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Structure determination of genomes and genomic domains by satisfaction of spatial restraints Marc A. Marti-Renom Genome Biology Group (CNAG) Structural Genomics Group (CRG) Friday, September 28, 12 Friday, September 28, 12 Integrative

SLIDE 1

Structure determination

f genomes and genomic

domains by satisfaction

f spatial restraints

Marc A. Marti-Renom

Genome Biology Group (CNAG) Structural Genomics Group (CRG)

Friday, September 28, 12

SLIDE 2

Friday, September 28, 12

SLIDE 3

f(·)

Experiments Computations Physics Evolution

Integrative Modeling Platform

GENERALIZE software development

http://www.integrativemodeling.org

Alber, F. et al. (2007). Nature, 450(7170), 695–701 Russel, D. et al. (2012). PLoS Biology, 10(1), e1001244. Friday, September 28, 12

SLIDE 4

“Simple” genomes “Complex” genomes

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SLIDE 5

Adapted from: Langowski and Heermann. Semin Cell Dev Biol (2007) vol. 18 (5) pp. 659-67

μ 10 10 10 Resolution s Time 10 10 10 10 10 10 10 10 μm Volume 10 10 10 10 10 DNA length nt 10 10 10 10

Knowledge

IDM INM

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SLIDE 6

Experiments Computation

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SLIDE 7

The “Chromatin Globule” model

D. Baù et al. Nat Struct Mol Biol (2011) 18:107-14
A. Sanyal et al. Current Opinion in Cell Biology (2011) 23:325–33.

Münkel et al. JMB (1999) Lieberman-Aiden et al. Science (2009)

PolII HBB Eraf Factory

a b

Osborne et al. Nat Genet (2004)

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SLIDE 8

Caulobacter crescentus 3D genome

M.A. Umbarger, et al. Molecular Cell (2011) 44:252–264

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SLIDE 9

Biomolecular structure determination 2D-NOESY data Chromosome structure determination 5C data

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SLIDE 10

5C technology

http://my5C.umassmed.edu

Dostie et al. Genome Res (2006) vol. 16 (10) pp. 1299-309

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SLIDE 11

Integrative Modeling

http://www.integrativemodeling.org

P1 P2 P1 P2 P1 P2

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SLIDE 12

169 5C primers on + strand 170 5C primers on – strand 28,730 chromatin interactions

~13Kb

The 3D architecture of Caulobacter Crescentus

4,016,942 bp & 3,767 genes

Ori Ter Ter Ori Ori Ori

0.0 0.5 1.1 1.7 2.1 2.5 3.0 3.5 4.0

Minus Probe Genome Position (mbp)

0.0 0.5 1.1 1.6 2.1 2.5 3.1 3.6 4.0

Plus Probe Genome Position (mbp)

7.5 x 10
1
2.81 x 10-1

1.88 x 10-1 6.56 x 10

1.12 x 10 1.59 x 10 2.06 x 10 2.53 x 10 3 x 10

5C interaction Z-scores

= - Strand = + Strand

Terminus Origin

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SLIDE 13

5C interaction matrix

ELLIPSOID for Caulobacter cresentus

Ori Ter Ter Ori Ori Ori

0.0 0.5 1.1 1.7 2.1 2.5 3.0 3.5 4.0

Minus Probe Genome Position (mbp)

0.0 0.5 1.1 1.6 2.1 2.5 3.1 3.6 4.0

Plus Probe Genome Position (mbp)

7.5 x 10
1
2.81 x 10-1

1.88 x 10-1 6.56 x 10-1 1.12 x 10 1.59 x 100 2.06 x 100 2.53 x 100 3 x 10

5C interaction Z-scores

Ori Ter

0.5 1 1.5 2 2.5 3 3.5 4 4.5

0.5 1 1.5 2 2.5 3 Genome Position (mbp) Contact Frequency

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SLIDE 14

3D model building with the 5C + IMP approach

0.0 0.5 1.1 1.7 2.1 2.5 3.0 3.5 4.0

Minus Probe Genome Position (mbp)

0.0 0.5 1.1 1.6 2.1 2.5 3.1 3.6 4.0

Plus Probe Genome Position (mbp)

7.5 x 10
1
2.81 x 10-1

1.88 x 10-1 6.56 x 10-1 1.12 x 10 1.59 x 100 2.06 x 100 2.53 x 100 3 x 10

5C interaction Z-scores

339 mers

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SLIDE 15

Genome organization in Caulobacter crescentus

Cluster 1

500 nm

180o

Cluster 2

500 nm

180o

Cluster 3

500 nm

180o

Cluster 4

500 nm

180o

Arms are helical

parS sites 25±17Kb from Ori

MIRRORS!

dif site 47±17Kb from Ter

Centromer-like Resolution

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SLIDE 16

parS sites initiate compact chromatin domain

0.5 1 1.5 2 2.5 3 3.5 4 4.5 4 2 0.2 0.4 0.6 0.8 1 1.2

Genome Position (mbp) Compaction Score

100-200Kb

Chromosome arms are equidistant to the cell center

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SLIDE 17

Moving the parS sites 400 Kb away from Ori

parS parS Wild-type ET166 PopZ ParB

?

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SLIDE 18

Moving the parS sites results in whole genome rotation!

0.0 0.5 1.1 1.7 2.1 2.5 3.0 3.5 4.0

Minus Probe Genome Position (mbp)

0.0 0.5 1.1 1.6 2.1 2.5 3.1 3.6 4.0

Plus Probe Genome Position (mbp)

7.5 x 10
1
2.81 x 10-1

1.88 x 10-1 6.56 x 10

1.12 x 10 1.59 x 10 2.06 x 10 2.53 x 10 3 x 10

5C interaction Z-scores

500 nm

Arms ¡are ¡STILL ¡helical ParS ¡sites Wild-‑type ET166

Structure & function PRESERVED!!!

Friday, September 28, 12

SLIDE 19

Moving the parS sites results in whole genome rotation!

0.0 0.5 1.1 1.7 2.1 2.5 3.0 3.5 4.0

Minus Probe Genome Position (mbp)

0.0 0.5 1.1 1.6 2.1 2.5 3.1 3.6 4.0

Plus Probe Genome Position (mbp)

7.5 x 10
1
2.81 x 10-1

1.88 x 10-1 6.56 x 10

1.12 x 10 1.59 x 10 2.06 x 10 2.53 x 10 3 x 10

5C interaction Z-scores

500 nm

Arms ¡are ¡STILL ¡helical ParS ¡sites Wild-‑type ET166

Structure & function PRESERVED!!!

Friday, September 28, 12

SLIDE 20

Genome architecture in Caulobacter

M.A. Umbarger, et al. Molecular Cell (2011) 44:252–264

ParS

dense

?

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SLIDE 21

From Sequence to Function

D. Baù and M.A. Marti-Renom Chromosome Res (2011) 19:25-35.

Function! Funtion!

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SLIDE 22

Acknowledgments

http://marciuslab.org http://integrativemodeling.org http://cnag.cat · http://crg.cat Davide Baù Staff Scientist CNAG Mark Umbarger PhD fellow Harvard Esteban Toro PhD fellow Stanford

Marc A. Marti-Renom

Genome Biology Group (CNAG) Structural Genomics Group (CRG) Barcelona, Spain.

Job Dekker

Program in Gene Function and Expression Department of Biochemistry and Molecular Pharmacology University of Massachusetts Medical School Worcester, MA, USA

George M. Church

Department of Genetics, Harvard Medical School, Boston, MA. USA

Lucy Shapiro

Department of Developmental Biology, Stanford University School of Medicine, Stanford, CA. USA

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