Title: A genomic code for nucleosome positioning DNA double heli
1A genomic code for nucleosome positioning
Felsenfeld Groudine, Nature (2003)
2Deciphering the nucleosome positioning code
- In vitro selection of nucleosome-favoring DNAs
- Isolation of natural nucleosome DNAs
3Physical selection for DNAs that attract
nucleosomes
Random sequence DNA synthesis (1 each of 5 x 1012
different DNA sequences)
Make many copies by PCR
Equilibrium selection of highest affinity 10
Extract DNA
Clone, sequence, analyze individuals
Lowary Widom, 1998
4Summary
- Differing DNA sequences exhibit a gt 5,000-fold
range of affinities for nucleosome formation
Lowary Widom, 1998 Thåström et al., 1999 Widom,
2001 Thåström et al., 2004
5DNA sequence motifs that stabilize nucleosomes
and facilitate spontaneous sharp looping
Thåström et al., 2004 Cloutier Widom 2004 Segal
et al., 2006
6Isolation of natural nucleosome DNAs
Digest unwrapped DNA
Extract protected DNA
Clone, sequence, analyze individuals
7The nucleosome signature in living yeast cells
- 10 bp periodicity of AA/TT/TA
- Same period for GC, out of phase with AA/TT/TA
- Same signals from the in vitro nucleosome
selection
- NO signal from randomly chosen genomic regions
Segal et al., 2006
8Two alignments of nucleosome DNAs
Wang Widom, 2005
9The nucleosome signature is common to yeast and
chickens
Chicken Yeast merge
Chicken (in vivo)
Yeast (in vivo)
Segal et al., 2006
10The nucleosome signature in vitro and in vivo
Segal et al., 2006
11Summary
Differing DNA sequences exhibit a gt 5,000-fold
range of affinities for nucleosome formation
We have a predictive understanding of the DNA
sequence motifs that are responsible
Sequences matching these motifs are abundant in
eukaryotic genomes, and are occupied by
nucleosomes in vivo
12Placing nucleosomes on the genome
A free energy landscape, not just scores and a
threshold !!
- Nucleosomes occupy 147 bp and exclude 157 bp
Segal et al., 2006
13Equilibrium configurations of nucleosomeson the
genome
- One of very many possible configurations
??P(S)
PB(S)
??P(S)
??P(S)
??P(S)
PB(S)
PB(S)
PB(S)
Chemical potential apparent concentration
Probability of placing a nucleosome starting at
each allowed basepair i of S
Probability of any nucleosome covering position i
(? average occupancy)
Locations i with high probability for starting a
nucleosome (? stable nucleosomes)
Segal et al., 2006
14Summary
Differing DNA sequences exhibit a gt 5,000-fold
range of affinities for nucleosome formation
We have a predictive understanding of the DNA
sequence motifs that are responsible
Sequences matching these motifs are abundant in
eukaryotic genomes, and are occupied by
nucleosomes in vivo
A model based only on these DNA sequence motifs
and nucleosome-nucleosome exclusion explains 50
of in vivo nucleosome positions
15Distinctive nucleosome occupancy adjacent to TATA
elements at yeast promoters
Segal et al., 2006
16Predicted nucleosome organization near 5 ends of
genes comparison to experiment
Segal et al., 2006 Fondufe-Mittendorf, Segal, JW
17Summary
Differing DNA sequences exhibit a gt 5,000-fold
range of affinities for nucleosome formation
We have a predictive understanding of the DNA
sequence motifs that are responsible
Sequences matching these motifs are abundant in
eukaryotic genomes, and are occupied by
nucleosomes in vivo
A model based only on these DNA sequence motifs
and nucleosome-nucleosome exclusion explains 50
of in vivo nucleosome positions
These intrinsically encoded nucleosome positions
are correlated with, and may facilitate,
essential aspects of chromosome structure and
function
18A genomic code for higher order chromatin
structure?
30 nm fiber
Felsenfeld Groudine, 2003
19Regular 3-d superstructures favor 10 bp
quantized linker DNA lengths
Widom, 1992
20Stable nucleosomes come in correlated groups
Segal et al., 2006
21Biochemical isolation of dinucleosomes
Clone sequence
Yao et al., 1990 Fondufe-Mittendorf, Wang,
Widom
22Linker lengths in purified dinucleosomes
- Biochemically isolate dinucleosomes
- Predict locations of the two nucleosomes
- Defines the linker DNA length and sequence
Duration HMM
Location mixture model
Frequency
Linker DNA length (bp)
Linker DNA length (bp)
Wang Widom
23A genomic code for nucleosome positioning
DNA
Nucleosomes
30 nm fiber
Felsenfeld Groudine, 2003
24Evolution of the nucleosome positioning code
Sandman Reeve, Curr. Op. Microbiol. 2006
25An elastic energy model for the
sequence-dependent cost of DNA wrapping
Morozov, Segal, Widom, Siggia
26DNA in nucleosomes is extremely sharply bent
Side view (Space filling representation)
Top view (Ribbon representation)
80 bp per superhelical turn
Luger et al., Nature (1997)
27An elastic energy model for the
sequence-dependent cost of DNA wrapping
Morozov, Segal, Widom, Siggia
28Elastic energy of dinucleotide step
- Knowledge-based harmonic potential
Olson et al., (1998)
29Basepair steps as fundamental units of DNA
mechanics
Zhurkin Olson
30Structural basis of sharp DNA bending in
nucleosomes
- Small distortions, and localized larger
distortions, along the full wrapped DNA length
Richmond Davey, 2003
31Correlated deformations for sharp DNA wrapping
Roll
Tilt
Shift
Slide
Twist
Richmond Davey, 2003
32Elastic energy model for nucleosomal DNA
E Eelastic Edeviation from superhelix
Ideal superhelix
Crystal structure
Morozov, Segal, Widom, Siggia
33DNA sequence motifs that stabilize nucleosomes
and facilitate spontaneous sharp looping
Thåström et al., 2004 Cloutier Widom 2004 Segal
et al., 2006
34Beyond dinucleotides
- Highly enriched tetranucleotides
plt108
Lowary Widom, 1998
35Acknowledgements
The genomic code for nucleosome positioning
Yvonne Fondufe-Mittendorf Irene Moore Lingyi
Chen Karissa Fortney Annchristine Thåström Peggy
Lowary Jiping Wang (Northwestern U.
Statistics) Eran Segal (Weizmann Inst.) Yair
Field (Weizmann Inst.) Eric Siggia (Rockefeller
U.) Alexandre Morozov (Rockefeller U.)