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, January 25, 2010
Aim Can we relate structure and expression? Simple genomes Complex genomes 2 Monday, January 25, 2010
Resolution Limited knowledge... Knowledge DNA length 100 103 106 109 nt Volume 10-9 10-6 10-3 100 103 μm3 Time 10-10 10-8 10-6 10-4 10-2 100 102 103 s Resolution 10-3 10-2 10-1 μ 3 Adapted from: Langowski and Heermann. Semin Cell Dev Biol (2007) vol. 18 (5) pp. 659-67 Monday, January 25, 2010
Structure determination Integrative Modeling Platform http://www.integrativemodeling.org Alber et al. Nature (2007) vol. 450 (7170) pp. 683-94 Biomolecular structure determination 2D-NOESY data Chromosome structure determination 5C data 4 Monday, January 25, 2010
Human α -globin domain ENm008 genomic structure and environment ENCODE Consortium. Nature (2007) vol. 447 (7146) pp. 799-816 p13.3 13.2 12.3 p12.1 16p11.2 11.1 q11.2 q12.1 13 16q21 22.1 q23.1 0| 50000| 100000| 150000| 200000| 250000| 300000| 350000| 400000| 450000| 500000| LOC1001134368 RAB11FIP3 C16ORF35 SNRNP25 ARHGDIG RHBDF1 MRPL28 POLR3K LUC7L ITFG3 RGS11 PDIA2 AXIN1 TMEM8 DECR2 HB � 2 HB � 1 MPG HB � HB � HB � HS48 HS46 HS40 HS33 HS10 HS8 GM12878 CTCF K562 GM12878 diff RNA K562 GM12878 CTCF K562 GM12878 H3K4me3 K562 GM06990 DNaseI K562 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). 5 Monday, January 25, 2010
5C experiments http://my5C.umassmed.edu B. R. Lajoie, N. L. van Berkum, A. Sanyal et al., Nat Methods 6 (10), 690 (2009). GM12878 K562 Formaldehyde Cross-linking Primer ligation PCR amplification Digestion Microarray Ligation DNA sequencing Reversal of Cross-links PCR Amplification 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) 6 Monday, January 25, 2010
Integrative Modeling http://www.integrativemodeling.org P1 P2 7 Monday, January 25, 2010
Representation Harmonic 2 ( ) 0 H i , j = k d i , j " d i , j i+1 Harmonic Lower Bound i i+2 $ 0 ; 2 ( ) 0 if d i , j " d i , j lbH i , j = k d i , j # d i , j & % 0 ; & if d i , j > d i , j lbH i , j = 0 ' i+n Harmonic Upper Bound $ 0 ; 2 ( ) 0 if d i , j " d i , j ubH i , j = k d i , j # d i , j & % 0 ; & if d i , j < d i , j ubH i , j = 0 ' 8 Monday, January 25, 2010
Scoring GM12878 70 fragments 1,520 restraints Harmonic Harmonic Upper Bound Harmonic Lower Bound K562 70 fragments 1,049 restraints 9 Monday, January 25, 2010
Optimization start CREATE PARTICLES 7.00E+06 ADD RESTRAINTS 6.00E+06 IMP Objective function SIMULATED ANEALING 5.00E+06 MONTE-CARLO 4.00E+06 LOCAL CONJUGATE GRADIENT 3.00E+06 5 steps 500 rounds 2.00E+06 1.00E+06 LOWEST OBJECTIVE FUNCTION 0.0E+00 0 50 100 150 200 250 300 350 400 450 500 Iteration end 10 Monday, January 25, 2010
Not just one solution GM12878 K562 11 Monday, January 25, 2010
Not just one solution and we can de-convolute them! 12 Monday, January 25, 2010
Consistency GM12878 K562 Cluster #1 Cluster #2 2780 model 314 model 910,280 IMP OF 232,673 IMP OF 150 nm 100 125 nm 80 100 nm 75 nm 60 50 nm 40 Consistency (%) 20 GM15878 0 100 150 nm 125 nm 80 100 nm 75 nm 60 50 nm 40 20 K562 0 Fragment 13 Monday, January 25, 2010
Regulatory elements GM12878 K562 Cluster #1 Cluster #2 2780 model 314 model 910,280 IMP OF 232,673 IMP OF 2.5 Promoters GM12878 Active genes CTCF sites DNaseI sites 2.0 H3K4me3 sites No-active genes Relative abundance 1.5 1,000 1.0 800 .5 Distance (nm) K562 600 .0 <50 <100 <150 <200 <250 <300 <350 <400 Distance to center (nm) 400 GM12878 2.50 Promoters K562 Active genes CTCF sites DNaseI sites 200 2.00 H3K4me3 sites No-active genes Relative abundance K562 0 1.50 GM12878 1.00 .50 .00 <50 <100 <150 <200 <250 <300 <350 <400 Distance to center (nm) 13 Monday, January 25, 2010
Compactness GM12878 K562 Cluster #1 Cluster #2 2780 model 314 model 910,280 IMP OF 232,673 IMP OF 110 Density (bp/1nm) 100 K562 GM12878 90 80 70 60 50 GM12878 40 K562 Fragment 13 Monday, January 25, 2010
Multi-loops GM12878 K562 Cluster #1 Cluster #2 2780 model 314 model 910,280 IMP OF 232,673 IMP OF 68Kb 64Kb 700 >=250 GM12878 44Kb 65Kb 50Kb 600 45Kb Distance between anchoring points (nm) Path length (nm) 52Kb 500 205 35Kb 20Kb 400 300 161 300 400 500 117 55Kb 30Kb 600 63Kb 64Kb K562 700 55Kb 68Kb 73 69Kb 13 Monday, January 25, 2010
Expression GM12878 K562 Cluster #1 Cluster #2 2780 model 314 model 910,280 IMP OF 232,673 IMP OF Increased in GM12878 = Increased in K562 13 Monday, January 25, 2010
Summary 5C data results in comprehensive interaction matrices to build a consistent 3D model 14 Monday, January 25, 2010
Summary Models allow for 5C data de-convolution 15 Monday, January 25, 2010
Summary Models allow for 5C data de-convolution 20 Monday, January 25, 2010
Summary Selected models reproduce known ( and new ) interactions 17 Monday, January 25, 2010
Summary Large-scale changes in conformation correlate with gene expression of resident genes 100 nm 100 nm LOC1001134368 RAB11FIP3 C16ORF35 ARHGDIG SNRNP25 RHBDF1 POLR3K MRPL28 LUC7L ITFG3 RGS11 PDIA2 AXIN1 TMEM8 DECR2 HB � 2 HB � 1 MPG HB � HB � HB � HS48 HS46 HS40 HS33 HS10 HS8 GM12878 diff RNA K562 18 Monday, January 25, 2010
Summary “ Chromatin Globule ” model � a b Factory Eraf � HBB PolII Münkel et al. JMB (1999) Osborne et al. Nat Genet (2004) Lieberman-Aiden et al. Science (2009) Phillips and Corces. Cell (2009) 19 Monday, January 25, 2010 � �
Acknowledgments Job Dekker Marc A. Marti-Renom Program in Gene Function and Expression Structural Genomics Unit Department of Biochemistry and Molecular Pharmacology Bioinformatics and Genomics Department University of Massachusetts Medical School Centro de Investigación Príncipe Felipe Worcester, MA, USA Valencia, Spain Amartya Sanyal Davide Baù Postdoctoral Fellow Postdoctoral fellow Dekker Lab Structural Genomics Unit Emidio Capriotti Bryan Lajoie Postdoctoral fellow Bioinformatician Structural Genomics Unit Dekker Lab Monday, January 25, 2010
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