1. Chromatin Structure & Genome Organization

2. Overview of Chromosome Structure Nucleosomes –~200 bp DNA in 120 Å diameter coil –3.4 Å /bp x 200 = 680 Å –680/120 = 5X compaction 30nm fiber –Coil of nucleosomes w/ 6/turn –1200bp/120 Å vs 4080 Å = 34X compaction Chromatin loops –30nm fiber is looped into 15- 100Kbp loops –7-8 loops form rosette w/ bases of loops attached to central core of scaffold proteins –300 Å /rosette, 800Kbp/rosette = 800kbp/300 Å vs 2720000 Å  9000X compaction

3. Nucleosomes Core of 8 proteins, 2 of each –H2A –H2B –H3 –H4 166 bp of DNA ~40bp between successive nucleosomes

4. Nucleosomes DNA associated with individual nucleosomes determined by DNAse I digestion

5. Nucleosome Each nucleosome contains 1 linker histone – H1 Linker histones can vary with cell types and differentiation states

6. Histone Post-translational Regulatory Modifications AcetylationPhosphorylation

7. The Histone Song (To the tune of "Flintstones") With Accompaniment With Accompaniment Histones! Meet the Histones! They're a basic protein family. There are Just four subtypes. They're conserved evolutionarily. Two each Of each histone Do their thing. Forming Just like beads upon a string. H1 Binds the complex. And it inhibits new transcription And the creation Of new mRNA.

8. Transcriptional Regulation by Histone Modification Histone acetyltransferase is component of transcriptional activation complexes

9. H1 Promotes Nucleosome Compaction H1 function thought to be regulated by phosphorylation on N and C terminal tails -H1 +H1

10. Heterochromatin vs Euchromatin Constitutive heterochromatin –Never transcribed DNA Facultative heterochromatin –DNA regions that can be switched between heterochromatin and euchromatin states –X inactivation Chromo domain proteins –Bind to DNA keeping in heterochromatin state Polycomb protein family in Drosophila

11. Heterochromatin vs Euchromatin Modifications to histones and DNA direct formation of heterochromatin Deacetylation of H4 Methylation of H3 Methylation of CpG islands

12. Loops & Chromosome Scaffolds Chromosome scaffold –Proteins at base of loops –Potentially regulate formation of loops and/or regulate global gene expression Components –DNA topoisomerase II –SMC proteins –HMGA DNA elements –S/MARS Sequences of DNA to which scaffold proteins bind –LCR DNA elements known to regulate expression of large regions of DNA containing multiple genes –Boundary elements scs elements flank puffs in Drosophila polytene chromosomes

13. Chromosome Loops

14. Chromosome Structure: The Metaphase Chromosome

15. Centromeres DNA sequence –Repetitive DNA elements –Constitutive heterochromatin Protein components –CENP-A, B & C

16. Centromeres Repetitive DNA of mammalian centromeres –  satellite DNA –171 bp unit –Several specific unit sequences –Multiple repeats of these units form arrays

17. Centromeres Centromere of S. cerevisiae –CEN DNA is 125bp element –3 regions - CDE I, II, & III –CDE's bound by special histone and other proteins and direct attachment of microtubule

18. Telomeres

19. Genome Organization Sequence composition –Unique sequences Genes –Low copy # elements rRNA, 5S, tRNA genes –High copy # repetitive DNA Retroelements –LINEs –SINEs Simple Sequence DNA –Minisatellites (VNTR) –Microsatelites

20. Retrotransposons, Retroelements & Transposons

21. Mouse Satellite DNA Repeating unit given by restriction enzyme digestion 4 Imperfect Repeating Units 23 – 9bp Repeats

22. VNTRs in DNA Fingerprinting