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 Resolution

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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

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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

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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

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

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Experiments Computation

Integrative and iterative approach

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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

  • RNA expression data from the transcriptome group at Affymetrix and Cold Spring Harbor Laboratories.
  • CTCF and histone modifications (H3K4me3) from the Broad Institute and the Bradley E. Bernstein Lab at the

Massachusetts General Hospital/Harvard Medical School.

  • DNaseI data from the Crawford Lab at Duke University and at the Collins Lab at NHGRI.
RAB11FIP3 DECR2 LOC1001134368 CTCF CTCF CTCF HS8 HS10 HS40 HS33 HS46 HS48 CTCF CTCF CTCF CTCF CTCF 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 CTCF

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

chr16:

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

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5C experiments

http://my5c.umassmed.edu

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GM12878 K562

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

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

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Integrative Modeling

http://www.integrativemodeling.org

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P1 P2
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K562 GM12878

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

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

GM15787

Fragment

Consistency

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K562 GM12878

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

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

K562 GM12878

Fragment

Compactness

K562 GM06990 DNaseI

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K562 GM12878

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

100 200 300 400 Distance (nm)

HSs CTCFs Non regulatory HSs CTCFs Non regulatory

100 150 200 250 Distance (nm) 20 10 10 20 %

  • α-globin K562
  • 200

400 600 800 1,000 Distance (nm)

* * * ** ** * * * * K562 GM12878

Regulatory elements

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K562 GM12878

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

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

Multi-loops

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K562 GM12878

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

Increased in K562 Increased in GM12878 =

Expression

K562 GM12878 RNA diff
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Summary

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

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Summary

Selected models reproduce known (and new) interactions

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RAB11FIP3 DECR2 LOC1001134368 CTCF CTCF CTCF HS8 HS10 HS40 HS33 HS46 HS48 CTCF CTCF CTCF CTCF CTCF 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 CTCF p13.3 13.2 12.3 p12.1 16p11.2 11.1 q11.2 q12.1 13 16q21 22.1 q23.1 chr16:
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Summary

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

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RAB11FIP3 DECR2 LOC1001134368 CTCF CTCF CTCF HS8 HS10 HS40 HS33 HS46 HS48 CTCF CTCF CTCF CTCF CTCF TMEM8 MRPL28 AXIN1 PDIA2 ARHGDIG RGS11 ITFG3 LUC7L HBQ HBA1 HBA2 HBM HBZ C16ORF35 POLR3K SNRNP25 RHBDF1 MPG CTCF

K562 GM12878 RNA diff

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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)

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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