Structure determination of genomes and genomic domains by - PowerPoint PPT Presentation

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 Modeling Platform GENERALIZE software development http://www.integrativemodeling.org Experiments Computations Physics Evolution f(·) Alber, F. et al. (2007). Nature , 450 (7170), 695–701 Russel, D. et al. (2012). PLoS Biology , 10 (1), e1001244. Friday, September 28, 12

“Complex” genomes “Simple” genomes Friday, September 28, 12

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 Adapted from: Langowski and Heermann. Semin Cell Dev Biol (2007) vol. 18 (5) pp. 659-67 Friday, September 28, 12

Experiments Computation Friday, September 28, 12

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. a b Factory Eraf HBB PolII Münkel et al. JMB (1999) Osborne et al. Nat Genet (2004) Lieberman-Aiden et al. Science (2009) Friday, September 28, 12

Caulobacter crescentus 3D genome M.A. Umbarger, et al. Molecular Cell (2011) 44:252–264 Friday, September 28, 12

Biomolecular structure determination 2D-NOESY data Chromosome structure determination 5C data Friday, September 28, 12

5C technology http://my5C.umassmed.edu Dostie et al. Genome Res (2006) vol. 16 (10) pp. 1299-309 Friday, September 28, 12

Integrative Modeling http://www.integrativemodeling.org P1 P2 P1 P2 P1 P2 Friday, September 28, 12

The 3D architecture of Caulobacter Crescentus 4,016,942 bp & 3,767 genes Ori Ter Ori Ori 0 3 x 10 0.0 Origin 0 2.53 x 10 0.5 Minus Probe Genome Position (mbp) 0 2.06 x 10 1.1 5C interaction Z-scores 0 1.59 x 10 1.7 = + Strand = - Strand Ter 0 2.1 1.12 x 10 -1 2.5 6.56 x 10 1.88 x 10 -1 3.0 Terminus 3.5 -2.81 x 10 -1 Ori -1 4.0 -7.5 x 10 0.0 0.5 1.1 1.6 2.1 2.5 3.1 3.6 4.0 Plus Probe Genome Position (mbp) 169 5C primers on + strand ~13Kb 170 5C primers on – strand 28,730 chromatin interactions Friday, September 28, 12

5C interaction matrix ELLIPSOID for Caulobacter cresentus Ori Ter Ori Ori 0 3 x 10 0.0 2.53 x 10 0 0.5 Ori Ter 2.06 x 10 0 Minus Probe Genome Position (mbp) 1.1 5C interaction Z-scores 3 1.59 x 10 0 2.5 1.7 2 Contact Frequency Ter 1.5 0 2.1 1.12 x 10 1 0.5 6.56 x 10 -1 2.5 0 ��� 5 1.88 x 10 -1 3.0 �� 0 0.5 1 1.5 2 2.5 3 3.5 4 4.5 Genome Position (mbp) 3.5 -2.81 x 10 -1 Ori -1 4.0 -7.5 x 10 0.0 0.5 1.1 1.6 2.1 2.5 3.1 3.6 4.0 Plus Probe Genome Position (mbp) Friday, September 28, 12

3D model building with the 5C + IMP approach 0 3 x 10 0.0 339 mers 2.53 x 10 0 0.5 Minus Probe Genome Position (mbp) 2.06 x 10 0 1.1 5C interaction Z-scores 1.59 x 10 0 1.7 0 2.1 1.12 x 10 6.56 x 10 -1 2.5 1.88 x 10 -1 3.0 3.5 -2.81 x 10 -1 -1 4.0 -7.5 x 10 0.0 0.5 1.1 1.6 2.1 2.5 3.1 3.6 4.0 Plus Probe Genome Position (mbp) Friday, September 28, 12

Genome organization in Caulobacter crescentus Arms are helical Resolution Centromer-like dif site 47±17Kb from Ter parS sites 25±17Kb from Ori Cluster 4 Cluster 1 Cluster 2 Cluster 3 180 o 180 o 180 o 180 o 500 nm 500 nm 500 nm 500 nm MIRRORS! Friday, September 28, 12

parS sites initiate Chromosome arms are compact chromatin domain equidistant to the cell center 1.2 1 0.8 Compaction Score 0.6 0.4 0.2 0 ��� 2 ��� 4 0 0.5 1 1.5 2 2.5 3 3.5 4 4.5 Genome Position (mbp) 100-200Kb 16 Friday, September 28, 12

Moving the parS sites 400 Kb away from Ori ParB PopZ parS parS ? Wild-type ET166 Friday, September 28, 12

Moving the parS sites results in whole genome rotation! Wild-­‑type 0 3 x 10 0.0 0 2.53 x 10 0.5 Minus Probe Genome Position (mbp) 0 2.06 x 10 1.1 5C interaction Z-scores 0 1.59 x 10 1.7 ParS ¡sites ET166 0 2.1 1.12 x 10 2.5 -1 6.56 x 10 1.88 x 10 -1 3.0 3.5 -2.81 x 10 -1 500 nm -1 4.0 -7.5 x 10 Arms ¡are ¡ STILL ¡helical 0.0 0.5 1.1 1.6 2.1 2.5 3.1 3.6 4.0 Plus Probe Genome Position (mbp) Structure & function PRESERVED!!! Friday, September 28, 12

Moving the parS sites results in whole genome rotation! Wild-­‑type 0 3 x 10 0.0 0 2.53 x 10 0.5 Minus Probe Genome Position (mbp) 0 2.06 x 10 1.1 5C interaction Z-scores 0 1.59 x 10 1.7 ParS ¡sites ET166 0 2.1 1.12 x 10 2.5 -1 6.56 x 10 1.88 x 10 -1 3.0 3.5 -2.81 x 10 -1 500 nm -1 4.0 -7.5 x 10 Arms ¡are ¡ STILL ¡helical 0.0 0.5 1.1 1.6 2.1 2.5 3.1 3.6 4.0 Plus Probe Genome Position (mbp) Structure & function PRESERVED!!! Friday, September 28, 12

Genome architecture in Caulobacter M.A. Umbarger, et al. Molecular Cell (2011) 44:252–264 dense ? dense ParS Friday, September 28, 12

From Sequence to Function D. Baù and M.A. Marti-Renom Chromosome Res (2011) 19:25-35. Function! Funtion! Friday, September 28, 12

Acknowledgments Mark Umbarger Esteban Toro Davide Baù PhD fellow PhD fellow Staff Scientist Harvard Stanford CNAG Job Dekker George M. Church Lucy Shapiro Marc A. Marti-Renom Program in Gene Function and Expression Department of Developmental Biology, Genome Biology Group (CNAG) Department of Genetics, Department of Biochemistry and Molecular Pharmacology Stanford University School of Medicine, Structural Genomics Group (CRG) Harvard Medical School, University of Massachusetts Medical School Stanford, CA. USA Barcelona, Spain. Boston, MA. USA Worcester, MA, USA http://marciuslab.org http://integrativemodeling.org http://cnag.cat · http://crg.cat Friday, September 28, 12