lo 1 1. How is mammalian chromatin structure organised?

What are the two main forms of chromatin originally distinguished cytologically?

Euchromatin and heterochromatin

What is euchromatin?

Decondensed chromatin

less intensely staining,

more open

transcriptionally active.

What is heterochromatin?

Condensed chromatin

intensely staining,

tightly packed

transcriptionally repressed.

What is a TAD?

megabases long sequences

separated by boundary regions

physically interact with themselves more frequently than with the rest of the genome.

How frequent are TADs across different cell types?

60-70% of TADs are invariant

What are the hierarchical layers of 3D genome organisation?

Chromosome territories → A/B compartments → TADs → DNA loops

What do chromatin compartments A and B represent?

Active and repressed chromatin regions

A compartments are

transcriptionally active regions,

while B compartments are

transcriptionally repressed regions.

What technique is used to study 3D genome organisation?

Hi-C

Hi-C is

a genome-wide derivative that reveals each interaction in the nuclear space,

Hi-C is

a genome-wide derivative

that reveals each interaction in the nuclear space,

resulting in

a 2D heat map

What does a Hi-C heat map show?

Frequency of interactions between genomic regions

Each data point in a Hi-C heat map indicates

the frequency of interaction between two points in the genome.

What are chromosome territories?

Distinct spatial regions occupied by each chromosome in the nucleus

Are TADs found in all species?

No, TADs are animal specific

Why might TADs not be needed in single-cell organisms?

They have highly compact genomes

Where do most enhancer-promoter interactions occur?

Within TADs

What is the approximate size of a TAD?

Megabases in length

What is CTCF in relation to TADs?

"insulator" protein that binds at TAD boundaries

What is the Cohesin complex?

A multisubunit ring-shaped complex that coordinates TAD spatial constraints