DNA double helix

1. Chromatin structure and cancer epigenetics DNA double helix Nucleosomes 30 nm fiber Chromosome Felsenfeld & Groudine, Nature (2003)

2. Chromatin structure and cancer epigenetics Two areas of opportunity in physical science Nucleosome Positioning • Molecular mechanics Epigenetic cell memory by nucleosome modification • Dynamical systems

3. The genomic code for nucleosome positioning Stretches of genomic DNA compete with each other for limiting numbers of nucleosomes DNA double helix Nucleosomes

4. Nucleosomes inhibit regulatory protein binding DNA is sterically occluded and highly distorted Side view (Space filling representation) Top view (Ribbon representation) Luger et al., Nature (1997)

5. GCN4; Ellenberger et al., Cell 71: 1223, 1992 NF-KB; Chen et al., Nature 391: 410, 1998 Many gene regulatory proteins wrap completely around their DNA target sites • Nucleosomes inhibit regulatory protein binding

6. AATTTA GC AATTTA GC AATTTA GC GC AATTTA AATTTA GC GC AATTTA AATTTA GC Deciphering the nucleosome positioning code • In vitro selection of nucleosome-favoring DNAs • Isolation of natural nucleosome DNAs

7. In vitro nucleosome occupancy compared to in vivo ~100 million mapped nucleosomes Chromosome 14: 187000-207000 2,000 bp Genes SLA2 ATG2 ZWF1 NAR1 LAP3 KEX2 YTP1 Model In vitro YPD in vivo EtOH in vivo Gal in vivo Moore, Fondufe-Mittendorf, Gossett, Kaplan, Lieb, Segal & JW

8. Nucleosome positioning and epigenetic gene silencing of the MLH1 1a tumor suppressor gene DNA unmethylated, gene active DNA methylated, gene inactive Lin, JC et al., Cancer Cell 2007

9. Nucleosome positioning and epigenetic gene silencing of the MLH1 1a tumor suppressor gene DNA unmethylated, Gene active DNA methylated, Gene inactive + 5-aza-2’-deoxycytidine DNA de-methylation precedes gene reactivation DNA unmethylated, Gene active Lin, JC et al., Cancer Cell 2007

10. AATTTA GC AATTTA GC AATTTA GC GC AATTTA AATTTA GC GC AATTTA AATTTA GC An elastic energy model for the sequence-dependent cost of DNA wrapping • Sequence specific, but without base-specific contacts • DNA is extremely sharply bent (~80 bp per turn) • Stable nucleosome formation  high cyclization probability Morozov, Fortney, Widom, & Siggia

11. AATTTA GC AATTTA GC AATTTA GC GC AATTTA AATTTA GC GC AATTTA AATTTA GC An elastic energy model for the sequence-dependent cost of DNA wrapping Morozov, Fortney, Widom, & Siggia

12. High resolution sequenced-based map of nucleosome positions in yeast Field et al. submitted

13. Favored and disfavored 5-mers in in vivo nucleosomes Field et al. submitted

14. The genomic code for nucleosome positioning DNA Nucleosomes 30 nm fiber Felsenfeld & Groudine, 2003

15. Chromatin structure and cancer epigenetics Two areas of opportunity in physical science Nucleosome Positioning • Molecular mechanics Epigenetic cell memory by nucleosome modification • Dynamical systems

16. Epigenetic cell memory by nucleosome modification Epigenetic states as attractors of dynamical systems Dodd, IB, et al., Cell 2007

17. Chromatin structure and cancer epigenetics DNA double helix Nucleosomes 30 nm fiber Chromosome Felsenfeld & Groudine, Nature (2003)