Chromatin is made up of DNA wound around histone proteins within the cell nucleus. It exists in a less condensed form, known as euchromatin, during interphase and a highly condensed form, known as heterochromatin, that is tightly packaged. Chromatin is organized into nucleosomes, which are further packaged into higher order structures like the 30nm fiber and solenoid to fully compact the DNA within a cell. This hierarchical packaging allows for the meters of DNA in a cell to fit within the nucleus.

1. Submitted by
Pradeep Kumar
M.Sc. (Ag.) Biotechnology

2. o Cells contain a nucleus surrounded by a nuclear membrane in eukaryotic cells,
and a nuclear region in the prokaryotic cells.
o In a non-dividing cell the nucleus is filled with a thread-like material known as
"chromatin".
o Chromatin is made up of DNA and proteins (mainly histones and some non-
histone acidic proteins).
o The chromosomes themselves are macromolecular entities that must be
synthesized, packaged, protected, and properly distributed to daughter cells at
cell division.

3. • The packaging of tremendous amount of genetic information into the small space
within a cell has been called the ultimate storage problem.
• Chromosomal DNA exist in the form of very long molecules, which must be
tightly packed to fit into the small confines of a cell.
• The structure of DNA can be considered at three hierarchical levels:
a. The primary structure of DNA is its nucleotide sequence
b. The secondary structure is the double stranded helix
c. The tertiary structure refers to higher order folding that allow DNA to be
packed into the confined space of a cell.

4. • One type of DNA tertiary structure is supercoiling which takes place when the
DNA helix is subjected to strain by being over wound or under wound.
• Energy is used to add or remove any turns, strains is placed on the molecule,
causing the helix to super coil, or twist on itself.
• Molecule that are over rotated exhibit positive supercoiling.
• Under rotated molecules exhibit negative supercoiling.
• Supercoiling is a partial solution to the cells DNA packing problem because
super coiled DNA occupies less space than relaxed DNA.

6. • Supercoiling relies on topoisomerases enzymes that add or remove rotation
from the DNA helix by temporarly breaking the nucleotide strand, rotating the
ends around each other, the rejoining the broken ends.
• Overrotation or underrotation of a DNA double helix places strain on the
molecule, causing it to supercoil.
• Supercoiling is controled by topoisomerase enzymes.
• Most cellular DNA is negetively supercoiled, which eases the seperation of
nucleotide strands during replication and transcription and allow DNA to be
packed into small spaces.

7. • Individual eukaryotic chromosome
contain enormous amounts of DNA.
• Chromosome are in an elongated
relatively uncondensed state during
interphase of the cell cycle.
p
q

8. • Walther Flemming first used the term Chromatin in 1882. At that time, Flemming
assumed that within the nucleus there was some kind of a nuclear-scaffold.
• Chromatin, which consists of DNA complexed to proteins, is the material that
makes up eukaryotic chromosomes.
• The most abundant of these proteins are the five types of positively charged
histone proteins H1, H2A, H2B, H3, and H4.
• Variant histones may at times be incorporated into chromatin in place of the
normal histones.
• In non-dividing cells there are two types of chromatin: euchromatin and
heterochromatin.

9. Electron micrographs of “chromatin” preparations
• Two classes of chromatin proteins:
a. Histones (core Histones H2A, H2B, H3, H4)
b. Non- histone proteins

10. Types of
Histone
Amino acid
composition
M.W.
No. of
A.A.
Variation
H1 Lysine rich 21,130 223 Wide
H2A
Slightly
lysine rich
13,960 129
Fairly
conserved
H2B
Slightly
lysine rich
13,774 125
Fairly
conserved
H3
Arginine
rich
15,273 135
Highly
conserved
H4
Arginine
rich
11,236 102
Highly
conserved

11. • The histone octamer and associated DNA that form the nucleosome combine
with histone H1 to form the chromatosome.
• The addition of H1 to a nucleosome results in protection of an additional 20 to
22 bp of linker DNA adjacent to the nucleosome, and thus H1 is often referred
to as the linker histone.
• Only one H1 subunit is present per chromatosome, unlike the core histones,
which are present in two copies each.
• DNA binding in H1 is intrinsic to the central globular region, which contains
two DNA-binding sites.
• H1 binds only one of the linker DNA strands, and the second DNA site in
histone H1 binds to the central region of the DNA supercoil in the nucleosome

12. • Histones are rich in the basic amino acids arginine and lysine, which together make up
about 25% of the amino acid residues in any given histone protein.
• Histone proteins are highly conserved among eukaryotic cells.
• Histones H3 and H4 are nearly identical in all eukaryotes, suggesting strict conservation of
their functions.
• Histones H1, H2A, and H2B show less sequence similarity, but on the whole, they are
more conserved than other types of proteins.
• Salt bridges between positively charged histones and negatively charges DNA play a major
role in stabilizing DNA-histone complex.

13. o H1, H2A & H2B, are rich in lysine whereas H3 & H4 are arginine rich H1 is
highly unconserved and mutable H3 & H4 are highly conserved molecules.
o According to molecular weight the relation is H1 > H3 >H2A >H2B >H4.
o Histones proteins lack Tryptophan amino acid.
o Histones octamer has a structural core of an H3.H4 tetramer associated with two
H2A.H2B dimmers.
o Each Histones is extensively interdigitated with its partner.
o All core Histones have the structural motif of the Histones fold.
o The Histones N-terminal tails extend out of the nucleosome.

14. Side view
Top view

15. • In chromatin, those protein which remain after the histone have been
removed as classified as non histone protein .
• Scaffold proteins, DNA polymerase, heterochromatin protein 1 and paycomb
are common non histone .
• Non-histone protein Higher molecular weight - Approximately 1.0 to 1.5
lakh dalton Acidic in nature Mostly act as enzyme Promotes gene action.

16. o DNA is roughly 3 meter long and it has to be packed in nucleus which is few
micrometres in diameter, hence higher order of packaging is required.
o There are various order of packaging
a. First order of packaging – Nucleosome
b. Second order of packaging – Solenoid fibre
c. Scaffold loop Chromatids Chromosome are third order of packaging.

18.  The nucleosome is basic repeating unit of
chromatin.
 It provides the lowest level of compaction
of double-strand DNA into the cell
nucleus.
 It often associates with transcription.
 1974: Roger Kornberg discovers
nucleosome who won Nobel Prize in
2006.

19. • The nucleosome consists of a core particle of eight histone proteins and DNA
that wraps around the core.
• Chromatosome, which are nucleosomes bound to an H1 histone, are separated
by linker DNA.
• Nucleosmes fold to form a 30-nm chromatin fiber, which appears as a series
of loops that pack to create a 250 nm wide fiber.
• Helical coiling of the 250 nm fiber produces a chromatid.

20. • Solenoid is known as Second level of packaging .
• Solenoid – Second level of packaging Proposed by Finch & Klug 6 nucleosome
together forms Solenoid Diameter is 30 nm H1 histone stabilizes the Structure.

21. o Super Solenoid : Super Solenoid The final level of packaging is
characterized by the 700 nm structure seen in the metaphase Chromosome
known as super solenoid structure.
o The condensed piece of chromatin has a characteristic scaffolding structure
that can be detected in metaphase chromosomes.
o This appears to be the result of extensive looping of the DNA in the
chromosome.

23.  Compaction level of interphase chromosomes is not
uniform
 Euchromatin
a. Less condensed regions of chromosomes
b. Transcriptionally active
c. Regions where 30 nm fiber forms radial loop domains
 Heterochromatin
a. Tightly compacted regions of chromosomes
b. Transcriptionally inactive (in general)
c. Radial loop domains compacted even further

24. Structure of heterochromatin and Euchromatin