Towards Cracking the Code of Chromatin and Transcriptional Regulation

1
Towards Cracking the Code of Chromatin and
Transcriptional Regulation
CTAACCTGGCTACAGAATCATAAGTTGAATTCGACAGGTTATCAGCAACA
ACACAGTCATATCCATTCTCAATTAGCTCTACCACAGTGTGTGAACCAAT
GTATCCAGCACCACCTGTAACCAAAACAATTTTAGAAGTACTTTCACTTT
GTAACTGAGCTGTCATTTATATTGAATTTTCAAAAATTCTTACTTTTTTT
TTGGATGGACGCAAAGAAGTTTAATAATCACTAACCTGGCTACAGAATCA
TAAGTTGAATTCGACAGGTTATCAGCAACAACACAGTCATATCCATTCTC
AATTAGCTCTACCACAGTGTGTGAACCAATGTATCCAGCACCACCTGTAA
CCAAAACAATTTTAGAAGTACTTTCACTTTGTAACTGAGCTGTCATTTAT
ATTGAATTTTCAAAAATTCTTACTTTTTTTTTGGATGGACGCAAAGAAGT
TTAATAATCATATTACATGGCATTACCACCATATACATATCCATATCTAA
TCTTACTTATATGTTGTGGAAATGTAAAGAGCCCCATTATCTTAGCCTAA
AAAAACCTTCTCTTTGGAACTTTCAGTAATACGCTTAACTGCTCATTGCT
ATATTGAAGTACGGATTAGAAGCCGCCGAGCGGGCGACAGCCCTCCGACG
GAAGACTCTCCTCCGTGCGTCCTCGTCTTCACCGGTCGCGTTCCTGAAAC
GCAGATGTGCCTCGCGCCGCACTGCTCCGAACAATAAAGATTCTACAATA
CTAGCTTTTATGGTTATGAAGAGGAAAAATTGGCAGTAACCTGGCCCCAC
AAACCTTCAAATTAACGAATCAAATTAACAACCATAGGATGATAATGCGA
TTAGTTTTTTAGCCTTATTTCTGGGGTAATTAATCAGCGAAGCGATGATT
TTTGATCTATTAACAGATATATAAATGGAAAAGCTGCATAACCACTTTAA
CTAATACTTTCAACATTTTCAGTTTGTATTACTTCTTATTCAAATGTCAT
AAAAGTATCAACAAAAAATTGTTAATATACCTCTATACTTTAACGTCAAG
GAGAAAAAACTATAATGACTAAATCTCATTCAGAAGAAGTGATTGTACCT
GAGTTCAATTCTAGCGCAAAGGAATTACCAAGACCATTGGCCGAAAAGTG
CCCGAGCATAATTAAGAAATTTATAAGCGCTTATGATGCTAAACCATATC
TAATCTTACTTATATGTTGTGGAAATGTAAAGAGCCCCATTATCTTAGCC
TAAAAAAACCTTCTCTTTGGAACTTTCAGTAATACGCTTAACTGCTCATT
GCTATATTGAAGTACGGATTAGAAGCCGCCGAGCGGGCGACAGCCACCTG
TAACCAAAACAATTTTAGAAGTACTTTCACTTTGTAACTGAGCTGTCATT
TATATTGAATTTTCAAAAATTCTTACTTTTTTTTTGGATGGACGCAAAGA
AGTTTAATAATCATATTACATGGCATTACCACCATATACATATCCATATC
TAATCTACCTGTAACCAAAACAATTTTAGAAGTACTTTCACTTTGTAACT
GAGCTGTCATTTATATTGAATTTTCAAAAATTCTTACTTTTTTTTTGGAT
GGACGCAAAGAAGTTTAATAATCATATTACATGGCATTACCACCATATAC
ATATCCATATCTAATCTTACTTATATGTTGTGGAAATGTAAAGAGCCCCA
TTATCTTAGCCTAAAAAAACCTTCTCTTTGGAACTTTCAGTAATACGCTT
AACTGCTCATTGCTATATTGAAGTACGGATTAGAAGCCGCCGAGCGGGCG
ACAGCCACCTGTAACCAAAACAATTTTAGAAGTACTTTCACTTTGTAACT
GAGCTGTCATTTATATTGAATTTTCAAAAATTCTTACTTTTTTTTTGGAT
GGACGCAAAGAAGTTTAATAATCATATTACATGGCATTACCACCATATAC
ATATCCATATCTAATCTTACTTATATGTTGTGGAAATGTAAAGAGCCCCA
TTATCTTAGCCTAAAAAAACCTTCTCTTTGGAACTTTCAGTAATACGCTT
AACTGCTCATTGCTATATTGAAGTACGGATTAGAAGCCGCCGAGCGGGCG
ACAGCCCTCCGACGGAAGACTCTCCTCCGTGCGTCCTCGTCTTCACCGGT
CGCGTTCCTGAAACGCAGATGTGCCTCGCGCCGCACTGCTCCGAACAATA
AAGATTCTACAATACTAGCTTTTATGGTTATGAAGAGGAAAAATTGGCAG
TAACCTGGCCCCACAAACCTTCAAATTAACGAATCAAATTAACAACCATA
GGATGATAATGCGATTAGTTTTTTAGCCTTATTTCTGGGGTAATTAATCA
GCGAAGCGATGATTTTTGATCTATTAACAGATATATAAATGGAAAAGCTG
CATAACCACTTTAACTAATACTTTCAACATTTTCAGTTTGTATTACTTCT
TATTCAAATGTCATAAAAGTATCAACAAAAAATTGTTAATATACCTCTAT
ACTTTAACGTCAAGGAGAAAAAACTATAATGACTAAATCTCATTCAGAAG
AAGTGATTGTACCTGAGTTCAATTCTAGCGCAAAGGAATTACCAAGACCA
TTGGCCGAAAAGTGCCCGAGCATAATTAAGAAATTTATAAGCGCTTATGA
TGCTAAACCGGATTTTGTTGCTAGATCGCCTGGTAGAGTCAATAAAAAAT
TGTTAATATACCTCTATACTTTAACGTCAAGGAGAAAAAACTATAATGAC
TAAATCTCATTCAGAAGAAGTGATTGTACCTGAGTTCAATTCTAGCGCAA
AGGAATTACCAAGACCATTGGCCGAAAAGTGCCCGAGCATAATTAAGAAA
TTTATAAGCGCTTATGATGCTAAACCGGATTTTGTTGCTAGATCGCCTGG
TAGAGTCAATCTAACCTGGCTACAGAATCATAAGTTGAATTCGACAGGTT
ATCAGCAACAACACAGTCATATCCATTCTCAATTAGCTCTACCACAGTGT
GTGAACCAATGTATCCAGCACCACCTGTAACCAAAACAATTTTAGAAGTA
CTTTCACTTTGTAACTGAGCTGTCATTTATATTGAATTTTCAAAAATTCT
TACTTTTTTTTTGACCGGATTTTGTTGCTAGATCGCCTGGTAGAGTCAAT
CTAACCTGGCTACAGAATCATAAGTTGAATTCGACAGGTTATCAGCAACA
ACACAGTCATATCCATTCTCAATTAGCTCTACCACAGTGTGTGAACCAAT
GTATCCAGCACCATATCTAATCTTACTTATATGTTGTGGAAATGTAAAGA
GCCCCATTATCTTAGCCTAAAAAAACCTTCTCTTTGGAACTTTCAGTAAT
ACGCTTAACTGCTCATTGCTATATTGAAGTACGGATTAGAAGCCGCCGAG
CGGGCGACAGCCACCTGTAACCAAAACAATTTTAGAAGTACTTTCACTTT
GTAACTGAGCTGTCATTTATATTGAATTTTCAAAAATTCTTACTTTTTTT
TTGGATGGACGCAAAGAAGTTTAATAATCATATTACATGGCATTACCACC
ATATACATATCCATATCTAATCTACCTGTAACCAAAACAATTTTAGAAGT
ACTTTCACTTTGTAACTGAGCTGTCATTTATATTGAATTTTCAAAAATTC
TTACTTTTTTTTTGGATGGACGCAAAGAAGTTTAATAATCATATTACATG
GCATTACCACCATATACATATCCATATCTAATCTTACTTATATGTTGTGG
AAATGTAAAGAGCCCCATTATCTTAGCCTAAAAAAACCTTCTCTTTGGAA
CTTTCAGTAATACGCTTAACTGCTCATTGCTATATTGAAGTACGGATTAG
AAGCCGCCGAGCGGGCGACAGCCACCTGTAACCAAAACAATTTTAGAAGT
ACTTTCACTTTGTAACTGAGCTGTCATTTATATTGAATTTTCAAAAATTC
TTACTTTTTTTTTGGATGGACGCAAAGAAGTTTAATAATCATATTACATG
GCATTACCACCATATACATATCCATATCTAATCTTACTTATATGTTGTGG
AAATGTAAAGAGCCCCATTATCTTAGCCTAAAAAAACCTTCTCTTTGGAA
CTTTCAGTAATACGCTTAACTGCTCATTGCTATATTGAAGTACGGATTAG
AAGCCGCCGAGCGGGCGACAGCCCTCCGACGGAAGACTCTCCTCCGTGCG
TCCTCGTCTTCACCGGTCGCGTTCCTGAAACGCAGATGTGCCTCGCGCCG
CACTGCTCCGAACAATAAAGATTCTACAATACTAGCTTTTATGGTTATGA
AGAGGAAAAATTGGCAGTAACCTGGCCCCACAAACCTTCAAATTAACGAA
TCAAATTAACAACCATAGGATGATAATGCGATTAGTTTTTTAGCCTTATT
TCTGGGGTAATTAATCAGCGAAGCGATGATTTTTGATCTATTAACAGATA
TATAAATGGAAAAGCTGCATAACCACTTTAACTAATACTTTCAACATTTT
CAGTTTGTATTACTTCTTATTCAAATGTCATAAAAGTATCAACAAAAAAT
TGTTAATATACCTCTATACTTTAACGTCAAGGAGAAAAAACTATAATGAC
TAAATCTCATTCAGAAGAAGTGATTGTACCTGAGTTCAATTCTAGCGCAA
AGGAATTACCAAGACCATTGGCCGAAAAGTGCCCGAGCATAATTAAGAAA
TTTATAAGCGCTTATGATGCTAAACCGGATTTTGTTGCTAGATCGCCTGG
TAGAGTCAATAAAAAATTGTTAATATACCTCTATACTTTAACGTCAAGGA
GAAAAAACTATAATGACTAAATCTCATTCAGAAGAAGTGATTGTACCTGA
GTTCAATTCTAGCGCAAAGGAATTACCAAGACCATTGGCCGAAAAGTGCC
CGAGCATAATTAAGAAATTTATAAGCGCTTATGATGCTAAACCGGATTTT
GTTGCTAGATCGCCTGGTAGAGTCAATCTAACCTGGCTACAGAATCATAA
GTTGAATTCGACAGGTTATCAGCAACAACACAGTCATATCCATTCTCAAT
TAGCTCTACCACAGTGTGTGAACCAATGTATCCAGCACCACCTGTAACCA
AAACAATTTTAGAAGTACTTTCACTTTGTAACTGAGCTGTCATTTATATT
GAATTTTCAAAAATTCTTACTTTTTTTTTGGATGGACGCAAAGAAGTTTA
ATAATCATATTACATGGCATTACCACCATATATATTACATGGCATTACCA
CCATATACATATCCATATCTAATCTTACTTATATGTTGTGGAAATGTAAA
GAGCCCCATTATCTTAGCCTAAAAAAACCTTCTCTTTGGAACTTTCAGTA
ATACGCTTAACTGCTCATTGCTATATTGAAGTACGGATTAGAAGCCGCCG
AGCGGGCGACAGCCCTCCGACGGAAGACTCTCCTCCGTGCGTCCTCGTCT
TCACCGGTCGCGTTCCTGAAACGCAGATGTGCCTCGCGCCGCACTGCTCC
GAACAATAAAGATTCTACAATACTAGCTTTTATGGTTATGAAGAGGAAAA
ATTGGCAGTAACCTGGCCCCACAAACCTTCAAATTAACGAATCAAATTAA
CAACCATAGGATGATAATGCGATTAGTTTTTTAGCCTTATTTCTGGGGTA
ATTAATCAGCGAAGCGATGATTTTTGATCTATTAACAGATATATAAATGG
AAAAGCTGCATAACCACTTTAACTAATACTTTCAACATTTTCAGTTTGTA
TTACTTCTTATTCAAATGTCATAAAAGTATCAACAAAAAATTGTTAATAT
ACCTCTATACTTTAACGTCAAGGAGAAAAAACTATAATGACTAAATCTCA
TTCAGAAGAAGTGATTGTACCTGAGTTCAATTCTAGCGCAAAGGAATTAC
CAAGACCATTGGCCGAAAAGTGCCCGAGCATAATTAAGAAATTTATAAGC
GCTTATGATGCTAAACCGGATTTTGTTGCTAGATCGCCTGGTAGAGTCAA
TCTAACCTGGCTACAGAATCATAAGTTGAATTCGACAGGTTATCAGCAAC
AACACAGTCATATCCATTCTCAATTAGCTCTACCACAGTGTGTGAACCAA
TGTATCCAGCACCACCTGTAACCAAAACAATTTTAGAAGTACTTTCACTT
TGTAACTGAGCTGTCATTTATATTGAATTTTCAAAAATTCTTACTTTTTT
TTTGGATGGACGCAAAGAAGTTTAATAATCATATTACATGGCATTACCAC
CATATACATATCCATATCTAATCTTACTTATATGTTGTGGAAATGTAAAG
AGCCCCATTATCTTAGCCTAAAAAAACCTTCTCTTTGGAACTTTCAGTAA
TACGCTTAACTGCTCATTGCTATATTGAAGTACGGATTAGAAGCCGCCGA
GCGGGCGACAGCCCTCCGACGGAAGACTCTCCTCCGTGCGTCCTCGTCTT
CACCGGTCGCGTTCCTGAAACGCAGATGTGCCTCGCGCCGCACTGCTCCG
AACAATAAAGATTCTACAATACTAGCTTTTATGGTTATGAAGAGGAAAAA
TTGGCAGTAACCTGGCCCCACAAACCTTCAAATTAACGAATCAAATTAAC
AACCATAGGATGATAATGCGATTAGTTTTTTAGCCTTATTTCTGGGGTAA
TTAATCAGCGAAGCGATGATTTTTGATCTATTAACAGATATATAAATGGA
AAAGCTGCATAACCACTTTAACTAATACTTTCAACATTTTCAGTTTGTAT
TACTTCTTATTCAAATGTCATAAAAGTATCAACAAAAAATTGTTAATATA
CCTCTATACTTTAACGTCAAGGAGAAAAAACTATAATGACTAAATCTCAT
TCAGAAGAAGTGATTGTACCTGAGTTCAATTCTAGCGCAAAGGAATTACC
AAGACCATTGGCCGAAAAGTGCCCGAGCATAATTAAGAAATTTATAAGCG
CTTATGATGCTAAACCGGATTTTGTTGCTAGATCGCCTGGTAGAGTCAAT
AAAAAATTGTTAATATACCTCTATACTTTAACGTCAAGGAGAAAAAACTA
TAATGACTAAATCTCATTCAGAAGAAGTGATTGTACCTGAGTTCAATTCT
AGCGCAAAGGAATTACCAAGACCATTGGCCGAAAAGTGCCCGAGCATAAT
TAAGAAATTTATAAGCGCTTATGATGCTAAACCGGATTTTGTTGCTAGAT
CGCCTGGTAGAGTCAATCTAACCTGGCTACAGAATCATAAGTTGAATTCG
ACAGGTTATCAGCAACAACACAGTCATATCCATTCTCAATTAGCTCTACC
ACAGTGTGTGAACCAATGTATCCAGCACCACCTGTAACCAAAACAATTTT
AGAAGTACTTTCACTTTGTAACTGAGCTGTCATTTATATTGAATTTTCAA
AAATTCTTACTTTTTTTTTGGATGGACGCAAAGAAGTTTAATAATCATAT
TACATGGCATTACCACCATATAGAGTTCAATTCTAGCGCAAAGGAATTAC
CAAGACCATTGGCCGAAAAGTGCCCGAGCATAATTAAGAAATTTATAAGC
GCTTATGATGCTAAACCGGATTTTGTTGCTAGATCGCCTGGTAGAGTCAA
TCTAACCTGGCTACAGAATCATAAGTTGAATTCGACAGGTTATCAGCAAC
AACACAGTCATATCCATTCTCAATTAGCTCTACCACAGTGTGTGAACCAA
TGTATCCAGCACCACCTGTAACCAAAACAATTTTAGAAGTACTTTCACTT
TGTAACTGAGCTGTCATTTATATTGAATTTTCAAAAATTCTTACTTTTTT
TTTGGATGGACGCAAAGAAGTTTAATAATCATATTACATGGCATTACCAC
CATATACATATCCATATCTAATCTTACTTATATGTTGTGGAAATGTAAAG
AGCCCCATTATCTTAGCCTAAAAAAACCTTCTCTTTGGAACTTTCAGTAA
TACGCTTAACTGCTCATTGCTATATTGAAGTACGGATTAGAAGCCGCCGA
GCGGGCGTATGGTTATGAAGAGGAAAAATTGGCAGTAACCTGGCCCCACA
AACCTTCAAATTAACGAATCAAATTAACAACCATAGGATGATAATGCGAT
TAGTTTTTTAGCCTTATTTCTGGGGTAATTAATCAGCGAAGCGATGATTT
TTGATCTATTAACAGATATATAAATGGAAAAGCTGCATAACCACTTTAAC
TAATACTTTCAACATTTTCAGTTTGTATTACTTCTTATTCAAATGTCATA
AAAGTATCAACAAAAAATTGTTAATATACCTCTATACTTTAACGTCAAGG
AGAAAAAACTATAATGACTAAATCTCATTCAGAAGAAGTGATTGTACCTG
AGTTCAATTCTAGCGCAAAGGAATTACCAAGACCATTGGCCGAAAAGTGC
CCGAGCATAATTAAGAAATTTATAAGCGCTTATGATGCTAAACCGGATTT
TGTTGCTAGATCGCCTGGTAGAGTCAATAAAAAATTGTTAATATACCTCT
ATACTTTAACGTCAAGGAGAAAAAACTATAATGACTAAATCTCATTCAGA
AGAAGTGATTGTACCTGAGTTCAATTCTAGCGCAAAGGAATTACCAAGAC
CATTGGCCGAAAAGTGCCCGAGCATAATTAAGAAATTTATAAGCGCTTAT
GATGCTAAACCGGATTTTGTTGCTAGATCGCCTGGTAGAGTCAATCTAAC
CTGGCTACAGAATCATAAGTTGAATTCGACAGGTTATCAGCAACAACACA
GTCATATCCATTCTCAATTAGCTCTACCACAGTGTGTGAACCAATGTATC
CAGCACCACCTGTAACCAAAACAATTTTAGAAGTACTTTCACTTTGTAAC
TGAGCTGTCATTTATATTGAATTTTCAAAAATTCTTACTTTTTTTTTGGA
TGGACGCAAAGAAGTTTAATAATCATATTACATGGCATTACCACCATATA
GAGTTCAATTCTAGCGCAAAGGAATTACCAAGACCATTGGCCGAAAAGTG
CCCGAGCATAATTAAGAAATTTATAAGCGCTTATGATGCTAAACCGGATT
TTGTTGCTAGATCGCCTGGTAGAGTCAATCTAACCTGGCTACAGAATCAT
AAGTTGAATTCGACAGGTTATCAGCAACAACACAGTCATATCCATTCTCA
ATTAGCTCTACCACAGTGTGTGAACCAATGTATCCAGCACCACCTGTAAC
CAAAACAATTTTAGAAGTACTTTCACTTTGTAACTGAGCTGTCATTTATA
TTGAATTTTCAAAAATTCTTACTTTTTTTTTGGATGGACGCAAAGAAGTT
TAATAATCATATTACATGGCATTACCACCATATACATATCCATATCTAAT
CTTACTTATATGTTGTGGAAATGTAAAGAGCCCCATTATCTTAGCCTAAA
AAAACCTTCTCTTTGGAACTTTCAGTAATACGCTTAACTGCTCATTGCTA
TATTGAAGTACGGATTAGAAGCCGCCGAGCGGGCGACAGCCCTCCGACGG
AAGACTCTCCTCCGTGCGTCCTCGTCTTCACCGGTCGCGTTCCTGAAACG
CAGATGTGCCTCGCGCCGCACTGCTCCGAACAAACGTTTGAGCGTCAGTG
GGAGCGTAAACT

• Eran Segal
• Weizmann Institute of Science

2
What Controls Nucleosome organizations in vivo?
3
An in vitro nucleosome map guided solely by
sequence preferences of nucleosomes
Purified histones
Purified genomic DNA
CTAACCTGGCTACAGAATCATAAGTTGAATTCGACAGGTTATCAGCAACA
ACACAGTCATATCCATTCTCAATTAGCTCTACCACAGTGTGTGAACCAAT
GTATCCAGCACCACCTGTAACCAAAACAATTTTAGAAGTACTTTCACTTT
GTAACTGAGCTGTCATTTATATTGAATTTTCAAAAATTCTTACTTTTTTT
TTGGATGGACGCAAAGAAGTTTAATAATCACTAACCTGGCTACAGAATCA
TAAGTTGAATTCGACAGGTTATCAGCAACAACACAGTCATATCCATTCTC
AATTAGCTCTACCACAGTGTGTGAACCAATGTATCCAGCACCACCTGTAA
CCAAAACAATTTTAGAAGTACTTTCACTTTGTAACTGAGCTGTCATTTAT
ATTGAATTTTCAAAAATTCTTACTTTTTTTTTGGATGGACGCAAAGAAGT
TTAATAATCATATTACATGG
H3
H4
H2A
H2B
4
Nucleosome sequence preferences are major
determinants of nucleosome organizations in vivo
2000 bp
SLA2
ATG2
ZWF1
NAR1
LAP3
KEX2
YTP1
In vitro
In vivo (YPD)
5
In vitro in vivo similarity is not due to MNAse
or to artifacts in parallel sequencing
Purified histones
40,000 ds-oligos of length 150bp
H3
H4
H2A
H2B
Assemble purified histones on double-stranded
oligos
Extract ds-oligos in reconstituted nucleosomes
6
Dissecting the relative contribution of factors
to nucleosome organizations in vivo

• Dictate much of the in vivo nucleosome
  organization

Can we build a predictive understanding (model)
of the nucleosome sequence preferences?
7
Nucleosomes exhibit position-specific
periodicities certain dinucleotides along the
nucleosome length
Center align all nucleosome reads from each map
8
Many sequences are generally favored or
disfavored for incorporation into nucleosomes
Histogram of average nucleosome occupancy of
every 5-mer in vitro
Depleted 5-mers
9
A Model of Nucleosome Sequence Preferences
Global nucleosome preferences
Position-specific nucleosome preferences
Depleted 5-mers
AAAAATTTTT
Nucleosome-DNA interaction model
AATTTA
GC
AATTTA
GC
AAAAAAA
TTAAAAA
AATTTA
GC
GC
AATTTA
AATTTA
GC
GC
AATTTA
AATTTA
GC
10
Predicting nucleosome organizations from a model
of nucleosome sequence preferences


AATTTA
GC
AATTTA
GC
AAAAAAA
TTAAAAA
AATTTA
GC
GC
AATTTA
AATTTA
GC
GC
AATTTA
AATTTA
GC


Statistical weight
?P(S1)
NucleosomeConcentration
NucleosomeBinding energy
11
Predicting nucleosome organizations from a model
of nucleosome sequence preferences


AATTTA
GC
AATTTA
GC
AAAAAAA
TTAAAAA
AATTTA
GC
GC
AATTTA
AATTTA
GC
GC
AATTTA
AATTTA
GC
Configuration Probability


P 0.08


P 0.01


P 0.19


P 0
12
Model predicts nucleosome organizationsin vitro
and in vivo with high accuracy
2000 bp
SLA2
ATG2
ZWF1
NAR1
LAP3
KEX2
YTP1
In vitro
In vivo (YPD)
Model(cross validation)
13
Model is significantly correlated with nucleosome
occupancy in C. elegans
In vitro in vivo comparison of 5-mer nucleosome
occupancy
R0.73
14
Dissecting the relative contribution of factors
to nucleosome organizations in vivo

• Dictate much of the in vivo nucleosome
  organization
• We have a predictive of the sequence
  preferences

What is the relative contribution of each factor
to observed patterns of in vivo nucleosome
organization?
15
Nucleosome depletion around factor sites is
partly encoded by the intrinsic nucleosome
organization
Observation 1 nucleosome depletion at TF
sites(Yuan et al. 05, Albert et al. 07, Lee et
al. 07)
16
Dissecting the relative contribution of factors
to nucleosome organizations in vivo

• Compete out nucleosomes from sites (Reb1, Abf1)

• Dictate much of the in vivo nucleosome
  organization
• We have a predictive of the sequence
  preferences
• Partly explain nucleosome depletion at factor
  sites

17
Nucleosome depletion at gene starts and ends is
partly encoded by nucleosome positioning signals
Observation 2 nucleosome depletion at gene
starts ends(Yuan et al. 05, Albert et al.
07, Lee et al. 07, Shivaswamy et al. 08)
In vivo (YPD)
In vivo (YPD)
Avg. nucleosome occupancy
0
0
-500
500
-500
500
Distance from translation end (bp)
Distance from transcription start (bp)
18
Dissecting the relative contribution of factors
to nucleosome organizations in vivo

• Compete out nucleosomes from sites (Reb1,
  Abf1)
• Compete out nucleosomes from gene start sites

• Dictate much of the in vivo nucleosome
  organization
• We have a predictive of the sequence
  preferences
• Partly explain nucleosome depletion at factor
  sites
• Partly explain depletion at gene start sites
• Largely explains depletion at gene end sites

• May cause nucleosome shift around gene starts

19
Nucleosome phasing around gene start sites is
partly encoded by nucleosome positioning signals
Observation 3 nucleosome phasing around gene
start sites(Yuan et al. 05, Lee et al. 07,
Mavrich et al. 08)
Nucleosome occupancy relative to transcription
start sites
In vivo (YPD)
In vitro
20
Dissecting the relative contribution of factors
to nucleosome organizations in vivo

• Compete out nucleosomes from sites (Reb1,
  Abf1)
• Compete out nucleosomes from gene start sites

• Dictate much of the in vivo nucleosome
  organization
• We have a predictive of the sequence
  preferences
• Partly explain nucleosome depletion at factor
  sites
• Partly explain depletion at gene start sites
• Largely explains depletion at gene end sites
• Partly explain nucleosome phasing at gene
  starts

• May cause nucleosome shift around gene starts

21
Active transcription influences thein vivo
nucleosome organization
In vitro in vivo correlation over gene coding
regions as a function of gene expression level
0.85
0.8
0.75
0.7
0.65
0.6
Higher expression
22
Dissecting the relative contribution of factors
to nucleosome organizations in vivo

• Compete out nucleosomes from sites (Reb1,
  Abf1)
• Compete out nucleosomes from gene start sites

• Dictate much of the in vivo nucleosome
  organization
• We have a predictive of the sequence
  preferences
• Partly explain nucleosome depletion at factor
  sites
• Partly explain depletion at gene start sites
• Largely explains depletion at gene end sites
• Partly explain nucleosome phasing at gene
  starts

• May cause nucleosome shift around gene starts

• May alter the nucleosome organization at gene
  coding regions

23
What are the functional consequences of the
DNA-encoded nucleosome organization?
24
DNA-encoded nucleosome organization may help in
differential activation of targets for the same
factor
Observation 1 targets for the same factor may
be activated with different kinetics
Induction kinetics of Pho4 targets(Lam et al.
08)

• Hypothesis behavior may be achieved by
• DNA-encoded nucleosome organization, if
• Intrinsic organization encodes different
  nucleosome occupancy at different TF sites
• TF sites with different nucleosome occupancy
  differ in their activation kinetics

25
Intrinsic organization encodes different
nucleosome occupancy at different TF sites
Nucleosome occupancy relative to a nucleosome
boundary
Factor sites near boundaries may be relatively
depleted of nucleosomes
26
Intrinsic organization encodes different
nucleosome occupancy at different TF sites
27
Intrinsic organization encodes different
nucleosome occupancy at different TF sites
CST6 ABF1 YAP7 MAC1 HSF1 RTG3 FHL1 ACE2 SPT23 RAP1
MET31 MBP1 ARR1 PHO2 SFP1 GCR2 SWI5 REB1 SWI6 FKH
2 RLM1 GCN4 STB1 FKH1 AZF1 HAP1 TEC1 NRG1 GLN3 SWI
4 SPT2 MOT3 CIN5 STP1 PHD1 CBF1 NDD1 YAP6 HAP2 MSN
4 SUT1 YAP5 MSN2 DIG1 ROX1 STE12 SKN7 SUM1 AFT2 SO
K2 DAL82
1
For every factor there is greater depletion over
the subset of its sites that are near boundaries
2
Nucleosome depletion

• Hypothesis behavior may be achieved by
• DNA-encoded nucleosome organization, if
• Intrinsic organization encodes different
  nucleosome occupancy at different TF sites
• TF sites with different nucleosome occupancy
  differ in their activation kinetics

28
Factor sites with different nucleosome occupancy
differ in their activation kinetics

• Hypothesis behavior may be achieved by
• DNA-encoded nucleosome organization, if
• Intrinsic organization encodes different
  nucleosome occupancy at different TF sites
• TF sites with different nucleosome occupancy
  differ in their activation kinetics

29
Functional consequences of the DNA-encoded
nucleosome organization
DNA-encoded organization may allow factors to
regulate targets with different kinetics
TF
TF
AAAAA
CCAAT
CCAAT
2
1
1
2
30
DNA-encoded nucleosome organizationmay affect
transcriptional noise
Observation 2 cell-to-cell expression
variability (noise) varies between genes(Raser
et al. 05, Newman et al. 06, Bar-even et al.
06)
31
DNA-encoded nucleosome organization ishighly
predictive of transcriptional noise
Type II
Type I

• No boundaries
• TATA

• No boundaries
• No TATA

• Boundaries
• TATA

• Boundaries
• No TATA

TATA
TATA
AAAAA
AAAAA
32
Functional consequences of the DNA-encoded
nucleosome organization
DNA-encoded organization may allow factors to
regulate targets with different kinetics
DNA-encoded organizationmay affect
transcriptional noise
TF
TF
AAAAA
CCAAT
CCAAT
2
1
1
2
33
DNA-encoded organization may explain target
specificity of chromatin remodelers
Observation 3 chromatin remodelers target
specific genes(Robert et al., 04, Whitehouse et
al., 06)
34
Functional consequences of the DNA-encoded
nucleosome organization
DNA-encoded organization may allow factors to
regulate targets with different kinetics
DNA-encoded organizationmay affect
transcriptional noise
TF
TF
AAAAA
CCAAT
CCAAT
2
1
1
2
DNA-encoded organization may explain target
specificity of chromatin remodelers
TATA
AAAAA
35
DNA-encoded nucleosome organization mayaffect
replication initiation efficiency
Observation 4 replication origins vary in their
initiation efficiency (Heichinger et al., 06)
36
Functional consequences of the DNA-encoded
nucleosome organization
DNA-encoded organization may allow factors to
regulate targets with different kinetics
DNA-encoded organizationmay affect
transcriptional noise
TF
TF
AAAAA
CCAAT
CCAAT
2
1
1
2
DNA-encoded organization may explain target
specificity of chromatin remodelers
DNA-encoded organization may affect replication
initiation efficiency
TATA
AAAAA
Efficient origins
Type II
Type I
37
Expression divergence may be partly achieved by
evolution of DNA-encoded organizations
Observation 5 some genes exhibit divergence in
their expression programs during evolution
(Ihmels et al., 05)
Hypothesis Such divergence may be partly
achieved by evolution of DNA-encoded nucleosome
organization
38
Summary
Dissecting the relative contribution of factors
to nucleosome organizations in vivo
Pol II
Nucleosome preferences
Transcription factor binding
Chromatin remodelers
Active transcription

• Compete out nucleosomes from sites (Reb1,
  Abf1)
• Compete out nucleosomes from gene start sites

• Dictate in vivo nucleosome organization
• We have a predictive of the sequence
  preferences
• Partly explain nucleosome phasing at gene
  starts, depletion at factor sites, gene
  start and end sites

• May alter the nucleosome organization at gene
  coding regions

• May cause nucleosome shift around gene starts

39
Have we Cracked the Code?
CTAACCTGGCTACAGAATCATAAGTTGAATTCGACAGGTTATCAGCAACA
ACACAGTCATATCCATTCTCAATTAGCTCTACCACAGTGTGTGAACCAAT
GTATCCAGCACCACCTGTAACCAAAACAATTTTAGAAGTACTTTCACTTT
GTAACTGAGCTGTCATTTATATTGAATTTTCAAAAATTCTTACTTTTTTT
TTGGATGGACGCAAAGAAGTTTAATAATCACTAACCTGGCTACAGAATCA
TAAGTTGAATTCGACAGGTTATCAGCAACAACACAGTCATATCCATTCTC
AATTAGCTCTACCACAGTGTGTGAACCAATGTATCCAGCACCACCTGTAA
CCAAAACAATTTTAGAAGTACTTTCACTTTGTAACTGAGCTGTCATTTAT
ATTGAATTTTCAAAAATTCTTACTTTTTTTTTGGATGGACGCAAAGAAGT
TTAATAATCATATTACATGGCATTACCACCATATACATATCCATATCTAA
TCTTACTTATATGTTGTGGAAATGTAAAGAGCCCCATTATCTTAGCCTAA
AAAAACCTTCTCTTTGGAACTTTCAGTAATACGCTTAACTGCTCATTGCT
ATATTGAAGTACGGATTAGAAGCCGCCGAGCGGGCGACAGCCCTCCGACG
GAAGACTCTCCTCCGTGCGTCCTCGTCTTCACCGGTCGCGTTCCTGAAAC
GCAGATGTGCCTCGCGCCGCACTGCTCCGAACAATAAAGATTCTACAATA
CTAGCTTTTATGGTTATGAAGAGGAAAAATTGGCAGTAACCTGGCCCCAC
AAACCTTCAAATTAACGAATCAAATTAACAACCATAGGATGATAATGCGA
TTAGTTTTTTAGCCTTATTTCTGGGGTAATTAATCAGCGAAGCGATGATT
TTTGATCTATTAACAGATATATAAATGGAAAAGCTGCATAACCACTTTAA
CTAATACTTTCAACATTTTCAGTTTGTATTACTTCTTATTCAAATGTCAT
AAAAGTATCAACAAAAAATTGTTAATATACCTCTATACTTTAACGTCAAG
GAGAAAAAACTATAATGACTAAATCTCATTCAGAAGAAGTGATTGTACCT
GAGTTCAATTCTAGCGCAAAGGAATTACCAAGACCATTGGCCGAAAAGTG
CCCGAGCATAATTAAGAAATTTATAAGCGCTTATGATGCTAAACCGGATT
TTGTTGCTAGATCGCCTGGTAGAGTCAATCTAACCTGGCTACAGAATCAT
AAGTTGAATTCGACAGGTTATCAGCAACAACACAGTCATATCCATTCTCA
ATTAGCTCTACCACAGTGTGTGAACCAATGTATCCAGCACCATATCTAAT
CTTACTTATATGTTGTGGAAATGTAAAGAGCCCCATTATCTTAGCCTAAA
AAAACCTTCTCTTTGGAACTTTCAGTAATACGCTTAACTGCTCATTGCTA
TATTGAAGTACGGATTAGAAGCCGCCGAGCGGGCGACAGCCACCTGTAAC
CAAAACAATTTTAGAAGTACTTTCACTTTGTAACTGAGCTGTCATTTATA
TTGAATTTTCAAAAATTCTTACTTTTTTTTTGGATGGACGCAAAGAAGTT
TAATAATCATATTACATGGCATTACCACCATATACATATCCATATCTAAT
CTACCTGTAACCAAAACAATTTTAGAAGTACTTTCACTTTGTAACTGAGC
TGTCATTTATATTGAATTTTCAAAAATTCTTACTTTTTTTTTGGATGGAC
GCAAAGAAGTTTAATAATCATATTACATGGCATTACCACCATATACATAT
CCATATCTAATCTTACTTATATGTTGTGGAAATGTAAAGAGCCCCATTAT
CTTAGCCTAAAAAAACCTTCTCTTTGGAACTTTCAGTAATACGCTTAACT
GCTCATTGCTATATTGAAGTACGGATTAGAAGCCGCCGAGCGGGCGACAG
CCACCTGTAACCAAAACAATTTTAGAAGTACTTTCACTTTGTAACTGAGC
TGTCATTTATATTGAATTTTCAAAAATTCTTACTTTTTTTTTGGATGGAC
GCAAAGAAGTTTAATAATCATATTACATGGCATTACCACCATATACATAT
CCATATCTAATCTTACTTATATGTTGTGGAAATGTAAAGAGCCCCATTAT
CTTAGCCTAAAAAAACCTTCTCTTTGGAACTTTCAGTAATACGCTTAACT
GCTCATTGCTATATTGAAGTACGGATTAGAAGCCGCCGAGCGGGCGACAG
CCCTCCGACGGAAGACTCTCCTCCGTGCGTCCTCGTCTTCACCGGTCGCG
TTCCTGAAACGCAGATGTGCCTCGCGCCGCACTGCTCCGAACAATAAAGA
TTCTACAATACTAGCTTTTATGGTTATGAAGAGGAAAAATTGGCAGTAAC
CTGGCCCCACAAACCTTCAAATTAACGAATCAAATTAACAACCATAGGAT
GATAATGCGATTAGTTTTTTAGCCTTATTTCTGGGGTAATTAATCAGCGA
AGCGATGATTTTTGATCTATTAACAGATATATAAATGGAAAAGCTGCATA
ACCACTTTAACTAATACTTTCAACATTTTCAGTTTGTATTACTTCTTATT
CAAATGTCATAAAAGTATCAACAAAAAATTGTTAATATACCTCTATACTT
TAACGTCAAGGAGAAAAAACTATAATGACTAAATCTCATTCAGAAGAAGT
GATTGTACCTGAGTTCAATTCTAGCGCAAAGGAATTACCAAGACCATTGG
CCGAAAAGTGCCCGAGCATAATTAAGAAATTTATAAGCGCTTATGATGCT
AAACCGGATTTTGTTGCTAGATCGCCTGGTAGAGTCAATAAAAAATTGTT
AATATACCTCTATACTTTAACGTCAAGGAGAAAAAACTATAATGACTAAA
TCTCATTCAGAAGAAGTGATTGTACCTGAGTTCAATTCTAGCGCAAAGGA
ATTACCAAGACCATTGGCCGAAAAGTGCCCGAGCATAATTAAGAAATTTA
TAAGCGCTTATGATGCTAAACCGGATTTTGTTGCTAGATCGCCTGGTAGA
GTCAATCTAACCTGGCTACAGAATCATAAGTTGAATTCGACAGGTTATCA
GCAACAACACAGTCATATCCATTCTCAATTAGCTCTACCACAGTGTGTGA
ACCAATGTATCCAGCACCACCTGTAACCAAAACAATTTTAGAAGTACTTT
CACTTTGTAACTGAGCTGTCATTTATATTGAATTTTCAAAAATTCTTACT
TTTTTTTTGGATGGACGCAAAGAAGTTTAATAATCATATTACATGGCATT
ACCACCATATATATTACATGGCATTACCACCATATACATATCCATATCTA
ATCTTACTTATATGTTGTGGAAATGTAAAGAGCCCCATTATCTTAGCCTA
AAAAAACCTTCTCTTTGGAACTTTCAGTAATACGCTTAACTGCTCATTGC
TATATTGAAGTACGGATTAGAAGCCGCCGAGCGGGCGACAGCCCTCCGAC
GGAAGACTCTCCTCCGTGCGTCCTCGTCTTCACCGGTCGCGTTCCTGAAA
CGCAGATGTGCCTCGCGCCGCACTGCTCCGAACAATAAAGATTCTACAAT
ACTAGCTTTTATGGTTATGAAGAGGAAAAATTGGCAGTAACCTGGCCCCA
CAAACCTTCAAATTAACGAATCAAATTAACAACCATAGGATGATAATGCG
ATTAGTTTTTTAGCCTTATTTCTGGGGTAATTAATCAGCGAAGCGATGAT
TTTTGATCTATTAACAGATATATAAATGGAAAAGCTGCATAACCACTTTA
ACTAATACTTTCAACATTTTCAGTTTGTATTACTTCTTATTCAAATGTCA
TAAAAGTATCAACAAAAAATTGTTAATATACCTCTATACTTTAACGTCAA
GGAGAAAAAACTATAATGACTAAATCTCATTCAGAAGAAGTGATTGTACC
TGAGTTCAATTCTAGCGCAAAGGAATTACCAAGACCATTGGCCGAAAAGT
GCCCGAGCATAATTAAGAAATTTATAAGCGCTTATGATGCTAAACCGGAT
TTTGTTGCTAGATCGCCTGGTAGAGTCAATCTAACCTGGCTACAGAATCA
TAAGTTGAATTCGACAGGTTATCAGCAACAACACAGTCATATCCATTCTC
AATTAGCTCTACCACAGTGTGTGAACCAATGTATCCAGCACCACCTGTAA
CCAAAACAATTTTAGAAGTACTTTCACTTTGTAACTGAGCTGTCATTTAT
ATTGAATTTTCAAAAATTCTTACTTTTTTTTTGGATGGACGCAAAGAAGT
TTAATAATCATATTACATGGCATTACCACCATATACATATCCATATCTAA
TCTTACTTATATGTTGTGGAAATGTAAAGAGCCCCATTATCTTAGCCTAA
AAAAACCTTCTCTTTGGAACTTTCAGTAATACGCTTAACTGCTCATTGCT
ATATTGAAGTACGGATTAGAAGCCGCCGAGCGGGCGACAGCCCTCCGACG
GAAGACTCTCCTCCGTGCGTCCTCGTCTTCACCGGTCGCGTTCCTGAAAC
GCAGATGTGCCTCGCGCCGCACTGCTCCGAACAATAAAGATTCTACAATA
CTAGCTTTTATGGTTATGAAGAGGAAAAATTGGCAGTAACCTGGCCCCAC
AAACCTTCAAATTAACGAATCAAATTAACAACCATAGGATGATAATGCGA
TTAGTTTTTTAGCCTTATTTCTGGGGTAATTAATCAGCGAAGCGATGATT
TTTGATCTATTAACAGATATATAAATGGAAAAGCTGCATAACCACTTTAA
CTAATACTTTCAACATTTTCAGTTTGTATTACTTCTTATTCAAATGTCAT
AAAAGTATCAACAAAAAATTGTTAATATACCTCTATACTTTAACGTCAAG
GAGAAAAAACTATAATGACTAAATCTCATTCAGAAGAAGTGATTGTACCT
GAGTTCAATTCTAGCGCAAAGGAATTACCAAGACCATTGGCCGAAAAGTG
CCCGAGCATAATTAAGAAATTTATAAGCGCTTATGATGCTAAACCGGATT
TTGTTGCTAGATCGCCTGGTAGAGTCAATAAAAAATTGTTAATATACCTC
TATACTTTAACGTCAAGGAGAAAAAACTATAATGACTAAATCTCATTCAG
AAGAAGTGATTGTACCTGAGTTCAATTCTAGCGCAAAGGAATTACCAAGA
CCATTGGCCGAAAAGTGCCCGAGCATAATTAAGAAATTTATAAGCGCTTA
TGATGCTAAACCGGATTTTGTTGCTAGATCGCCTGGTAGAGTCAATCTAA
CCTGGCTACAGAATCATAAGTTGAATTCGACAGGTTATCAGCAACAACAC
AGTCATATCCATTCTCAATTAGCTCTACCACAGTGTGTGAACCAATGTAT
CCAGCACCACCTGTAACCAAAACAATTTTAGAAGTACTTTCACTTTGTAA
CTGAGCTGTCATTTATATTGAATTTTCAAAAATTCTTACTTTTTTTTTGG
ATGGACGCAAAGAAGTTTAATAATCATATTACATGGCATTACCACCATAT
AGAGTTCAATTCTAGCGCAAAGGAATTACCAAGACCATTGGCCGAAAAGT
GCCCGAGCATAATTAAGAAATTTATAAGCGCTTATGATGCTAAACCGGAT
TTTGTTGCTAGATCGCCTGGTAGAGTCAATCTAACCTGGCTACAGAATCA
TAAGTTGAATTCGACAGGTTATCAGCAACAACACAGTCATATCCATTCTC
AATTAGCTCTACCACAGTGTGTGAACCAATGTATCCAGCACCACCTGTAA
CCAAAACAATTTTAGAAGTACTTTCACTTTGTAACTGAGCTGTCATTTAT
ATTGAATTTTCAAAAATTCTTACTTTTTTTTTGGATGGACGCAAAGAAGT
TTAATAATCATATTACATGGCATTACCACCATATACATATCCATATCTAA
TCTTACTTATATGTTGTGGAAATGTAAAGAGCCCCATTATCTTAGCCTAA
AAAAACCTTCTCTTTGGAACTTTCAGTAATACGCTTAACTGCTCATTGCT
ATATTGAAGTACGGATTAGAAGCCGCCGAGCGGGCGTATGGTTATGAAGA
GGAAAAATTGGCAGTAACCTGGCCCCACAAACCTTCAAATTAACGAATCA
AATTAACAACCATAGGATGATAATGCGATTAGTTTTTTAGCCTTATTTCT
GGGGTAATTAATCAGCGAAGCGATGATTTTTGATCTATTAACAGATATAT
AAATGGAAAAGCTGCATAACCACTTTAACTAATACTTTCAACATTTTCAG
TTTGTATTACTTCTTATTCAAATGTCATAAAAGTATCAACAAAAAATTGT
TAATATACCTCTATACTTTAACGTCAAGGAGAAAAAACTATAATGACTAA
ATCTCATTCAGAAGAAGTGATTGTACCTGAGTTCAATTCTAGCGCAAAGG
AATTACCAAGACCATTGGCCGAAAAGTGCCCGAGCATAATTAAGAAATTT
ATAAGCGCTTATGATGCTAAACCGGATTTTGTTGCTAGATCGCCTGGTAG
AGTCAATAAAAAATTGTTAATATACCTCTATACTTTAACGTCAAGGAGAA
AAAACTATAATGACTAAATCTCATTCAGAAGAAGTGATTGTACCTGAGTT
CAATTCTAGCGCAAAGGAATTACCAAGACCATTGGCCGAAAAGTGCCCGA
GCATAATTAAGAAATTTATAAGCGCTTATGATGCTAAACCGGATTTTGTT
GCTAGATCGCCTGGTAGAGTCAATCTAACCTGGCTACAGAATCATAAGTT
GAATTCGACAGGTTATCAGCAACAACACAGTCATATCCATTCTCAATTAG
CTCTACCACAGTGTGTGAACCAATGTATCCAGCACCACCTGTAACCAAAA
CAATTTTAGAAGTACTTTCACTTTGTAACTGAGCTGTCATTTATATTGAA
TTTTCAAAAATTCTTACTTTTTTTTTGGATGGACGCAAAGAAGTTTAATA
ATCATATTACATGGCATTACCACCATATAGAGTTCAATTCTAGCGCAAAG
GAATTACCAAGACCATTGGCCGAAAAGTGCCCGAGCATAATTAAGAAATT
TATAAGCGCTTATGATGCTAAACCGGATTTTGTTGCTAGATCGCCTGGTA
GAGTCAATCTAACCTGGCTACAGAATCATAAGTTGAATTCGACAGGTTAT
CAGCAACAACACAGTCATATCCATTCTCAATTAGCTCTACCACAGTGTGT
GAACCAATGTATCCAGCACCACCTGTAACCAAAACAATTTTAGAAGTACT
TTCACTTTGTAACTGAGCTGTCATTTATATTGAATTTTCAAAAATTCTTA
CTTTTTTTTTGGATGGACGCAAAGAAGTTTAATAATCATATTACATGGCA
TTACCACCATATACATATCCATATCTAATCTTACTTATATGTTGTGGAAA
TGTAAAGAGCCCCATTATCTTAGCCTAAAAAAACCTTCTCTTTGGAACTT
TCAGTAATACGCTTAACTGCTCATTGCTATATTGAAGTACGGATTAGAAG
CCGCCGAGCGGGCGACAGCCCTCCGACGGAAGACTCTCCTCCGTGCGTCC
TCGTCTTCACCGGTCGCGTTCCTGAAACGCAGATGTGCCTCGCGCCGCAC
TGCTCCGAACAA
40
Acknowledgements

• Northwestern University
• Jonathan Widom
• Yvonne Mittendorf
• Irene Moore

• U. North Carolina
• Jason Lieb
• Andrea Gossett

• University of Toronto
• Tim Hughes
• Desiree Tillo

• Weizmann Institute
• Yair Field
• Noam Kaplan

• Tali Sadka
• Michal Levo