Centromeres
Heterochromatin
Kinetochore - spindle fiber attachment
No universal DNA sequences
Repeat sequences - CENs - 5 to 170 bp – humans, alphoid satellite repeats
Specific associated proteins

•About 15,000 bp in humans
•Lagging strand problem
•Telomere shortening
•Hayflick – and then we die
•Cancer, AIDs, stem cells

• Gene rich chromosomes toward center
• Gene poor chromosomes toward periphery
• Centromeres are not the determining factor
• Chromosomes with adjacent positions more likely to interact cytolologically

• Previously it was predicted that active genes would be located at the surface of chromosome territories.
• Now, it appears that they are also in the interior
• Some are also found on loops outside of the territory

In order for DNA to physically fit into a nucleus, several levels of packing are necessary.
How is the DNA packaged in this way and how is it available for replication and transcription if it is tightly packed?

Histones
• folding and coiling chromosomes
• 45% of the total mass
• 60 million molecules of each type per cell

• Histones are highly conserved across all eukaryotic organisms
• Histones are small basic proteins (102-135 aa) rich in lysine and arginine
• Each histone contains a region that folds in a characteristic structure called the histone fold and a tail region
• Tail region is post translationally modified in various ways to control many aspects of chromatin structure

Core particle - Approximately 1.8 turns of DNA
(consisting of 146 bp) wound around the outside of the histone octamer.

Note that other chromatin modifying complexes include kinases, methylases and ubiquitin conjugating proteins.
Acetylation typically correlates with transcriptional activation while deacetylation correlates with repression.

Histone “tails” stick out between the coil of DNA
Post-translational chemical modification of the tails controls function.
Modification patterns comprise the “ histone code ” .

• Non-histone proteins (NHPs, acidic proteins, nonhistone chromosomal proteins, NHC proteins)
– help regulate DNA transcription and replication
– at least 30 types

“Chromatin remodeling complexes” and “Chromatin modifying complexes” are important for transcriptional activation
Chromatin modifying complex

Chromatin decondensation appears to require two types of protein complexes each made of several polypeptide subunits:
1. Histone acetylase complexes.
These are often referred to as HATS for histone acetylases.
2. Chromatin remodeling factors.
These are often refered to as Swi/Snf factors because they were first identified as yeast mutants defective in mating type switching and in the ability to metabolize sucrose (sucrose non-fermenting).

Chromatin remodeling factors use energy from
ATP hydrolysis to rearrange the packing of nucleosomes in higher order chromatin structures
There are several different chromatin remodeling complexes in cells.
Some of these bind to activation domains and de-condense the associated chromatin.
Some bind to repression domains and condense the associated chromatin.

Nucleosomes + 60 (approx) bp DNA

A eukaryotic gene of 10,000 bp will be associated with about 50 nucleosomes. A human cell contains 3 x 10 7 nucleosomes.
One molecule of histone H1 and the nucleososome is sometimes referred to as the chromatosome.

Most interphase chromatin is condensed into 30nm coils?

Most interphase chromatin is condensed into 30nm coils?
A model for the structure of an interphase chromosome

Lampbrush chromosomes (amphibian oocyte, immature eggs)

In mitotic chromosomes, a scaffold is formed, and matrix attachment sites correspond to sites of chromatin attachment to the scaffold?

Histone depleted metaphase chromosomes

Scaffold Attachment Regions (SARs)?
Regions of the chromosomes with sequences specific for topoisomerase, HMG protein, and histone H1 binding
Found only in untranscribed regions of the eukaryotic chromosomes
Spaced along the chromosomes, with the intervening regions containing one or more genes?
Highly AT rich (65%) and may be several hundred bp long

Discrete loops of DNA appear to be connected at both ends to the scaffold

Quaternary structure: final folding into chromosome shape