3D folding of chromosomal domains in relation to gene expression - - PowerPoint PPT Presentation

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3D folding of chromosomal domains in relation to gene expression - - PowerPoint PPT Presentation

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3D folding of chromosomal domains in relation to gene expression Marc A. Marti-Renom http://sgu.bioinfo.cipf.es Structural Genomics Unit Bioinformatics & Genomics Department Prince Felipe Research Center (CIPF), Valencia, Spain Monday,

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Marc A. Marti-Renom

http://sgu.bioinfo.cipf.es

Structural Genomics Unit Bioinformatics & Genomics Department Prince Felipe Research Center (CIPF), Valencia, Spain

3D folding of chromosomal domains in relation to gene expression

Monday, January 25, 2010

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Complex genomes Simple genomes

Aim

Can we relate structure and expression?

Monday, January 25, 2010

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Resolution

Limited knowledge...

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

μ 10-1 10-2 10-3 Resolution s Time 103 102 100 10-2 10-4 10-6 10-8 10-10 μm3 Volume 103 100 10-3 10-6 10-9 DNA length nt 109 106 103 100

Knowledge

Monday, January 25, 2010

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Structure determination

Integrative Modeling Platform

http://www.integrativemodeling.org

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Alber et al. Nature (2007) vol. 450 (7170) pp. 683-94

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

Monday, January 25, 2010

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Human α-globin domain

ENm008 genomic structure and environment

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ENCODE Consortium. Nature (2007) vol. 447 (7146) pp. 799-816

The ENCODE data for ENm008 region was obtained from the UCSC Genome Browser tracks for: RefSeq annotated genes, Affymetrix/CSHL expression data (Gingeras Group at Cold Spring Harbor), Duke/NHGRI DNaseI Hypersensitivity data (Crawford Group at Duke University), and Histone Modifications by Broad Institute ChIP-seq (Bernstein Group at Broad Institute of Harvard and MIT).

RAB11FIP3 DECR2 LOC1001134368 HS8 HS10 HS40 HS33 HS46 HS48 TMEM8 MRPL28 AXIN1 PDIA2 ARHGDIG RGS11 ITFG3 LUC7L HB HB1 HB2 HB HB C16ORF35 500000| 450000| 400000| 350000| 0| 300000| 250000| 200000| 150000| 100000| 50000| POLR3K SNRNP25 RHBDF1 MPG

p13.3 13.2 12.3 p12.1 16p11.2 11.1 q11.2 q12.1 13 16q21 22.1 q23.1

K562 GM06990 DNaseI K562 GM12878 H3K4me3 CTCF K562 GM12878 K562 GM12878 RNA diff CTCF

K562 GM12878

Monday, January 25, 2010

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5C experiments

http://my5C.umassmed.edu

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  • B. R. Lajoie, N. L. van Berkum, A. Sanyal et al., Nat Methods 6 (10), 690 (2009).

GM12878 K562

Grow GM12878 and K562 cells Perform 3C analysis Perform 5C analysis with 30+25 primers Analyze 5C products by paired-end Solexa sequencing (131,947 paired end reads per library)

Formaldehyde Cross-linking Digestion Ligation Reversal of Cross-links PCR Amplification

Primer ligation PCR amplification

Microarray DNA sequencing

Monday, January 25, 2010

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Integrative Modeling

http://www.integrativemodeling.org

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P1 P2

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Representation

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i i+2 i+1 i+n

Harmonic Lower Bound Harmonic Upper Bound Harmonic

Hi, j = k di, j " di, j

( )

2

if di, j " di, j

0 ;

lbHi, j = k di, j # di, j

( )

2

if di, j > di, j

0 ;

lbHi, j = 0 $ % & ' & if di, j " di, j

0 ;

ubHi, j = k di, j # di, j

( )

2

if di, j < di, j

0 ;

ubHi, j = 0 $ % & ' &

Monday, January 25, 2010

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Scoring

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Harmonic Harmonic Lower Bound Harmonic Upper Bound

GM12878 K562

70 fragments 1,520 restraints 70 fragments 1,049 restraints

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Optimization

CREATE PARTICLES ADD RESTRAINTS SIMULATED ANEALING MONTE-CARLO LOCAL CONJUGATE GRADIENT LOWEST OBJECTIVE FUNCTION start end 500 rounds 5 steps

50 100 150 200 250 300 350 400 450 500 Iteration 0.0E+00 1.00E+06 2.00E+06 3.00E+06 4.00E+06 5.00E+06 6.00E+06 7.00E+06 IMP Objective function

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Not just one solution

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GM12878 K562

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Not just one solution

and we can de-convolute them!

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K562 GM12878

Cluster #2 314 model 232,673 IMP OF Cluster #1 2780 model 910,280 IMP OF

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Consistency

Consistency (%)

20 40 60 80 100

50 nm 75 nm 100 nm 125 nm 150 nm

K562

150 nm

20 40 60 80 100

50 nm 75 nm 100 nm 125 nm

GM15878

Fragment

Monday, January 25, 2010

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K562 GM12878

Cluster #2 314 model 232,673 IMP OF Cluster #1 2780 model 910,280 IMP OF

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Regulatory elements

200 400 600 800 1,000 Distance (nm)

K562 GM12878

K562 GM12878

Relative abundance

Promoters Active genes No-active genes DNaseI sites CTCF sites H3K4me3 sites

Distance to center (nm) <400 <300 <350 <250 <200 <150 <100 <50

K562 GM12878

Distance to center (nm) <400 <300 <350 <250 <200 <150 <100 <50 Relative abundance

Promoters Active genes No-active genes DNaseI sites CTCF sites H3K4me3 sites

.0 .5 1.0 1.5 2.0 2.5 .00 .50 1.00 1.50 2.00 2.50

Monday, January 25, 2010

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K562 GM12878

Cluster #2 314 model 232,673 IMP OF Cluster #1 2780 model 910,280 IMP OF

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Compactness

K562 GM12878

40 50 60 70 80 90 100 110 Density (bp/1nm)

K562 GM12878

Fragment

Monday, January 25, 2010

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K562 GM12878

Cluster #2 314 model 232,673 IMP OF Cluster #1 2780 model 910,280 IMP OF

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Multi-loops

Path length (nm)

Distance between anchoring points (nm) 73 117 161 205 >=250

700 600 500 400 300 300 400 500 600 700

44Kb 20Kb 68Kb 52Kb 64Kb 45Kb 35Kb 65Kb 50Kb 55Kb 30Kb 68Kb 63Kb 69Kb 64Kb 55Kb

K562 GM12878

Monday, January 25, 2010

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K562 GM12878

Cluster #2 314 model 232,673 IMP OF Cluster #1 2780 model 910,280 IMP OF

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Expression

Increased in K562 Increased in GM12878 =

Monday, January 25, 2010

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Summary

5C data results in comprehensive interaction matrices to build a consistent 3D model

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Monday, January 25, 2010

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Summary

Models allow for 5C data de-convolution

Monday, January 25, 2010

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Summary

Models allow for 5C data de-convolution

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Monday, January 25, 2010

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Summary

Selected models reproduce known (and new) interactions

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Monday, January 25, 2010

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Summary

Large-scale changes in conformation correlate with gene expression of resident genes

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100 nm 100 nm

K562 GM12878 RNA diff

RAB11FIP3 DECR2 LOC1001134368 HS8 HS10 HS40 HS33 HS46 HS48 TMEM8 MRPL28 AXIN1 PDIA2 ARHGDIG RGS11 ITFG3 LUC7L HB HB1 HB2 HB HB C16ORF35 POLR3K SNRNP25 RHBDF1 MPG

Monday, January 25, 2010

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Summary

“Chromatin Globule” model

Münkel et al. JMB (1999) Lieberman-Aiden et al. Science (2009) Phillips and Corces. Cell (2009)

  • PolII

HBB Eraf Factory

a b

Osborne et al. Nat Genet (2004)

Monday, January 25, 2010

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Acknowledgments

Marc A. Marti-Renom

Structural Genomics Unit Bioinformatics and Genomics Department Centro de Investigación Príncipe Felipe Valencia, Spain

Job Dekker

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

Davide Baù

Postdoctoral fellow Structural Genomics Unit

Emidio Capriotti

Postdoctoral fellow Structural Genomics Unit

Bryan Lajoie

Bioinformatician Dekker Lab

Amartya Sanyal

Postdoctoral Fellow Dekker Lab

Monday, January 25, 2010