DNA double helix

Nucleosomes

ChromosomeFelsenfeld & 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 otherfor 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, 1998 GCN4; 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

AATTTA

AATTTA

AA

TTTA

AATTTA

AATTTA

AA TT TA

AA

TT

TA

GC

GC

GC

GC

GC

GC

GC

2,000 bpChromosome 14: 187000-207000

YPD in vivo

Gal in vivo

EtOH in vivo

Genes

In vitro

SLA2 ATG2 ZWF1 NAR1 LAP3 KEX2 YTP1

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 silencingof 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 silencingof the MLH1 1a tumor suppressor gene

Lin, JC et al.,Cancer Cell 2007

DNA unmethylated,Gene active

DNA methylated,Gene inactive

DNA de-methylationprecedes genereactivation

DNA unmethylated,Gene active

+ 5-aza-2’-deoxycytidine

AATTTA

AATTTA

AA

TTTA

AATTTA

AATTTA

AA TT TA

AA

TT

TA

GC

GC

GC

GC

GC

GC

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

An elastic energy model for the sequence-dependent cost of DNA wrapping

AATTTA

AATTTA

AA

TTTA

AATTTA

AATTTA

AA TT TA

AA

TT

TA

GC

GC

GC

GC

GC

GC

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

ChromosomeFelsenfeld & Groudine, Nature (2003)

Chromatin structure and cancer epigenetics

30 nm fiber