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

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

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

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

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

Deciphering the nucleosome positioning code In vitro selection of nucleosome-favoring DNAs Isolation of natural nucleosome DNAs AA TT TA GC

2,000 bp Chromosome 14: YPD in vivo Gal in vivo EtOH in vivo Genes In vitro SLA2ATG2ZWF1NAR1LAP3 KEX2YTP1 Model Moore, Fondufe-Mittendorf, Gossett, Kaplan, Lieb, Segal & JW In vitro nucleosome occupancy compared to in vivo ~100 million mapped nucleosomes

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

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

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

AA TT TA GC Morozov, Fortney, Widom, & Siggia

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

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

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

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

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

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