Organizing cellular DNA into chromosomes

1. Nucleosomes and Chromatin Structure Lodish Chapter 10.4 Organizing cellular DNA into chromosomes • Most bacterial chromosomes are circular with one replication origin • Eukaryotic chromosomes each contain one linear DNA molecule and multiple origins of replication • Bacterial DNA is associated with polyamines • Eukaryotic DNA associates with histones to form chromatin

11. Nucleosomes are complexes of DNA and histones

13. Epigenetics: changes in gene expression caused by mechanisms other than changes in the underlying DNA sequence Histone modifications  acetylation (histone acetyl-transferases – HATs); associated with active chromatin  de-acetylation (histone deacetylases – HDACs); associated with inactive chromatin (new generation of anti-cancer drugs: HDAC inhibitors)  methylation (can be associated with active or inactive, depending on site of modification)  phosphorylation (metaphase chromosomes) DNA methylation  DNA methyltransferases (Dnmt1, 3a, 3b) associated with inactive chromatin)

14. Histone modifications

15. Histone H3 Modifications

16. DNA can be condensed to heterochromatin Euchromatin Heterochromatin

17. Giemsa stained bone marrow stem cell

21. Lack of telomeres facilitates chromosome fusion Visualizing telomeres by fluorescent in situ hybridization (FISH)

22. Each chromosome has a characteristic banding pattern Organization of metaphase chromosome: • Chromosome bands: • Common technique is G-banding (Giemsa). Chromosomes prepared from metaphase cells, stained with Giemsa. Dark bands are called G bands, pale bands are G negative. Dark bands are generally late replicating, contain more condensed chromatin and are less transcriptionally active while light bands are the opposite.

23. Organization of metaphase chromosome Common technique is G-banding (Giemsa). Dark bands are called G bands (heterochromatin), pale bands are G negative (euchromatin).

24. Nomenclature: p (pepit) arm = short arm; q=long arm. • Band numbering proceeds outwards from the • centromere e.g., bands p11 (one-one NOT eleven) • or p23(p two-three NOT twenty three)

25. Chromosomal aberations are most easily observed by spectral karyotyping (SKY)

26. Chromosome translocations are often reciprocal

28. Chromosome translocations can also play a role in evolution Tree shrew SNL crew

29. Genome sizes of different model organisms Yeast 12M bp/ 16 chromosomes Flies 180 Mbp/ 3 autosomes, X and Y Zebrafish 1,700 Mbp/ 25 chromosomes Mice 2,600 Mbp/ 19 autosomes, X and Y Humans 3,900 Mbp/ 22 autosomes, X and Y

30. What you need to know: DNA is wrapped around histones Loops in 300 nm fiber bring regions that are largely spaced apart into close proximity (will be important for transcriptional regulation) Dimension of beads on a string = 11 nm; chromtin fiber = 30 nm) Histones: 5 histone proteins (H1, H2a, H2b, H3, H4) H1 is linker histone tightens DNA around histone core Histone octamer composed of 2a, 2b, 3, 4 TWO copies each Histone octamer plus DNA is a nucleosome. Histones are important for compaction of DNA but do also serve regulatory functions by means of modification Which histone modifications are associated with active/inactive chromatin (acetylation, methylation, phosphorylation. Metaphase chromosomes are usually phosphorylated-facilitates condensation) Euchromatin (active), Heterochromatin (more condensed, inactive) Chromosome nomenclature (p and q arms) Telomere function- protect chromosome ends from fusing Genome sizes of different organisms