Chromatin Structure and Histones Code

Question 1

What makes up chromatin?

Answer 1

DNA, histones, RNA

Question 2

What is chromatin?

Answer 2

A nuclear complex of DNA and associated proteins that forms chromosomes within the nucleus of eukaryotic cells

Question 3

What is the function of chromatin?

Answer 3

Packaging long DNA molecules into more compact and denser shape to fit into the nucleus and to protect the DNA structure and sequence

Question 4

What are the 4 levels of chromatin

Answer 4

1st: DNA and histones to form nucleosomes
Increases DNA packaging 7-fold
Final size is 10nm
2nd: Nucleosomes pack themselves in fibres
Increases DNA packaging 6-fold
30nm
3rd: Fibres pack themselves into loops and TADs and form chromatin
Increase packaging 3-fold
100-250nm
4th: Represented by the mitotic chromosome
Means 1000-fold packaging
700-1000nm

Question 5

When does chromatin condense?

Answer 5

Chromatin condensation begins during the prophase and chromosomes become visible

Question 6

How is chromatin organised during interphase?

Answer 6

Euchromatin and heterochromatin

Question 7

What are the characteristics of euchromatin and heterochromatin?

Answer 7

Euchromatin: Low compacticity, 10nm fibre-beads on a string
Lightly staining areas of chromatin
Rich in genes
Accessible to the enzymes involved in DNA transcription, replication or repair
Heterochromatin (10%): Highly condensed, 30nm fibre
Darkly staining areas of chromatin often associated with nuclear envelope
Gene poor
There are two types- constitutive and facultative

Question 8

What is the difference between constitutive and facultative heterochromatin?

Answer 8

Constitutive heterochromatin is invariably heterochromatin containing highly repetitive sequences of DNA which are genetically inactive and serves as structural elements of the chromosome e.g. telomeres and centromeres
Facultative consists of regions on chromosomes which becomes heterochromatin in certain cells and tissues (heterochromatin that can become euchromatin in certain cells)
e.g. inactivates X chromosome in female somatic cells

Question 9

How does chromatin show plasticity?

Answer 9

It is enabled by choice of histone variants, modifications of DNA bases and reversible post-translational modifications (PTM) of histone tails

Question 10

What is a nucleosome?

Answer 10

A fundamental structural unit of chromatin

It is composed of a little DNA wrapped around proteins called histones

Question 11

How are nucleosomes formed?

Answer 11

1. Histones assemble to form an octamer core:
   H2A, H2B, H3 and H4 (2 of each). N-terminal tails stay outside the octamer core
2. 146bp of DNA around the histones core (1.7 turns of DNA)
3. H1 protein wraps another 20 base pairs of linker DNA resulting in two full turns around the octamer. It helps stabilise the zig-zagged 30nm chromatin
4. Nucleosomes are joined by linker DNA (20bp) that runs between them. Long chain of nucleosomes gives the appearance of beads on a string
5. Nucleosomes tightly pack together into a fibre of 30nm
6. Chromatin loop formation
7. Organisation in Topologically Associating Domains (TADs)
8. Chromosome territories

Question 12

How is the core histone octamer structured?

Answer 12

The core histone octamer is composed of central H3 H4 tetramer and 2 flanking H2A and H2B dimers
Each of the core histones contain a common structural motive that is called the histone fold which facilitates the interactions between the individual core histones

Question 13

What are the dynamics of the nucleosome?

Answer 13

During transcription, or DNA replication, they must be removed from the DNA in front of the polymerase, and replaced behind the polymerase

Question 14

What is chromatin loop formation? (and cohesion)

Answer 14

Looping occurs when stretches of genomic sequence that lie on the same chromosome are in close physical proximity to each other
Cohesion- protein ring that binds to DNA and facilitates loops
a) the cohesion rings binds bind to DNA
b) the cohesion rings slide over the CTCF molecules whose binding sequence point away from the loop. The loop continues to grow
c) loop formation stops when each of the rings has reached an inward-directed CTCF sequence

Question 15

What’s the purpose of looping?

Answer 15

Chromatin loops provide a favourable environment to processes such as DNA replication, transcription and repair as it brings elements such as the enhancer together with the promoter
Enhancers can also interact with silencers
Insulators can interact with another insulator and insulate genes from being regulated by regulators of the proxy genes

Question 16

What are Topologically Associating Domains?

Answer 16

TADs are highly conserved chromatin domains that shape functional chromosomal organisation
Function is not fully understood but their disruption leads to disease

Question 17

What are chromosome territories?

Answer 17

Non-overlapping domains/regions of the nucleus occupied by uncondensed chromosomes
They are composed of TADs

Question 18

Define epigenetics

Answer 18

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 a development program

Question 19

What is histone methylation?

Answer 19

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 causes chromatin decondensation e.g. H3K9me1
Effect may vary if residue is mono-, di- or tri-methylated

Question 20

What is histone acetylation?

Answer 20

Histone tails are acetylated by histone acetyl transferases (HATs) and deacetylated by histone deacetylases (HDACs)
Mose common is acetylation of lysines
Acetylated histones are generally associated with relaxed chromatin and gene expression and deacetylated histones with closed chromatin and 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

Question 21

What is histone phosphorylation?

Answer 21

Histone tails are phosphorylated by protein kinases and dephosphorylated by proteases
Can occur on serines, threonines and tyrosines
Phosphorylation of H3S10 and H3S28 is involved in chromatin condensation during mitosis and meiosis as well as in chromatin relaxation linked to transcription activation

Question 22

What is histone ubiquitylation?

Answer 22

Ubiquitin ligases and deubiquitinating enzymes
Primarily on lysines of histones H2A and H2B
H2Aub is more frequently correlated with gene silencing, while H2Bub is mostly associated with transcription activation

Question 23

What is the histone code and how does it work?

Answer 23

A combination of post-translational modifications on the same histone tail(s)
Code readers are protein complexes that read combinations of marks
Chromodomains specifically recognise methylated residues, while bromodomains bind acetylated residues
This read leads to chromatin remodelling (opening or closing)