Chromatin Structure

and
Histones Code

Dr Clara Cieza-Borrella
Senior Lecturer in Molecular Biology
ccieza-b@sgul.ac.uk
 Learning objectives

- Understand the main functions and properties of the chromatin.

- Explain the structure of a nucleosome.

- Describe the different levels of DNA organisation in the nucleus:

from nucleosome to chromosome.

- Understand the main mechanisms of chromatin remodelling –

histones modifications and their functions in transcription
regulation.
 Overview
1. Introduction to chromatin

2. From nucleosomes to chromosome territories

2.1 Nucleosomes

2.2 Chromatin loops

2.3 Topologically Associated Domains (TADs)

2.4 Chromosome territories

3. Epigenetics

3.1 Histone modifications

4. Summary

5. Key references
 Overview
1. Introduction to chromatin

2. From nucleosomes to chromosome territories

2.1 Nucleosomes

2.2 Chromatin loops

2.3 Topologically Associated Domains (TADs)

2.4 Chromosome territories

3. Epigenetics

3.1 Histone modifications

4. Summary

5. Key references
1. Introduction to chromatin
1. Introduction to chromatin
 1. Introduction to chromatin

DNA (spaghettis) + histones (meatballs) + RNA = Chromatin

- Chromatin: nuclear complex of DNA and associated proteins that

forms chromosomes within the nucleus of eukaryotic cells.

- Function: Packaging long DNA molecules into more compact and

denser shape (small volume) to fit into the nucleus and to protect
the DNA structure and sequence.
 1. Introduction to chromatin

Rosalind Franklin, 1952 (Kings College, London)

http://biologicalphysics.iop.org
 1. Introduction to chromatin
- 4 levels of packaging:

By Richard Wheeler

1st level 2nd level 3rd level 4th level

- DNA+histones = nucleosomes
- Nucleosomes pack themselves
- Fibersinpack
fibers - Represented
themselves by the mitotic
into loops and
- Increases DNA packaging
- Increases
7-fold DNA packaging 6-fold chromosome
TADs and form chromatin
- ≈10nm - 30nm - Means
- Increases DNA packaging 1000-fold packaging
3-fold
- 100-250nm - 700-1000nm
 1. Introduction to chromatin

- Chromatin condensation begins during prophase and

chromosomes become visible.

www.sciencehq.com
 1. Introduction to chromatin
- In interphase chromatin is organised in euchromatin and
heterochromatin.

www.mechanobio.info

www.mechanobio.info
 1. Introduction to chromatin
- Euchromatin:
• Low compacticity, 10nm fiber -”beads on a string”.
• Lightly staining areas of chromatin.
• Rich in genes.
 1. Introduction to chromatin
- Euchromatin is accessible to the enzymes involved in DNA transcription, replication, or
repair.

www.mechanobio.info
 1. Introduction to chromatin
- Euchromatin:
• Low compacticity, 11nm fiber -”beads on a string”.
• Lightly staining areas of chromatin.
• Rich in genes.

- Heterochromatin (10%):
• Highly condensed, 30nm fiber.
• Darkly staining areas of chromatin often associated with
nuclear envelope.
• Gene poor.
• Constitutive or facultative
 1. Introduction to chromatin
- Constitutive heterochromatin: invariably heterochromatin containing highly repetitive
sequences of DNA which are genetically inactive and serves as structural element of the
chromosome. Telomeres and centromeres.

- Facultative heterochromatin: regions on chromosomes which become euchromatin in

certain cells and tissues (heterochromatin that can become euchromatin in certain cells).
Potential for expression at a particular point of the development. Inactivates X
chromosome in female somatic cells.
 1. Introduction to chromatin
- Chromatin shows plasticity: enabled by choice of histone variants, modifications of
DNA bases, and reversible posttranslational modifications (PTM) of histone tails.
 Overview
1. Introduction to chromatin

2. From nucleosomes to chromosome territories

2.1 Nucleosomes

2.2 Chromatin loops

2.3 Topologically Associated Domains (TADs)

2.4 Chromosome territories

3. Epigenetics

3.1 Histone modifications

4. Summary

5. Key references
 2. From nucleosomes to chromosome territories

Hansen et al. 2018 Nucleus

 2.1 Nucleosomes
- First level of chromatin packing is the nucleosome.

courses.lumenlearning.com

- Nucleosome: fundamental structural unit of chromatin. Composed of a little

DNA wrapped around proteins called histones.
 2.1 Nucleosomes
a) Histones* assemble to form an octamer core:
• H2A, H2B, H3 and H4 (2 molecules each)
• N-terminal tails stay outside the octamer core

H2B
H2B H3
N +
++ + H2A H4 H3
+
++ + ++
N H4
H2A

*Histones: Main proteins in chromatin whose function is packaging DNA into nucleosomes.
 2.1 Nucleosomes
b) 146bp of DNA wrapped around the histones core (1.7 turns of DNA).
c) H1 protein works like a clip and keeps DNA wrapped around nucleosome

2nm

www.philpoteducation.com
 2.1 Nucleosomes
b) 146bp of DNA wrapped around the histones core (1.7 turns of DNA).
c) H1 protein works like a clip and keeps DNA wrapped around nucleosome
d) Linker DNA 38-53bp DNA that interconnects two adjacent nucleosomes. It helps to
stabilize the zig-zagged 30 nm chromatin fiber.

ib.bioninja.com.au
 2.1 Nucleosomes
d) Nucleosomes are joined by linker DNA that runs between them. Long chain of
nucleosomes gives the appearance of ”beads on a string” (10nm).

Nature Education
 2.1 Nucleosomes
d) Nucleosomes are joined by linker DNA that runs between them. Long chain of
nucleosomes gives the appearance of ”beads on a string” (10nm).
e) Nucleosomes tightly pack together into a fiber of 30nm (2nd level).

Nucleosomes

Histone
N-terminal DNA
tails

Nature Education
 2.1 Nucleosomes
- Nucleosomes dynamics: during transcription, or DNA replication, they must be
removed from the DNA in front of the polymerase, and replaced behind the
polymerase.

Alabert C et al. Adv Exp Med Biol. 2017

 2.2 Chromatin loops

f) Chromatin loop formation (looping): occurs when stretches

of genomic sequence that reside on the same chromosome
are in close physical proximity to each other.
- Cohesin: protein ring that binds to DNA and
facilitates loops

By Morelntpul
Fraser J et al. Microbiol Mol Biol Rev. 2015.
 2.2 Chromatin loops

- Chromatin loops provide favourable environment to processes such as DNA

replication, transcription, and repair.
 2.3 TADs

g) Organisation in Topologically
Associating Domains (TADs):
Highly conserved chromatin
domains that shape functional
chromosomal organization.
Function not fully understood,
their disruption lead to diseases.

Matharu N and Ahituv N. PLOS Gen. 2015

2.4 Chromosome territories

h) Chromosome territories: non-overlapping

domains/regions of the nucleus occupied by
uncondensed chromosomes. They are composed
of TADs.

Fraser J et al. Microbiol Mol Biol Rev. 2015.

2. From nucleosomes to chromosome territories

Fraser J et al. Microbiol Mol Biol Rev. 2015.

 Overview
1. Introduction to chromatin

2. From nucleosomes to chromosome territories

2.1 Nucleosomes

2.2 Chromatin loops

2.3 Topologically Associated Domains (TADs)

2.4 Chromosome territories

3. Epigenetics

3.1 Histone modifications

4. Summary

5. Key references
 3. Epigenetics
- Heritable and reversible changes in gene expression which do not involve a
change in the DNA sequence.

- Results from external or environmental factors or, as part of development

program.

Chen W et al. Adv Protein Chem Struct Biol. 2017

 3.1 Histone modifications

Covalent modifications in histones

- Histone methylation

- Histone acetylation

- Histone phosphorylation

- Histone ubiquitylation

A, acetyl; C, carboxyl terminus; E, glutamic acid; M, methyl;

N, amino terminus; P, phosphate; S, serine; Ub, ubiquitin.
Marks PA et al. Nat Rev Cancer, 2001
 3.1 Histone modifications
- Histone methylation
- Histone tails are methylated by histone methyl transferases (HMTs) and
demethylated by histone demethylases (HDMs).
- Most common: mono-, di- or tri- methylation of lysines and arginines.

- Methylation of some lysine residues causes

chromatin condensation (e.g. H3K9me3).

- Methylation of other lysine residues causes

HMTs HDMs chromatin decondensation (e.g. H3K9me1).

- Effect may also vary if residue is mono-, di- or tri-

methylated.
 3.1 Histone modifications
- Histone acetylation
- Histone tails are acetylated by histone acetyl transferases (HATs) and deacetylated by
histone deacetylases (HDACs).
- Most common: acetylation of lysines.
- Acetylated histones are generally associated with
relaxed chromatin and gene expression and
deacetylated histones with closed chromatin,
silencing of genes.

- Aberrant acetylation is associated with several

solid tumours and haematological malignancies.

- HDACi as emerging drugs in cancer treatment (e.g.

vorinostat (SAHA) in T-cell lymphoma).
 3.1 Histone modifications
- Histone phosphorylation - Histone ubiquitylation

- Histone tails are phosphorylated by - Ubiquitin ligases and deubiquitinating

protein kinases and dephosphorylated enzymes.
by proteases. - Primarily on lysines of histones H2A and
- Can occur on serines, threonines and H2B.
tyrosines.

Jeusset LMP et al.

Cells 2019.

- Phosphorylation of H3S10 and H3S28 is - H2Aub is more frequently correlated with

involved in chromatin condensation during gene silencing, while H2Bub is mostly
mitosis and meiosis, as well as in chromatin associated with transcription activation.
relaxation linked to transcription activation.
 3.1 Histone modifications

- Histone code: combinations of post-translational modifications

on the same histone’s tail/s.

- Code readers- protein complexes that

read combinations of marks:
chromodomains specifically recognize
methylated residues, while
bromodomains bind acetylated
residues. This read leads to chromatin
remodelling (open or close).

Bannister AJ & Kouzarides T. Cell Research, 2011.

 Overview
1. Introduction to chromatin

2. From nucleosomes to chromosome territories

2.1 Nucleosomes

2.2 Chromatin loops

2.3 Topologically Associated Domains (TADs)

2.4 Chromosome territories

3. Epigenetics

3.1 Histone modifications

4. Summary

5. Key references
 4. Summary
- Chromatin is a nuclear complex of DNA and proteins whose function is to compact and
protect DNA molecules within the nucleus.

- The 4 levels of nuclear DNA packaging are: nucleosomes (structural unit), fibers,
chromatin loops and TADs and mitotic chromosomes.

- Histones are 5 nuclear proteins that pack DNA into nucleosomes.

- Chromatin can be remodelled by post-translational/epigenetic covalent

modifications of the N-terminal tails of the histones: methylation, acetylation,
phosphorilation and ubiquitylation.

- Histone code is determined by the combination of epigenetic modifications in histones.

 Overview
1. Introduction to chromatin

2. From nucleosomes to chromosome territories

2.1 Nucleosomes

2.2 Chromatin loops

2.3 Topologically Associated Domains (TADs)

2.4 Chromosome territories

3. Epigenetics

3.1 Histone modifications

4. Summary

5. Key references
 5. Key references

- McGinty RK and Tan S. Nucleosome Structure and Function. Chem Rev. 2015.
doi: 10.1021/cr500373h

- Alabert C, Jasencakova Z and Groth A. Chromatin Replication and Histone Dynamics. DNA
Replication. Adv Exp Med Biol. 2017. doi: 10.1007/978-981-10-6955-0_15

- Deakin JE et al. Chromosomics: Bridging the Gap between Genomes and Chromosomes. Genes
(Basel). 2019. doi: 10.3390/genes10080627

- Li Y and Seto E. HDACs and HDAC Inhibitors in Cancer Development and Therapy. Cold Spring Harb
Perspect Med. 2016. doi: 10.1101/cshperspect.a026831

- Molecular Biology of the Cell (6th edn) Alberts et al. (Eds). Garland Science, New York. QH581
ALB.
Thank you!

Dr Clara Cieza-Borrella
Senior Lecturer in Molecular Biology
ccieza-b@sgul.ac.uk
Supplementary Information

Pediaa.com

lifescience.roche.com
 Supplementary Information

Li B et al. Cell, 2007