Marc A. Marti-Renom Genome Biology Group (CNAG) Structural Genomics - PowerPoint PPT Presentation

Determining the 3D structure of genomes and genomic domains. � Marc A. Marti-Renom Genome Biology Group (CNAG) Structural Genomics Group (CRG)

Whale sperm myoglobin structure (1960)

STRUCTURE FUNCTION alpha-globin genomic domain structure (2011) human genome (2011)

Resolution Gap Marti-Renom, M. A. & Mirny, L. A. PLoS Comput Biol 7, e1002125 (2011) Knowledge IDM INM DNA length 10 10 10 10 nt Volume 10 10 10 10 10 μ m Time 10 10 10 10 10 10 10 10 s Resolution 10 10 10 μ

Hybrid Method Baù, D. & Marti-Renom, M. A. Methods 58, 300–306 (2012). Experiments Computation

Hi-C technology Lieberman-Aiden, E. et al. Science 326, 289–293 (2009). http://3dg.umassmed.edu A Chr.18 (Hind III) B C D

Biomolecular structure determination 2D-NOESY data Chromosome structure determination 3C-based data

P1 P2 Normalization � TAD identification P1 P2 i+1 P1 P2 i i+2 3D Modeling i+n Extract structural � properties

On TADs and hormones Miguel Beato & Guillaume Filion Gene Regulation, Stem Cells and Cancer François le Dily Davide Baù François Serra Centre de Regulació Genòmica Barcelona, Spain

Progesterone-regulated transcription in breast cancer > ¡2,000 ¡genes ¡ Up -­‑regulated ¡ > ¡2,000 ¡genes ¡ Down -­‑regulated ¡ Regulation in 3D? Vicent) et#al# 2011,))Wright) et#al# 2012,)Ballare) et#al# 2012)

Experimental design HiC libraries ChIP-Seq � RNA-Seq � Hi-C Chr.18 (Hind III) Chr.18 (NcoI)

Are there TADs? how robust? C. Mb) Size (M >2,000 detected TADs 1 3 5 7 9 11 13 15 17 19 21 X Chromosome Chr.18 -Pg +Pg 8% 12% 80% conserved 1 0 0 k b ± 2 0 0 k b o r m o r e 0 10 15 25 >30 0 10 15 25 >30

Are TADs homogeneous? -Pg +Pg/-Pg Chr.2 Chr.2 H3K36me2 H3K4me3 H3K4me1 H3K14ac H3K9me3 H3K27me3 HP1 H1.2 5 Mb 5 Mb Correlation coefficient Correlation coefficient -1.0 -0.5 0.0 0.5 1.0 -1.0 -0.5 0.0 0.5 1.0 Same TAD Same TAD *** *** Consecutive TADs Consecutive TADs *** *** *** *** Inter-TADs Inter-TADs Same random TAD Same random TAD

Do TADs respond differently to Pg treatment? 8 2.0 4 TAD 469 TAD 821 -Pg -Pg 7 +Pg +Pg 3 1.5 Expression levels (Log 2 RPKM) Expression levels (Log 2 RPKM) Observed/expected ratio (Log 2 ) 6 2 5 1.0 4 1 3 0.5 0 2 0.0 1 -1 0 -0.5 -2 -1 -2 -3 -1.0 Log 2 fold change Log 2 fold change 0 30 4 Frequencies Observed 3 Expected 20 -1 2 10 1 -2 0 0 0-10% 100-90 MRFAP1 S100P MRFAP1L1 BLOC1S4 KIAA0232 TBC1D14 CCDC96 TADA2B GRPEL1 ZBTB2 RMND1 C6orf211 CCDC170 ESR1 SYNE1 100-90 0-10 % of genes per TAD with positive or negative fold change

Do TADs respond differently to Pg treatment? 8 4 2.0 -Pg -Pg 7 +Pg +Pg 3 1.5 Expression levels (Log 2 RPKM) Expression levels (Log 2 RPKM) Observed/expected ratio (Log 2 ) 6 5 2 1.0 4 1 3 0.5 0 2 0.0 1 -1 0 -0.5 -2 -1 -2 -3 -1.0 Log 2 fold change Log 2 fold change 4 0 30 Frequencies Observed 3 Expected 20 -1 2 10 1 -2 0 0 MRFAP1 S100P MRFAP1L1 BLOC1S4 KIAA0232 TBC1D14 CCDC96 TADA2B GRPEL1 ZBTB2 RMND1 C6orf211 CCDC170 ESR1 SYNE1 0-10% 100-90 100-90 0-10 % of genes per TAD with positive or negative fold change Pg induced fold change per TAD (6h) Mean Replicate 1 Replicate 2 Activated Repressed Other TADs TADs TADs Fold change 1h Pg Fold change 6h Pg 1.5 3.0 2.0 3.00 Pg induced fold change (log 2 ) per gene Pg induced fold change (log 2 ) per TAD *** *** *** intra-TAD interactions (Z-score) *** *** *** *** *** Fold change per TAD (Log 2 ) *** 2.00 1.0 2.0 Pg induced changes in 1.0 1.00 non-coding 0.5 1.0 0.0 0.00 0.0 0.0 -1.00 -1.0 -0.5 -1.0 -2.00 -2.0 -3.00 -1.0 -2.0 Repressed Other Activated Repressed Other Activated Repressed Other Activated Repressed Other Activated Repressed Other Activated TADs TADs TADs TADs TADs TADs TADs TADs TADs TADs TADs TADs TADs TADs TADs

Modeling 3D TADs 61 genomic regions containing 209 TADs covering 267Mb Chr1:26,800,000-28,700,000 1.5 1-5 2-4 2-3 0.9 0.6 pool 1 3-4 2 3 4 FISH (micra) 1.0 pool 2 1 5 2.2 0.5 2 4 3 r= 0.94 0.0 0.0 0.5 1.0 1.5 models (micra)

dRMSD (nm) 0 50 100 150 200 cl12 [13] Pg -Pg How TADs respond structurally to Pg? cl14 [10] mixt cl17 [10] Pg cl11 [30] Pg cl2 [267] Pg Pg induced changes in radius or giration Chr2:9,600,000-13,200,000 cl13 [11] Pg 1.00 1.05 1.10 Chr2 U170 (activated) .95 cl1 [297] Pg Repressed TADs cl10 [69] Pg cl9 [84] Pg Other TADs *** cl16 [10] Pg + ** Activated cl4 [172] Pg + TADs cl6 [142] Pg + cl7 [89] Pg + cl3 [176] Pg + PG induced changes in accessibility cl8 [85] Pg + 0.8 0.9 1.0 1.1 1.2 +Pg Repressed cl15 [10] Pg + TADs cl5 [144] Pg + dRMSD (nm) Other *** TADs 0 50 100 150 200 ** cl19 [14] Pg Activated -Pg cl16 [15] Pg TADs cl10 [20] Pg cl6 [32] Pg cl7 [32] Pg cl18 [15] Pg cl25 [10] Pg cl17 [15] Pg Chr6:71,800,000-76,500,000 Particle accessibility (%) cl20 [12] Pg cl3 [73] Pg 100 20 40 60 80 cl14 [16] Pg 0 Chr6 U767 (repressed) cl22 [12] Pg non-TSS cl13 [16] Pg cl1 [118] Pg *** cl12 [17] Pg cl4 [46] Pg TSS cl11 [18] Pg cl15 [16] Pg cl2 [112] Pg cl8 [25] Pg cl23 [11] Pg + cl24 [10] Pg + cl5 [34] Pg + cl26 [10] Pg + +Pg cl27 [10] Pg + cl28 [10] Pg + cl21 [12] Pg + cl9 [21] Pg +

Model for TAD regulation Repressed TAD chr1 U41 H3K27me3 H3K36me2 H3K4me1 H3K4me3 H3K14ac H3K9m3 MNAse DHS H1.2 HP1 H2A Structural P g + transition Activated TAD chr2 U207 H2A DHS HP1 H1.2 MNAse H3K27me3 H3K9m3 H3K14ac H3K4me1 H3K36me2 H3K4me3 Nucleosome Histones H2A/H2B Histone H1 Progesteone Receptor

STRUCTURE FUNCTION

Structure >> Function! ESR1 promoter new enhancer +Pg represses � ESR1 gene

Acknowledgments Davide Baù François le Dily François Serra � David Dufour Mike Goodstadt Gireesh Bogu Francisco Martínez-Jiménez Job Dekker Kerstin Bystricky Miguel Beato & Guillaume Filion Program in Systems Biology Chromatin and gene expression Gene Regulation, Stem Cells and Cancer Department of Biochemistry and Molecular Pharmacology Laboratoire de Biologie Moléculaire Eucaryote - CNRS Centre de Regulació Genòmica University of Massachusetts Medical School Toulouse, France Barcelona, Spain Worcester, MA, USA http://marciuslab.org http://3DGenomes.org http://cnag.cat · http://crg.cat