This document discusses the organization of chromatin and DNA packaging in the cell nucleus. It describes four main levels of chromatin organization: 1) DNA wraps around histone proteins to form nucleosomes, the basic unit of chromatin, 2) Nucleosomes further organize into 30nm fibers, 3) The 30nm fibers then organize into looped domains, and 4) During cell division, the loops compact into mitotic chromosomes. Nucleosomes consist of about 150 base pairs of DNA wrapped around an octamer of core histone proteins, and act to tightly package DNA inside the nucleus.

1. ORGANIZATION OF
CHROMATIN
DR. ANU P. ABHIMANNUE
ASST. PROFESSOR,
DEPARTMENT OF BIOTECHNOLOGY,
ST.MARY’S COLLEGE, THRISSUR.

2. INTRODUCTION
• An average human cell
contains about 6.4 billion base
pairs of DNA divided among 46
chromosomes.
• When stretched it would
constitute 2 m long.
• How is it possible to fit 2
meters of DNA into a nucleus
only 10µm in diameter??

3. DNA PACKAGING
The answers lie in the
remarkable manner in
which a DNA molecule
is packaged.

4. LEVELS OF ORGANIZATION OF
CHROMATIN
The DNA molecules are tightly compacted inside the nucleus.
Various hierarchical levels are observed
1. Naked DNA molecules are wrapped around histones to form
nucleosomes, which represent the lowest level of chromatin
organization.
2. Nucleosomes are organized into 30-nm fibers.
3. 30-nm fibers are in turn organized into looped domains.
4. When cells prepare for mitosis, the loops become further compacted
into mitotic chromosomes

5. ORGANIZATION OF CHROMATIN

6. NUCLEOSOME
• The fundamental structural unit of DNA packaging or
Chromosome Organization
• DNA is compacted into nucleosomes to fit in nucleus.
• Nucleosome contains a segment of DNA wound around
histone proteins.
• About two turns of DNA is wrapped around a set of
eight histones, and hence known as a histone octamer.

7. DISCOVERY - NUCLEOSOMES
• Nucleosomes - first observed by Don and Ada
Olins in 1974.

8. NUCLEOSOME - STRUCTURE
American biochemist (born April 24, 1947).
Awarded Nobel Prize in Chemistry in 2006 for
his studies of the process by which genetic
information from DNA is copied to RNA.
Described by Roger David Kornberg

9. NUCLEOSOME STRUCTURE
• Kornberg observed that chromosomal DNA upon
nuclease activity yielded fragments of 200 bp.
• While naked DNA yielded random fragments.
• It was presumed that proteins associated with the DNA
were providing the protection and are organized into
repeating subunits, called nucleosomes.

10. NUCLEOSOME STRUCTURE
• Early 1970s, it was found that when chromatin was treated with
nonspecific nucleases, most of the DNA was converted to
fragments of approximately 200 base pairs in length.
• In contrast, a similar treatment of naked DNA produced a
randomly sized population of fragments.
• This finding suggested that chromosomal DNA was protected at
certain periodic sites where histones were present.

11. HISTONES
• Group of small proteins found inside the nucleus of
eukaryotic cells.
• Possess high content of the basic amino acids arginine and
lysine.
• Their positive charges allow them to associate with
negatively charged DNA.
• Histones are divided into five classes on the basis of
arginine/lysine ratio

12. TYPES OF HISTONES
Histone residues
(kD)
Mass
(KDa)
%Arg %Lys UEP*
of (10_6
year)
H1 215 23.0 1 29 8
H2A 129 14.0 9 11 60
H2B 125 13.8 6 16 60
H3 135 15.3 13 10 330
H4 102 11.3 14 11 600
Unit evolutionary period: the time for a protein’s amino acid sequence to change by 1 percent
after two species have diverged.

13. NUCLEOSOME CORE PARTICLE
• Nucleosome core particle consist of supercoiled DNA wrapped
twice around a disk-shaped complex of eight histone
molecules
• Histone octamer consists of two copies each of histones H2A,
H2B, H3, and H4 assembled
• Octamer is organized into four heterodimers: two H2A-H2B
dimers and two H3-H4 dimers

14. H1 HISTONE
H1 Histone resides outside the nucleosome core particle and
serve as a linker connecting DNA between nucleosome core
particle

15. DNA – HISTONE INTERACTION
• DNA and core histones are held together by
several types of noncovalent bonds, including
ionic bonds between negatively charged
phosphates of the DNA backbone and
positively charged residues of the histones.

16. 30-nm CHROMATIN FIBERS
• Nucleosomal filament is further coiled into higher order
thicker fibers of the 30-nm diameter.
• This assembly increases the DNA-packing ratio to a 6-
fold or even 40-fold times
• 2 models have been explained:
»Zig-zag model
»Solenoid model

17. SOLENOID
• Linker DNA curves between
consecutive core particles, which
are organized into a single,
continuous helical array
containing about 6–8
nucleosomes per turn.
ZIG-ZAG
• Linker DNA is present in a
straight, criss-cross extended line
between consecutive core
particles, which are organized
into two separate stacks of
nucleosomes.

18. INTERACTIONS
• Interactions are facilitated by both Linker histones and core
histones.
• Linker histones are very fundamental in making 30 nm
nucleosomal filaments.
• Core histones interact with adjacent nucleosomes with the
help of their long, flexible tails.
• For eg: N-terminal tail of an H4 histone can interact with both
the linker DNA and H2A/H2B dimer of adjacent nucleosomes

19. CHROMATIN LOOPED DOMAINS
• 30-nm chromatin fiber is further supercoiled into 80–100 nm
thick loops.
• These DNA loops are tethered at their bases to type II
topoisomerase which regulates the degree of supercoiling.
• Chromatin fibers are spread out within the nucleus and cannot
be easily visualized

20. MITOTIC CHROMOSOME
• Ultimate in chromatin
compactness
• 1 µm of mitotic
chromosome = 1 cm of
DNA, ie, a 10,000:1 packing
ratio.

21. HETEROCHROMATIN AND EUCHROMATIN
• After mitosis, chromatin in form of chromosomes returns to
its diffuse interphase condition.
• However, approximately 10 percent remains in condensed,
compacted form throughout interphase and is located at
the periphery of the nucleus and is called heterochromatin.
• The other that returns to a dispersed state is Euchromatin.

22. CONSTITUTIVE HETEROCHROMATIN
• Constitutive heterochromatin remains in the compacted
inactive state in all cells at all times.
• It represents DNA that is permanently silenced.
• In mammalian cells, it is commonly found in
– Region flanking telomeres and centromere of chromosome
– Distal arm of the Y chromosome in male mammals.

23. CONSTITUTIVE HETEROCHROMATIN
• DNA of Constitutive heterochromatin consists of repeated
sequences and few genes.
• Active genes when move into a position adjacent to
heterochromatin they tend to become transcriptionally
silenced, a phenomenon known as position effect

24. FACULTATIVE HETEROCHROMATIN
• Facultative heterochromatin is specifically inactivated during
certain phases of an organism’s life or in certain types of
differentiated cells

25. REFERENCES
• https://en.wikipedia.org/wiki/Nucleosome#:~:tex
t=A%20nucleosome%20is%20the%20basic,the%2
0fundamental%20subunit%20of%20chromatin.
• https://www.mechanobio.info/genome-
regulation/what-are-nucleosomes/
• Gerald Karp (2010). Cell and molecular biology:
concepts and experiments (6th ed.). John Wiley &
sons. ISBN-13 978-0-470-48337-4.