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免疫学信息网 http://www.immuneweb.com
Interference Footprinting
DNA + MMS
+ Saturating [Protein]
Gel Shift
14
Cleave backbone @ modified bases
免疫学信息网 http://www.immuneweb.com
“Chromatin is the last refuge of scoundrels”
免疫学信息网 http://www.immuneweb.com
A Mitotic Human Chromosome
DNA length: 4.6 x 107 bp = 1.5 cm Chromosome length: 2 µm
Compaction ratio = 8000 1
免疫学信息网 http://www.immuneweb.com
Chromatin
DNA Compaction
DNA AccessibilityChromatin
RemodelingMachines
NIH
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Basic Unit of Chromatin Structure: Polynucleosome
2Compaction ratio = 6
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Limited Micrococcal Nulcease Digestion of Chromatin Generates a ~200 bp Ladder
3
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H1 H1
H1 H1
H1
H1
Micrococcal Nuclease Digestion Time
Mononucleosome Chromatosome Core Particle
Linker DNA (variable)
Operational Definititions of Nucleosome Particles
Chromatin
4
免疫学信息网 http://www.immuneweb.com
The 30 nm Chromatin Fiber
5Compaction ratio = 50
免疫学信息网 http://www.immuneweb.com
A Mitotic Human Chromosome
DNA length: 4.6 x 107 bp = 1.5 cm Chromosome length: 2 µm
Compaction ratio = 8000 1
30 nm filament
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Nuclear Scaffold/Matrix
DNA Loops (5-200 kb)
SAR/MAR
6
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The Nucleosome146 bp DNA 2X H3, H4, H2A, H2B
H4
H2B
H2A
H3
Not in Handout
免疫学信息网 http://www.immuneweb.com
Identities = 74/82 (90%), Positives = 79/82 (96%)
Query: 22 ILRDNIQGITKPAIRRLARRGGVKRISGLIYEEVRAVLKSFLESVIRDSVTYTEHAKRKT 81 +LRDNIQGITKPAIRRLARRGGVKRISGLIYEE R VLK FLE+VIRD+VTYTEHAKRKTSbjct: 21 VLRDNIQGITKPAIRRLARRGGVKRISGLIYEETRGVLKVFLENVIRDAVTYTEHAKRKT 80
Query: 82 VTSLDVVYALKRQGRTLYGFGG 103 VT++DVVYALKRQGRTLYGFGGSbjct: 81 VTAMDVVYALKRQGRTLYGFGG 102
Blast Search with S. cerevisiae Histone H4
Query: S. cerevisiaeSubject: H. sapiens
Not in Handout
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MW Chromosomal Proteins200,000
36,000
97,000
66,000
55,000
31,000
21,000
14,000
116,000
H4H2A
H2B/H3
Histones are Low MW Chromosomal Proteins
7
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Domain Structure of Histones
1 2 3L1 L2N C
Core Domain
8
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H2B
H2A
H3
H4
23
1
23
12
3
1
23
1
9
L1L2
N
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H3
H4
10
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4 helix-bundle
H3
H4
H3’
H4’
11
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4 helix-bundle H4H2B
H2A
12
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H4
H2B
H2A
H3
Not in Handout
免疫学信息网 http://www.immuneweb.com
H4
H2B
H2A
H3
Diameter = 110 Aº
13
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H4
H2B
H2A
H3
Width = 45 Aº
14
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H4
H2B
H2A
H3
15
Axis of dyad symmetry
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Histone CoreTilt
+Roll
Tilt
-Roll
15A
Tilt
Roll
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H2B
H2A
L1-L2Minor groove
1- 1Minor groove
L1-L2Minor groove
16
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H2B
H2A
Not in Handout
DNA entry
DNA exit
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N-term helix
H2B
H2A
H3
Not in Handout
DNA entry
DNA exit
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N-term helix
N-term helix
H2B
H2A
H3
Not in Handout
DNA entry
DNA exit
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Energetic and TopologicalConsequences of DNA Wrapping
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Basepair: 1 5 10 15
HistoneCore
Translational and Rotational Positioning
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Basepair: 1 5 10 15
HistoneCore
Translational and Rotational Positioning
免疫学信息网 http://www.immuneweb.com
Basepair: 1 5 10 15
HistoneCore
Translational and Rotational Positioning
ARECOUPLED!
免疫学信息网 http://www.immuneweb.com 19
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Are Nucleosomes “Positioned?”
1. Sequence at Unique Position
2. Micrococcal Nuclease Digest
3. Restriction Digest
4. Southern Blot
Discrete Band PositioningSmear Random Orientation
17
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Implications of Translational Positioning
18
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N-ARTKQTARKSTGGKAPRKQLATKAARKSAPATGGVKKPHRYRPGTVALREIRRYQKSTE- H3
N-SGRGKGGKGLGKGGAKRHRKVLRDNIQ - H4
N-SGRGKQGGKTRAKSKTRSSRAGL- H2A
N-SDPAKSAPAAKKGSKKAVTKTQKKDGKKRRKSRKES- H2B
H3 -ERA-C
H4 -RTLYGFGG-C
H2A -ELNKLLGGVTIAQGGVLPNIQSVLLPKKTESSKSTKSK-C
H2B -PGELAKHAVSEGTKAVTKYTSAK-C
Core
Core
Histones Have Variable Length Tails
20
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H4
H2B
H2A
H3
H3 N-terminus
H3 N-terminus
21
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H4
H2B
H2A
H3
H2B N-terminus
22
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H4
H2B
H2A
+++
_
__
23
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N-SGRGKGGKGLGKGGAKRHRKVLRDNIQ -H4
P
AcAc AcAc
N-ARTKQTARKSTGGKAPRKQLATKAARKSAPATGGVKKPHRYRPGTVALREIRRYQKSTE- H3
Core P P
10 28
Ac Ac Ac Ac AcAc
N-SGRGKQGGKTRAKSKTRSSRAGL-H2A
P
Ac Ac
N-SDPAKSAPAAKKGSKKAVTKTQKKDGKKRRKSRKES-H2B
P
AcAcAcAc Ac Ac23A
Newly-synthesized histones
M M M
M
M
K79
Activeregion
InactiveRegion (heterochromatin, X-inactivation)
Activeregion
Mitosis(Aurora B)
SSN6/TUP1
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???
“Beads on a String” 30 nm Filament
24
Low salt High salt
How does chromatin become compacted??
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The “Linker” Histone H1/H5
• Largest histone (21 kD), less conserved
• Binds 165 bp: “Chromatosome”
• Facilitates chromatin compaction
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Histone H5 reduces salt requirement for chromatin compaction
25
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Helix III - Major groove binding
Loop(Secondary DNA binding site)
Globular domain of Histone H5“winged helix-turn-helix domain”
26
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NC
C
C
C
C
C
26Zhou et al., 1998 Nature 395, 402
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The Solenoid Model for the 30 nm Fiber
26A
Histone H1
免疫学信息网 http://www.immuneweb.com
The 30 nm Chromatin Fiber
5Compaction ratio = 50
免疫学信息网 http://www.immuneweb.com
Condensins
Condensins Are Required for Mitotic ChromosomeCondensation
Hirano and Mitchison, Cell 79, 449
Condensin-Depleted
Mock-Depleted
Hirano et al., Cell 89, 511
27