomes
• Majority of the DNA in eukaryotic cell is packaged into
nucleosomes
• It is composed of a core of eight histone protein molecules,
these being two each of histones H2A, H2B, H3 and H4.
Their positively charged amino acids bind tightly to
negatively charged DNA
• The DNA between each nucleosome is called the linker
DNA
• By assembling into nucleosomes, DNA is compacted
approximately six fold. This far less than 1000 – 10,000-
fold compaction generally observed in eukaryotic cells. This
first stage DNA packaging is essential for all the remaining
levels of DNA compaction
• The DNA most tightly associated with the nucleosome,
called core DNA, is wound ~1.75 times around the outside
of the histone octamer like thread around a spool
A K A Mandal 6
 Eukaryotic chromosomal organization

• Between 140 and 150 bp

of DNA (depending on the
species) are associated
with the nucleosome
particle, and each An array of nucleosomes separated
by linker DNA

nucleosome is separated
by 20–60 bp of linker DNA,
giving the repeat length of
190–220 bp

A K A Mandal 7
Eukaryotic chromosomal organization
• In any cell there are stretches of DNA that are not packaged into
nucleosomes, typically these are regions of DNA engaged in gene
expression, replication, or recombination. These sites are
typically associated with non-histone proteins that are either
regulating or participating in these events
• As well as the proteins of the core octamer, there is a group of
additional histones, all closely related to one another and collectively
called linker histones. In vertebrates these include histones H1a-e,
H1°, H1t and H5
• A single linker histone is attached to each nucleosome, to form the
chromatosome, but the precise positioning of this linker histone is
not known.
• Unfolded chromatin has the appearance of beads on a string, a
nucleosome, in which DNA winds around a core of histone
proteins.
• https://www.youtube.com/watch?v=Pj9cdVeIntY
A K A Mandal 8
 Eukaryotic chromosomal organization
• The ‘beads-on-a-string’ structure is thought to
represent an unpacked form of chromatin that
occurs only infrequently in living nuclei.
• The beaded string coils to form the 30-nm
chromatin fiber (it is approximately 30 nm in width).
• The exact way in which nucleosomes associate to
form the 30 nm fiber is not known, but several
models have been proposed, the most popular of
which is the solenoid structure. The individual
nucleosomes within the 30 nm fiber may be held
together by interactions between the linker The solenoid model for
histones, or the attachments may involve the core the 30 nm chromatin
histones, whose protein ‘tails’ extend outside the fiber
nucleosome.
• The 30 nm fiber is probably the major type of
chromatin in the nucleus during interphase

A K A Mandal 9
• This fiber forms looped domains
attached to a scaffold of nonhistone
proteins (Human chromosomes contain
about 2000 looped domains)
• Compaction continues by forming
looped domains from the 30 nm
chromatin, which seems to compact the
DNA to 300 nm chromatin
• DNA in looped domains are attached to
the nuclear matrix via DNA sequences
called MARs (matrix attachment
regions)
• In a mitotic chromosome, the looped
domains coil and fold to produce the
characteristic metaphase
chromosome.
• These packing steps are highly specific
and precise with particular genes
located in the same places 10
Fig. 8.21 Model for the organization of 30-nm chromatin fiber into
looped domains
that are anchored to a nonhistone protein chromosome
scaffold

A K A Mandal 11
Eukaryotic chromosomal organization

• During division, the DNA adopts a more

compact form of packaging, resulting in the highly
condensed metaphase chromosomes that can
be seen with the light microscope and which have
the appearance generally associated with the
word ‘chromosome.
• They form at a stage in the cell cycle after DNA
replication has taken place and so each one
contains two copies of its chromosomal DNA
molecule. The two copies are held together at the
centromere, which has a specific position within
each chromosome.

A K A Mandal 12
 Eukaryotic chromosomal organization

• Interphase chromatin is generally much less

condensed than the chromatin of mitosis
• The chromatin of each chromosome
occupies a restricted area within the
interphase nucleus.
• Interphase chromosomes have areas that
remain highly condensed heterochromatin,
and less compacted areas euchromatin
13
 Prokaryotic chromosome structure

A K A Mandal 14
 Prokaryotic Chromosome

• Although prokaryotic cells have typically

smaller genomes, the need to compact
their DNA is still substantial. An E. coli
must pack its 1 mm chromosome into a
small cell that is only 1 µm long
• Bacteria have no histones or
nucleosomes, but they do have other
smaller basic proteins that may serve
similar functions

A K A Mandal 15
 Prokaryotic Chromosome
• Genomes of prokaryotes are organized
differently from that of eukaryotes
• Genome contained in a single
chromosome, which is usually
circular DNA molecule,
morphologically different from that of
eukaryotes
• In prokaryotes, there is considerable
variation in genome length bearing
genes
– Smallest genome length in RNA viruses,
provided with only a few genes in its
chromosome
– The number of gene may be as high as 150
in some larger bacteriophage genome
– In E.coli, about 3000 to 4000 genes are 16
organized into its one circular chromosome.
 Prokaryotic Chromosome
• The chromosome exists as a highly
folded and coiled structure dispersed
throughout the cell.
• The folded nature of chromosome is
due to the incorporation of RNA with
DNA
• These loops are highly twisted or
supercoiled structure with about four
million nucleotide pairs.
• Its molecular weight is about 2.8 X109

A K A Mandal 17
 Prokaryotic Chromosome

• Observed under electron microscope

• 50-100 domains or loops per E. coli chromosome, with
50-100 kb/loop
•The ends of loops are
constrained by binding to
a structure which
probably consists of
proteins attach to part
of the cell membrane.

A K A Mandal 18
Mechanism of folding of a bacterial chromosome

•There are many supercoiled loops (~100 in E. coli)

attached to a central core.
•Each loop can be independently relaxed or condensed.
•Topoisomerase enzyme – (Type I and II) that
introduce or remove supercoilling 19
 Mechanism of folding of a bacterial chromosome
DNA-binding proteins
• Several DNA binding proteins with superficial resemblance with
eukaryotic chromosomal proteins have been isolated
• Histone-like proteins essential for DNA packaging to stabilize and
constrain the supercoiling
– HU: a small basic dimer protein, non-specific binding to DNA, most
abundant , condenses DNA, possibly wrapping it into a beadlike structure
– H-NS (protein H1): neutral monomeric, partially non-specific binding
(interacting preferentially with the sequences that are bent). There are
about 20,000 H-NS molecules per E. coli cell, enough for one H-NS dimer
per ≈400 base pairs of DNA
• Site-specific DNA binding proteins important for organization of DNA
domains (RNA polymerases, IHF etc)
• Finally, E. coli chromosomal DNA is tightly supercoiled — that is,
twisted upon itself
• An E. coli enzyme called DNA gyrase uses energy from ATP hydrolysis
to wind supercoils into DNA. Supercoiling contributes to the
compaction necessary to fit chromosomal DNA into the bacterial
cell
A K A Mandal 20
 Prokaryotic Chromosome -
Supercoling of the genome
• DNA supercoiling refers to the
over- or under-winding of a DNA
strand, and is an expression of the
strain on the polymer
• E. coli chromosome as a whole is
negatively supercoiled
• Individual domains may be
supercoiled independently
(topological independent).
• Direct biochemical evidence is
lacking for different level of
supercoiling in different domains

A K A Mandal 21
 Supercoiling

Most common type

of supercoiling

Helix twists on
itself in the opposite
direction; twists to
A K A Mandal
the left 22
 Mitotic chromosome
Additional information on SUPER COILING

Super coiling..\..\Videos\Chromosome_Videos\Super Coiling of DNA.flv

..\..\Videos\Chromosome_Videos\Chromosome to DNA.flv

https://www.youtube.com/watch?v=lUESmHDrN40

https://www.youtube.com/watch?v=DXznYpXZu3M

https://www.youtube.com/watch?v=rMz1tQRGirk

23
 References
• Text Books
– 1. Nelson,D.N. and Michal M.C. 2007. Lehninger. Principles of
Biochemistry. W.H. Freeman publications.
– 2. Gardner, E.J., Simmons, M.J., and Snustad. D.P. 2005.
Principles of genetics. 8th edition. Wiley India, Nice Printing
press, New Delhi
– 3. James D. Watson et al.,2004. Molecular biology of the gene.
Pearson education Inc.
• References
– 1. Benjamin Lewin. 2004. Genes VIII. Pearson Education, Inc.
– 2. Geoffrey M. Cooper. 2000. The Cell: A Molecular Approach.
2nd Edition. Sinauer Associates, Inc.
– 3. Lodish H. et. al., 2004. Molecular Cell Biology, 5th Edition,
W.H. Freeman & Co.
A K A Mandal 24