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

4. Telomeres

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

10. The structure and organization of chromosomes change during the course of the cell cycle.

13. Nonrandom chromosome positioning
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

14. How porous are territories?
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

18. 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?

19. The 4 nm DNA filament

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

21. Histones are highly conserved across all eukaryotic organisms
Histones are small basic proteins ( 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

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

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

27. The 10 nm nucleoprotein fibril
Nucleosomes + 60 (approx) bp DNA

29. A eukaryotic gene of 10,000 bp will be associated with about 50 nucleosomes. A human cell contains 3 x 107 nucleosomes. One molecule of histone H1 and the nucleososome is sometimes referred to as the chromatosome.

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

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

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

35. 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).

36. 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.

41. Most interphase chromatin is condensed into 30nm coils.

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

43. Lampbrush chromosomes (amphibian oocyte, immature eggs)

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

45. Histone depleted metaphase chromosomes

47. 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
Scaffold Attachment Regions (SARs)

48. Spaced along the chromosomes, with the intervening regions containing one or more genes?
Highly AT rich (65%) and may be several hundred bp long

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

53. Quaternary structure:
final folding into chromosome shape