Download Chromatin: a multi-scale jigsaw puzzle

Chromatin: a multi-scale jigsaw puzzle
Helmut Schiessel
Universiteit Leiden
Instituut Lorentz
The Netherlands
Numbers
human DNA per cell:
2 × human genome (2.9 × 109 bp)
= 2 m DNA in total
= 46 chromosomes of length ≈ 4 cm
46⇥
random chromosomal DNA coil
cell nucleus
densely packed DNA
100 µm
10 µm 2 µm
5 µm
500 nm
DNA chains
nucleosome
20 µm
nucleus
chromatin fiber
60 nm
basepair
DNA doublehelix
2 nm
20 nm
Hierarchical folding
chromatin:
2 nm
10 nm
33 nm
chromatin fiber
DNA
doublehelix
library:
Habe nun, ach! Philosophie,
line
300 nm
folded fiber
string of
nucleosomes
1.4 µnm
mitotic
chromosome
Habe nun, ach! Philosophie,
Juristerei und Medizin,
Und leider auch Theologie!
Durchaus studiert, mit hei!em Bemühn.
Da steh’ ich nun, ich armer Tor!
Und bin so klug als wie zuvor;
Hei!e Magister, hei!e Doktor gar,
Und ziehe schon an zehen Jahr,
Herauf, herab und quer und krumm,
Meine Schüler an der Nase herum "
Und sehe, da! wir nichts wissen können!
Das will mir schier das Herz verbrennen.
Zwar bin ich gescheiter als alle die Laffen,
Doktoren, Magister, Schreiber und Pfaffen;
Mich plagen keine Skrupel noch Zweifel,
Fürchte mich weder vor Hölle noch Teufel "
Dafür ist mir auch alle Freud’ entrissen,
Bilde mir nicht ein, was Rechts zu wissen,
Bilde mir nicht ein, ich könnte was lehren
Die Menschen zu bessern und zu bekehren.
Auch hab ich weder Gut noch Geld,
Noch Ehr’ und Herrlichkeit der Welt;
Es möchte kein Hund so länger leben!
page
book
bookshelf
Overview
2 nm
10 nm
2
3
1
33 nm
3
1.4 µnm
4
chromatin fiber
DNA
doublehelix
300 nm
folded fiber
string of
nucleosomes
1
The mechanical genome
2
DNA as a wormlike chain
3
Nucleosome unspooling
4
Packing nucleosomes
mitotic
chromosome
Artwork: Amar van Leewaarde & Marco Tompitak
The chromatin complex
2 nm
nucleosome
10 nm
33 nm
?
300 nm
chromatin fiber
DNA
doublehelix
string of
nucleosomes
folded fiber
1 3/4 turns, 147 bp
14 binding sites
1.4 µnm
mitotic
chromosome
from: H. Schiessel:
Biophysics for Beginners:
a Journey through the Cell Nucleus
(Pan Stanford Publishing, 2014)
Vol 442|17 August 2006|doi:10.1038/nature04979
ARTICLES
A genomic code for nucleosome
positioning
Eran Segal1, Yvonne Fondufe-Mittendorf2, Lingyi Chen2, AnnChristine Thåström2, Yair Field1, Irene K. Moore2,
Ji-Ping Z. Wang3 & Jonathan Widom2
Eukaryotic genomes are packaged into nucleosome particles that occlude the DNA from interacting with most DNA
binding proteins. Nucleosomes have higher affinity for particular DNA sequences, reflecting the ability of the sequence
to bend sharply, as required by the nucleosome structure. However, it is not known whether these sequence preferences
have a significant influence on nucleosome position in vivo, and thus regulate the access of other proteins to DNA. Here
we isolated nucleosome-bound sequences at high resolution from yeast and used these sequences in a new
computational approach to construct and validate experimentally a nucleosome–DNA interaction model, and to predict
the genome-wide organization of nucleosomes. Our results demonstrate that genomes encode an intrinsic nucleosome
organization and that this intrinsic organization can explain ,50% of the in vivo nucleosome positions. This nucleosome
positioning code may facilitate specific chromosome functions including transcription factor binding, transcription
initiation, and even remodelling of the nucleosomes themselves.
On July 18, the scientific community lost Professor in the Departments of Chemone of its most creative and influential istry, Biochemistry, and Biophysics and
thinkers and experimentalists. Jonathan the Beckman Institute at the University of
Widom, William Deering Professor of Illinois at Urbana-Champaign while a
Molecular Biosciences in the Weinberg graduate student and was promoted to
College of Arts and Sciences at North- Associate Professor with tenure in 1991.
western University, passed away unex- He later joined the Departments of Biopectedly of a heart attack while at his chemistry, Molecular Biology, and Cell
lab. He was 55 years old. Anyone with Biology and of Chemistry at Northwestern
a general interest in protein-DNA interac- University, where his star continued to
tions and chromatin structure has doubt- rise.
It is fair to say that chromatin was not
lessly been influenced by Jon’s many
seminal contributions, which have shaped a popular field of research in the earlythe field of chromatin and will live on for late 1980s and early 1990s. Undaunted
decades to come. Those of us who had by fashion trends, Jon published many
the privilege of seeing him in action at prescient and influential papers on the
meetings and poster sessions will miss conformation of linker DNA and on linker
his beautifully crafted presentations, his warm personality,
and his insightful and always
respectful contributions and
criticism. To those of us who
enjoyed his friendship, the
loss is deeply personal.
Jon was born in Ithaca, NY,
on October 25, 1955. His
approach to science appears
to have been shaped by his
parents, Joanne and Benjamin Widom, both of whom
are scientists. This resulted
in a powerful quantitative approach to investigating biology that pervaded all of his
research. Jon received his
BA in Chemistry at Cornell
University and a PhD with
Buzz Baldwin at Stanford
University, with whom he
published several seminal
papers on DNA packaging.
This work no doubt planted
the seeds for his lifelong
interest in DNA packaging in
eukaryotes. He spent the
years of 1983–1985 in England as a postdoc with Sir
Aaron Klug. There, he published the first of many papers
to come on the organization
of eukaryotic chromatin. Jon
Jonathan Widom
Photo by Rick Gaber, Northwestern University
was recruited as an Assistant
Jonathan Widom
“Genomes care
where nucleosomes are on average
determine the destinations of the nucleosomes that they mobilize.
Rather, the remodelling complexes may allow nucleosomes to sample
and so genomes
encode
information
to bias
alternative
positions rapidly, explicit
resulting in a thermodynamic
equilibrium between the nucleosomes and the site-specific DNA binding
proteins [their
that compete positions].”
with nucleosomes for occupancy along the
genome. In this view, nucleosome positions are regulated in cis by
Eukaryotic genomic DNA exists as highly compacted nucleosome
arrays called chromatin. Each nucleosome contains a 147-base-pair
(bp) stretch of DNA, which is sharply bent and tightly wrapped
around a histone protein octamer1. This sharp bending occurs at
every DNA helical repeat (,10 bp), when the major groove of
the DNA faces inwards towards the histone octamer, and again
,5 bp away, with opposite direction, when the major groove faces
outward. Bends of each direction are facilitated by specific dinucleotides2,3. Neighbouring nucleosomes are separated from each other by
10–50-bp-long stretches of unwrapped linker DNA4; thus, 75–90% of
genomic DNA is wrapped in nucleosomes. Access to DNA wrapped
in a nucleosome is occluded1 for polymerase, regulatory, repair and
recombination complexes, yet nucleosomes also recruit other proteins through interactions with their histone tail domains5. Thus, the
detailed locations of nucleosomes along the DNA may have important inhibitory or facilitatory roles6,7 in regulating gene expression.
DNA sequences differ greatly in their ability to bend sharply2,3,8.
their intrinsic sequence preferences, which would then have significant regulatory roles. In this cis regulation model, we expect the
genome to encode a nucleosome organization, intrinsic to the DNA
sequence alone, comprising sequences with both low and high
affinity for nucleosomes. Many of the high-affinity sequences should
then be occupied by nucleosomes in vivo. Moreover, the detailed
distribution of nucleosome positions encoded by the genome should
significantly influence chromosome functions genome-wide.
Here we report the results of a combined experimental and
computational approach to detect the DNA sequence preferences
of nucleosomes and the intrinsic nucleosome organization of the
histone H1. His work on the transie
site exposure of nucleosomal DN
shaped our view of nucleosomes like n
other; as of now, this concept represen
the most conclusive mechanism for th
regulation of DNA accessibility in a chro
matin context. This discovery was mad
at a time when the chromatin field wa
focused almost exclusively on structur
and static aspects of this complex. Jo
recognized that the nucleosomal DNA
wrapped around the histone octamer b
a large number of weak interactions (Po
lach and Widom, 1995). This allows th
nucleosome to be very stable, since the
is a very low probability that the DNA w
fully unwrap; at the same time, the nucl
osome is still dynamic, sinc
there is a significant chanc
that the DNA will partia
unwrap. He termed this prop
erty of the nucleosome ‘‘si
accessibility’’ and later we
on to demonstrate that si
accessibility allows for tra
scription factors to bind (
and Widom, 2004) and th
typical unwrapping even
occur rapidly at many time
a second (Li et al., 2005).
However, it is Jon’s tru
groundbreaking work in th
mid 1990s on nucleosom
positioning sequences th
made him a household nam
in countless chromatin labo
ratories worldwide. Throug
out his career, Jon ha
worked extensively to unde
stand the rules of nucleo
some formation within chro
mosomes. He had th
brilliant idea to use SELE
to ‘‘evolve’’ the most stab
nucleosome positioning s
quence possible, realizin
that such research would b
highly informative for devisin
rules for the features (
absence of site-specific co
tacts between DNA an
histones) that would mak
Molecular Cell 43, September 2, 2011 ª2011 Elsevier Inc. 69
1955-2011
The sequence space
How many sequences can be wrapped around a nucleosome?
147
4
(about 5 times the volume of the Milky Way)
The sequence space
Baker’s Yeast 12 Mb
The sequence space
Human 3.2 Gb
The sequence space
high affinity
sequences
Random Pool 5 Tb
Lowary & Widom 1998
The sequence space
107
high affinity
sequences
Mutation Monte Carlo method
The genomic code for nucleosome positioning
Satchwell, Drew & Travers, J. Mol. Biol. 191 (1986) 659
AA + TT + TA
0.30
0.25
0.20
0.15
GC
0.10
0.05
70
50
30
10
10
bp position
30
50
70
Segal et al., Nature, 2006
Our questions:
Can the positioning rules be explained by a purely mechanical model?
Can mechanical information be multiplexed with classical genetic information?
s
’
g
n
o
H
l
o
e
h
C
k
o
e
S
o
y
a
see als
d
r
e
t
s
e
y
m
o
r
f
lecture
What is a gene
Historical background
?
Somehow properties are inherited by the daughter cells...
Via DNA? No, boring molecule
Via Proteins? Yes! Very rich class of extremely diverse
molecules!
Genes are special sets of protein molecules!
How to test this idea?
DNA is the carrier of the genetic information
Oswald T. Avery, 1944
The discovery of the DNA double helix
Maurice Wilkins
Rosalind Franklin
X ray diffraction
DNA forms helix
James D. Watson
Francis Crick
model building
The alpha helix in proteins
Pauling & Corey, 1951
Linus Pauling
A wrong DNA double helix
Watson & Crick, 1951, not published
A wrong DNA triple helix
Pauling & Corey, Feb. 1953
three intertwined chains with the sugarphosphate backbones in the middle
major mistake: phosphate groups
assumed to be uncharged!
Published in PNAS
(cited 86 times…)
Base pairing
How to get the charged backbone to the outside?
Somehow the backbone should be of similar size.
The solution: Watson-Crick base-pairs (found by playing with paper
cutouts of the bases)
Consistent with the Chargaff rules:
for any DNA sample: #A = #T and #C = #G
The correct double helix
Watson & Crick, 1953
Model building
Watson & Crick, 1953
Central dogma
replication
Crick, 1956
RNA transcript
DNA
gene 1
gene 2
gene 3
RNA polymerase
protein
transcription
RNA 1
translation
attached amino acid (F)
DNA
ribosome
RNA 2
tRNA
protein
RNA
attached amino acid (F)
tRNA
tRNA
ribosome
3
anticodon (GAA)
tRNA
anticodon (GAA)
mRNA
protein 1
protein 2
mRNA
protein 3
codon cube:
negatively charged aa
C
G
2
T
A
D:
E:
aspartic acid (Asp)
glutamic acid (Glu)
positively charged aa
STOP
H:
K:
R:
histidine (His)
lysine (Lys)
arginine (Arg)
uncharged polar aa
N:
Q:
S:
T:
Y:
STOP
A T G C
nonpolar aa
1
C
G
2
T
A
A:
C:
F:
G:
I:
L:
M:
V:
P:
W:
STOP
STOP
A
T
1
G
asparagine (Asn)
glutamine (Gln)
serine (Ser)
threonine (Thr)
tyrosine (Tyr)
C
alanine (Ala)
cysteine (Cys)
phenylalanine (Phe)
glycine (Gly)
isoleucine (Ile)
leucine (Leu)
methionine (Met)
valine (Val)
proline (Pro)
tryptophan (Trp)
from: H. Schiessel, Biophysics
for Beginners: a Journey though
the Cell Nucleus
Why does DNA form a double helix?
Calladine, Drew, Luisi, Travers, Understanding DNA
base
sugar
phosphate
P
S
P
B
B
P
S
P
B
B
P
S
P
l = 6.5Å
S
S
S
P
B
B
3.2Å
3.3Å
S
holes
P
B
P
S
P
18Å
negatively charged
uncharged polar
nonpolar
P8
P9
The DNA double helix:
P7
P10
P6
P11
9Å
✓
P5
P1
lxy = 5.6Å
P2
P4
P3
. = 2 arcsin
✓
lxy
2 ⇥ 9 Å
◆
⇡ 36
minor groove
P11
P10
P9
P8
P7
l = 6.5Å
lxy
lz = 3.3Å
= 5.6Å
P6
P5
major groove
P4
A
P3
B-DNA
N
P2
N
T
H
N
+
H
N
+
H
N
N
N
P1
S
CH3
O
O
S
The genomic code for nucleosome positioning
Satchwell, Drew & Travers, J. Mol. Biol. 191 (1986) 659
AA + TT + TA
0.30
0.25
0.20
0.15
GC
0.10
0.05
70
50
30
10
10
bp position
30
50
70
Segal et al., Nature, 2006
The rigid base-pair representation
P8
P9
P7
P10
y
z
x
y
z
P6
P11
x
9Å
P5
P1
lxy = 5.6Å
Shift
✓
P2
P4
P3
. = 2 arcsin
✓
lxy
2 ⇥ 9 Å
◆
⇡ 36
Tilt
minor groove
P11
y
z
x
y
z
P10
P9
P8
P7
l = 6.5Å
x
lxy
lz = 3.3Å
= 5.6Å
P5
major groove
Slide
P6
P4
Roll
A
P3
N
P2
N
T
H
N
+
H
N
+
H
N
N
N
P1
y
z
x
y
z
x
Rise = 0.34 nm
Twist = 36
Rise
Twist
S
CH3
O
O
S
B-DNA
The rigid base-pair representation
y
z
x
y
Shift
z
x
R
25
R
25
0
250
Tilt
25
y
z
x
y
Slide
z
R
2
R=9
bp step
5
5
0
0
5
5
10
10
bp step
15
15
x
Roll
(a)
y
z
Rise
x
y
z
Twist
x
0
2
A local harmonic model
y
z
x
y
z
x
~x = [Tilt, Roll, Twist, Shift, Slide, Rise]
y
Shift
Tilt
z
z
x
y
Slide
x
Roll
1
1
Estep E
=stepk=
~x Tr ~x~x0
B Tr k B
2
2
T
0 T
~x
Q ~x Q ~x~x0
~x0
protein-DNA cocrystals
Olson, Gorin, Lu, Hock & Zhurkin
PNAS 95 (1998) 11163
y
z
x
y
z
x
all atom MD simulations
Lavery et al.
Nucleid Acids Res. 38 (2010) 299
Rise
Twist
The mysterious GC step
160
200
150
100
−0.02
−0.01 roll0
GC−0.03
peaks
at positive
0
q1 (rad)
−2
Q22
(k
T
.
rad
)
roll stiffness
B
a)
−2
Q11 (kBT . rad )
250
0.01
AA
AC
AG
AT
CA
CC
CG
GA
GC
TA
b)
140
120
100
80
60
0.02 0.04 0.06 0.08 0.1
intrinsic
q0 (rad)roll
2
Our nucleosome model
Eslami-Mossalam, Schram, Tompitak, van Noort & Schiessel
AT: blue/yellow
GC: green/white
similar models:
Tolstorukov et al., J. Mol. Biol. 2007
Vaillant, Audit & Arneodo, 2007
Morozov et al., Nucl. Acids Res. 2009
Becker & Everaers, Structure 2009
Fathizadeh, Besya, Ejtehadi & Schiessel, EPJE 2013
The two Mutation Monte Carlo moves
configurational move
The two Mutation Monte Carlo moves
configurational move
point mutation
Mutation Monte Carlo method
107
high affinity
sequences
Recovering the positioning rules
10 million sequences at 100 K
GC steps peak at their least favorite positions. Why?
GC brings in good neighbors, e.g. AGCT
Our questions:
Yes, the positioning rules can be explained by a purely mechanical model.
Can mechanical information be multiplexed with classical genetic information?
Elastic energy (k
T) energy (k T)
Elastic
B
B Frequency
0.1 a)
0.30
The 0energy
−5 −4 −3 −2 −1
1
2landscape
3
4
5
Deviation from the experimental position (bp)
0.2
80
0.1 b)
700
80
60
70
of a gene
−5 −4 −3 −2 −1
0
1
2
3
4
5
Deviation from the experimental position (bp)
YAL002W
b)
550
600
650
700 750 800
Position (bp)
850
900
950
550
600
650
700 750 800
Position (bp)
850
900
950
60
Nucleosome mapping at basepair resolution in Saccharomyces cerevisiae
Brogaard, Xi, Wang & Widom
Nature 486 (2012) 496
Synonymous Mutation Monte Carlo
… GTA CTC ACA ACT ACA CAT TTT GCC CTT ATT …
… Val Leu Thr Thr Thr His Phe Ala Leu Ile …
allowed
mutations
GTA
GTT
GTG
GTC
TTA
TTG
CTA
CTT
CTG
CTC
ACA
ACT
ACG
ACC
ACA
ACT
ACG
ACC
ACA CAT TTT GCA TTA ATA
ACT CAC TTC GCT TTG ATT
ACG
GCG CTA ATC
ACC
GCC CTT
CTG
CTC
70
b)
550
600
650
700 750 800
Position (bp)
850
900
950
550
600
650
700 750 800
Position (bp)
850
900
950
60
75
65
55
75
65
55
75
65
55
75
65
55
75
65
55
75
65
55
810
820
830
Position (bp)
840
Elastic energy (kBT)
Elastic energy (kBT)
Elastic energy (k
T)
Elastic
B
80
60
Our questions:
Yes, the positioning rules can be explained by a purely mechanical model.
Yes, mechanical and genetic information can be multiplexed together.
New question:
How do you multiplex those two types of genetic information?
Three mechanisms allow for multiplexing
1
protein sequences highly degenerate
C
G
2
T
A
negatively charged aa
D:
E:
aspartic acid (Asp)
glutamic acid (Glu)
positively charged aa
STOP
H:
K:
R:
histidine (His)
lysine (Lys)
arginine (Arg)
uncharged polar aa
STOP
A T G C
1
N:
Q:
S:
T:
Y:
asparagine (Asn)
glutamine (Gln)
serine (Ser)
threonine (Thr)
tyrosine (Tyr)
from: H. Schiessel:
Biophysics for Beginners:
nonpolar aa
a Journey through the Cell Nucleus
(Pan Stanford
Publishing, 2014)
A:
alanine (Ala)
C: cysteine (Cys)
F:
phenylalanine (Phe)
G: glycine (Gly)
I:
isoleucine (Ile)
Three mechanisms allow for multiplexing
2
genomes not selected for highest affinity
low affinity position
Elastic energy (kBT)
90
80
70
60
50
40
−10 −8 −6 −4 −2 0 2
Position (bp)
free mutations at low T
4
6
8
10
3
75
65
55
plasticity due to mechanical nature of DNA readout
75
65
55
Elastic energy (kBT)
75
65
55
75
65
55
Elastic energy (kBT)
75
65
55
Three mechanisms allow for multiplexing
75
65
55
810
820
830
840
Position (bp)
75
65
55
75
65
55
Elastic energy (kBT)
Elastic energy (kBT)
75
65
55
… GAA ACT …
… Glu Thr …
75
65
55
810
820
830
840
Position (bp)
suboptimal location of a good basepair step
GAA ACA
GAG ACT
ACG
ACC
Three mechanisms allow for multiplexing
1
2
3
protein sequences highly degenerate
genomes not selected for highest affinity
plasticity due to mechanical nature of DNA readout
Molecular Cell
Obituary
Jonathan Widom
1955–2011
On July 18, the scientific community lost Professor in the Departments of Chemone of its most creative and influential istry, Biochemistry, and Biophysics and
thinkers and experimentalists. Jonathan the Beckman Institute at the University of
Widom, William Deering Professor of Illinois at Urbana-Champaign while a
Molecular Biosciences in the Weinberg graduate student and was promoted to
College of Arts and Sciences at North- Associate Professor with tenure in 1991.
western University, passed away unex- He later joined the Departments of Biopectedly of a heart attack while at his chemistry, Molecular Biology, and Cell
lab. He was 55 years old. Anyone with Biology and of Chemistry at Northwestern
a general interest in protein-DNA interac- University, where his star continued to
tions and chromatin structure has doubt- rise.
It is fair to say that chromatin was not
lessly been influenced by Jon’s many
seminal contributions, which have shaped a popular field of research in the earlythe field of chromatin and will live on for late 1980s and early 1990s. Undaunted
decades to come. Those of us who had by fashion trends, Jon published many
the privilege of seeing him in action at prescient and influential papers on the
meetings and poster sessions will miss conformation of linker DNA and on linker
his beautifully crafted presentations, his warm personality,
and his insightful and always
respectful contributions and
criticism. To those of us who
enjoyed his friendship, the
loss is deeply personal.
Jon was born in Ithaca, NY,
on October 25, 1955. His
approach to science appears
to have been shaped by his
parents, Joanne and Benjamin Widom, both of whom
are scientists. This resulted
in a powerful quantitative approach to investigating biology that pervaded all of his
research. Jon received his
BA in Chemistry at Cornell
University and a PhD with
Buzz Baldwin at Stanford
University, with whom he
published several seminal
papers on DNA packaging.
This work no doubt planted
the seeds for his lifelong
interest in DNA packaging in
eukaryotes. He spent the
years of 1983–1985 in England as a postdoc with Sir
Aaron Klug. There, he published the first of many papers
to come on the organization
of eukaryotic chromatin. Jon
Jonathan Widom
Photo by Rick Gaber, Northwestern University
was recruited as an Assistant
Jonathan Widom
“nucleosome positioning” at the KITP conference
“Soft Matter Physics Approaches to Biology”
Santa Barbara, May 23rd 2011
histone H1. His work on the transient
site exposure of nucleosomal DNA
shaped our view of nucleosomes like no
other; as of now, this concept represents
the most conclusive mechanism for the
regulation of DNA accessibility in a chromatin context. This discovery was made
at a time when the chromatin field was
focused almost exclusively on structural
and static aspects of this complex. Jon
recognized that the nucleosomal DNA is
wrapped around the histone octamer by
a large number of weak interactions (Polach and Widom, 1995). This allows the
nucleosome to be very stable, since there
is a very low probability that the DNA will
fully unwrap; at the same time, the nucleosome is still dynamic, since
there is a significant chance
that the DNA will partially
unwrap. He termed this property of the nucleosome ‘‘site
accessibility’’ and later went
on to demonstrate that site
accessibility allows for transcription factors to bind (Li
and Widom, 2004) and that
typical unwrapping events
occur rapidly at many times
a second (Li et al., 2005).
However, it is Jon’s truly
groundbreaking work in the
mid 1990s on nucleosome
positioning sequences that
made him a household name
in countless chromatin laboratories worldwide. Throughout his career, Jon had
worked extensively to understand the rules of nucleosome formation within chromosomes. He had the
brilliant idea to use SELEX
to ‘‘evolve’’ the most stable
nucleosome positioning sequence possible, realizing
that such research would be
highly informative for devising
rules for the features (in
absence of site-specific contacts between DNA and
histones) that would make
Molecular Cell 43, September 2, 2011 ª2011 Elsevier Inc. 691
Summary of what we found so far:
The nucleosome positioning rules are mechanical in nature.
Classical genetic and mechanical information can be multiplexed,
based on three different mechanisms.
Does this mean that we have proven
the existence of a mechanical genome, which
would be the result of the mechanical evolution of
DNA molecules?
No!
Unfortunately not!
Alternative scenario
Genomes do not care where nucleosomes are.
The mechanical variations along DNA molecules are
just random site products of given sequences.
Nucleosomes bind where the mechanical energy is lowest
and experimentalists map these positions.
AA + TT + TA
0.30
0.25
0.20
0.15
GC
0.10
0.05
70
50
30
10
10
bp position
30
50
70
The two scenarios
no multiplexing
multiplexing
outside gene
nucleosome
gene
pamino acid
gene
pamino acid
bp
bp
Direct test for multiplexing
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The three domains of life
bacteria
archaea
eukaryotes
E. coli after lysis
“proto-nucleosome”
nucleosome
http://www.pitt.edu/~mcs2/ecoli.html
Talbet & Henikoff, 2010
Luger et al., 1997
Summary:
mechanical information can be written into DNA molecules, even on
top of genes
the higher order structures of real DNA molecules (nucleosomes, supercoils,…) is to a substantial extent encoded in mechanical genomes