CHROMATIN STRUCTURE

Eukaryotic chromatin = DNA (1 part) + proteins (2 parts)

The human genome is about 2 yards long but the average size of a nucleus is 10Ám (microns) in diameter.

What happens to chromatin structure during transcription and replication?

Enzymes need access to DNA, which is never naked, so changes are necessary in chromatin structure for these processes to take place.

Levels of Organization — the Packing Ratio

 

Packing Ratio

Linear DNA

1

Nucleosome

6X

Nucleosomes around 30 nm fiber

40X

Attachment of 30 nm fiber to matrix/core

1000X (interphase nucleus, which is when transcription and replication occur)

Mitotic chromosome

10000X (mitotic chromosome is even more condensed so that it can be packaged during cell division)

Nucleosome — 67 nm DNA around 11 nm histone core (beads on a string), the fundamental unit of organization, the 6X comes from 67/11

EXPERIMENTS FROM THE TEXTBOOK

To Analyze the Nucleosome (FIGURE 19.17)

beads = histone core

fiber = linker DNA

Spacing of Nucleosomes

400 bp = dinucleosome

600 bp = tirnucleosome etc…

How is long is the linker and how long is the DNA around the histone core?

What’s in a nucleosome?

Nucleosome = core particle + linker DNA

200 bp DNA = 67 nm (6X packing)

FIGURE 19.4

DNA wraps almost twice around when its 67 nm of DNA is wound around 11 nm core.

FIGURE 19.5

DNA’s two turns, each diameter, take up almost all the 6nm height of the nucleosome

FIGURE 19.6

Two regions that are 80 bp apart on linear DNA are close to together on the nucleosome.

DNA helix with 10.5 bp per turn is wrapped around nucleosome. Is the DNA at every point in this wrapping equivalent in structure? Nope.

To determine if DNA at all points in wrapping is equivalent

FIGURE 19.14

FIGURE 19.13

TAKE HOME MESSAGE: THIS HAS IMPLICATIONS FOR DNA BINDING PROTEINS.

What’s the role of H1?

FIGURE 19.19

FIGURE 19.20

Is there a consensus sequence for attachment to the matrix? What’s the sequence? What are the proteins that make up the matrix?

FIGURE 18.8

MARs = SARs (scaffold attachment regions)

The Histone Octamer

FIGURE 19.21

FIGURE 19.23

FIGURE 19.25

How does transcription machinery deal with chromatin structures? How does RNA polymerase deal with nucleosomes? How do DNA-binding proteins (tx factors) interact with DNA?

FIGURE 19.29 and 19.30

How can we tell if nucleosomes are in specific positions?

Two Types of Nucleosome Positioning

FIGURE 19.31

Translational positioning

FIGURE 19.32

Rotational positioning

Changes in positioning are associated with transcription.

Experiment:

FIGURE 19.38

OFF è ON è OFF

Hypersensitive Sites

FIGURE 19.41

DNAase Sensitivity

FIGURE 19.42