NUCLEOSOMES

General structure of nucleosome

- One copy of the human genome, which has three billion base pairs, can stretch to a length of more than 2m.
However, it needs to be contained within a cell nucleus that has an average diameter of less than 10 μm.

- To create this kind of compaction and preserve accessibility, organisms arrange their genomes into a polymeric
complex known as chromatin.

- The nucleosome, a fundamental building block of chromatin polymers, replicates every 160–240 base pairs
throughout the genome. The nucleosome core, which is made up of an octameric complex of the core histone
proteins, is present in every nucleosome and forms a spool that can wrap 145–147 bp of DNA.

- Linker DNA binds to the linker histone protein, which connects the nucleosome core to the nucleosome core next
to it. The chromatosome is made up of the linker histone and the nucleosome core, which together contain about 165
bp of DNA. A nucleosome is made up of linker DNA and the chromatosome.
 Histones
There are 4 major histones. H2a, H2b, H3 and H4. There is
also a linker histone (H1) which binds the nucleosome at the
entry and exit sites of the DNA.
Figure 2A
The basic structure of a histone is a folding region and then
an N terminal tail. The tail length is variable between
different histones, but they are very basic due to presence of Histone modification
lysine and arginine residues. Their positive charges interact
with the negatively charged DNA backbone. Many post-translational modifications can happen with
the histone tails, changing the accessibility of the
Many hydrogen bonds also form between the phosphodiester DNA.
backbone of DNA and the histones, holding the DNA in
tightly. Modifications include acetylation, methylation,
phosphorylation or ubiquitination.

These changes are reversible.

H2a and H2b structure
H2a and H2b exist as a dimer.

Two of these dimers are found as part of the

nucleosome core.

Column chromatography was used to identify these

proteins, the H2 fraction was very rich in lysine.
Density gradient centrifugation then showed there
were 2 types of H2 histones.

H2a has an additional C terminal which is useful in

attaching the H3-H4 tetramer with the H2a-H2b dimer.
 H3 structure
• The average number of amino acid residues in H3 histone
proteins is 135.

• Has a long N-terminal tail.

• Large amounts of variation occur in the structure of the

H3 histone, resulting in multiple different variants in humans,
e.g., H3.1, H3.2, H3.3, and H3.4. H3.7 and H3.1 share similar
structures; the same can be said for H3.3, H3.6, and H3.8.

• The variants are found at different stages of the cell cycle and
may only differ by a single amino acid residue, e.g., H3.1 and
H3.2, which are both found in S-phase. However, the H3.3
histone is found throughout interphase in small quantities, as it
helps maintain the nucleosome density.
 H4 structure
• H4 histone proteins only contain 102 amino acids.

• Forms a dimer with H3. Two dimers are then used to

form a tetramer. Hydrogen bonds hold the histone
proteins together.

• Tertiary structure comprises of 3 alpha-helices connected

by two loops.

• Very little variation can be seen in the primary structure

of the H4 histone – there is only one known variant,
H4G. There is also little variation between species,
e.g., there are two amino acid substitutions found in the
primary structure of the H4 histone in peas compared to
the primary structure found in the human version.
Interactions within the nucleosome
- DNA- histone interactions: A structure known as a nucleosome core particle is formed
when DNA encircles an octamer of histone proteins. Tight binding is made possible by
interactions between the positively charged amino acids of histones and the negatively
charged phosphate groups of DNA.

- Histone-Histone Interaction: Four pairs of histone proteins—H2A, H2B, H3, and H4

—are found inside the nucleosome core particle. A histone octamer is formed by these
histones. Via a variety of forces (such as ionic, hydrogen and vdw forces) the histones
interact with one another and support the overall stability of the nucleosome structure.

- Linker DNA: Linker DNA is the DNA that joins neighbouring nucleosome core
particles. It is more flexible and less closely linked to histones. The entire chromatin
structure may be impacted by variations in the linker DNA's length.
 The Role of Nucleosomes - Figure 9A

Genomic Compaction
First level of Compaction
- The DNA double helix is wrapped around a set of eight histone proteins (H2a x2, H2b x2, H3 x2, H4 x2) at
regular intervals throughout the entire length of DNA - CHROMATIN

- A nucleosome is the histone-DNA complex and the DNA connecting the nucleosomes are known as linker
DNA

Next level of Compaction – Chromosome (e.g. in Mitosis)

- Nucleosomes and its linker DNA are then coiled into a 30 nanometre chromatin fibre (McGinty and Tan, 2014)

Why is this important?

- Protects DNA from damage/ easier to move DNA in mitosis or meiosis – Next level of Compaction

- Allows for all the information necessary for cellular function to be accessible and present in a small area
(namely the nucleus)

Figure 9B
 The Role of Nucleosomes in Epigenetic
Gene Regulation
Histone tails are regions of each of the histones, that protrude out of the nucleosome - specifically the N-
terminal domain of all four histones and the C-terminal domain of H2A and H2B. (Look at Figure 10A ) Figure 10A

Histone Modifications
Different chemical groups added to the histone tails (which is an example of post-translational modification) can change how
accessible regions of DNA, as well as how compacted the chromatin, is through altering the electrostatic forces within the
nucleosome.

DNA is negatively charged due to its phosphate ions and histones have a positive charge due to their high content of arginine and
lysine residue. (Lee et al., 2020b). This allows for nucleosomes to be held together through electrostatic forces of attraction and
other interactions. The strength of attraction - as well as other interactions (polarity) - defines how tightly the DNA is wound
around the histones. (Simpson, Tupper and Al Aboud, 2022)

- Euchromatin – DNA is loosely wound around the histone proteins

- Heterochromatin - DNA is tightly wound around the histone proteins, silencing gene expression

Figure 10B - (Anon, 2022)

 The Role of Nucleosomes in Epigenetic
Gene Regulation
Examples of Histone Modifications

- Acetylation – the positive charges on lysine residues are neutralised, this decreases the electrostatic forces Figure 10B
of attraction between DNA and the histones. Therefore, the DNA is more loosely wrapped around the histones.
This catalysed by histone acetyltransferases located in the nucleus allowing the transfer on an acetyl group from
acetyl- CoA. (Cavalieri, 2021)

- Methylation – Unlike acetylation, methylation does not affect the charge of the histone. During methylation, methyl
groups can be added to either the lysine residue or the arginine residue of histones H3 AND H4. Arginine
methylation promotes the transcription, whilst lysine methylation represses transcription. (Cavalieri, 2021)

- Phosphorylation – The addition of phosphate ions onto histone residues, this is catalysed by kinases. As
phosphates are negatively charged, the addition of the ions allows for the histone protein to become less negative.
This decreasing the forces of attraction between the DNA and the histones, allowing for euchromatin to form. This
allows for greater gene expression due to an increased accessibility to the DNA. Histone Phosphorylation have
roles in chromatin condensation during Mitosis (Lowndes et al., 2005, Pinto et al., 2010)
 Interactions with other proteins
(functional interactions for gene expression)

RNA polymerase 2 (RNAPII)
transcribes wound DNA by pulling the
DNA away from the nucleosome
during the elongation phase of
transcription (McGinty and Tan, 2014)
 During the elongation phase RNAPII pauses at multiple points in order to
allow time for co-transcriptional events such as, in some cases, pre-
mRNA splicing (Neugebauer, 2002)
 PTMs of histone tails are mainly added through an interaction between
itself and chromatin remodeling enzymes (Swygert and Peterson, 2014)
for example a histone methyltransferase which adds a methyl group
(Husmann and Or Gozani, 2019)

(Tomoya Kujirai et al., 2023)

 Interactions with other proteins
(structural interactions for dynamic change)
RNAPII can also cause the displacement of the
nucleosome moving it “upstream” of the DNA
which is one way of organising and restructuring
the chromatin
 The way this process works is, after DNA is
transcribed and the DNA is peeled from a
nucleosome, the peeled DNA can bind to the
nucleosome “downstream” of it and create a
loop which pulls the nucleosome in (McGinty
and Tan, 2014)
Chromatin remodeling enzymes is a broad term describing a
large family of proteins and enzymes however a commonality
that they share would be that they all induce changes in the
chromatin whether it be changing the position, conformation or
composition of nucleosomes which all provide an aspect of
dynamism and ability for adaptation within the chromatin to a
cell’s environment
 The chromatin factors that affect nucleosomes normally bind in
certain locations, these being: histone tails, nucleosomal DNA,
and the “disk” faces of the core octamer particle itself (McGinty
and Tan, 2014), for example a protein that binds to a PTM on a
histone tail would be a malignant brain tumour repeats (Grimm et
al., 2007) which mostly bind to Methyl-Lysine side chains
 POSSIBLE ERRORS AND HOW THEY WORK
How can chromatin alterations cause disease
Chromatin deregulation in disease -Cancer is both an epigenetic disease (caused by external factors) and genetic
-This causes defects in gene regulation disease (caused by genes).
and abnormalities in gene activity -As chromatin controls the cells homeostasis in cancers this can become un-
-It is caused by genes that are inherited recognizable.
from parents that modify histones and This can lead to hypomethylation (chromosomal instability) and a dense
alter DNA therefore altering chromatin hypermethylation (gene silencing) of the genome
structure These changes can lead to mutations causing malignant tumors.
-This can lead to neurodevelopment
disorders as well as intellectual Press speaker
disabilities. icon to hear
-These diseases can be either presentation
monogenic (controlled by a single gene)
or multifactorial (controlled by multiple
genes)
-The epigenome is directly linked to
genomic malfunction e.g. malnutrition
can lead to disease
 Consequence to error
DNA methylation diagram

Methylation is shown to be correlated with many human diseases, such as; cancer, Huntington’s disease, schizophrenia and autoimmune diseases.
Methylation levels play an integral role in DNA repair, cell division, cell apoptosis and cell division.

Cancer

• Hypermethylation can occur in promoter regions of tumour suppressor genes therefore in-operating some of their functions. DNA methylation
proves to be a critical mechanism in the origination, continuation and progression of cancer. Recent research has found that measuring
methylation levels have enabled early diagnosis of cancer in patients and increased survival rates.

Huntington’s disease

• Huntington’s is a monogenic inherited disease and is fatal. DNA methylation represses transcription as it inhibits transcriptional activators from
binding. Complex and genome wide DNA methylation changes were found when researching transcriptional activity and genome stability in
patients with the disease.
Reference list

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