Does color have structure? Modeling 3D domains of the fly genome. Marc A. Marti-Renom Genome Biology Group (CNAG) Structural Genomics Group (CRG)
http://3DGenomes.org FastQ files to Maps Map analysis i+1 i i+2 Model building i+n Model analysis
Structuring the COLORs of chromatin
Fly Chromatin COLORs Filion et al. (2010). Cell, 143(2), 212–224. drawing by Guillaume Filion A Position on chr2L (kb) B 16000 16200 16400 16600 16800 17000 Principal component analysis MRG15 SU(VAR)3 − 7 SU(VAR)3 − 9 HP6 PC2 HP1 LHR − 15 − 10 − 5 0 5 10 15 CAF1 ASF1 MUS209 TOP1 RPII18 20 SIR2 RPD3 CDK7 DSP1 10 DF31 MAX PCAF ASH2 53 chromatin proteins PC1 HP1c 0 CtBP JRA BRM ECR − 10 BCD MED31 SU(VAR)2 − 10 LOLAL GAF − 20 CG31367 ACT5C TIP60 10 MNT SIN3A TBP DWG PHOL 5 PROD BEAF32b SU(HW) LAM 0 D1 PC3 H1 SUUR EFF − 5 IAL GRO PHO CTCF − 10 PC E(Z) PCL SCE − 15 + Genes - − 15 − 10 − 5 0 5 10 15 PC2 type C PC1 PC2 PC3 Hidden Markov model 16000 16200 16400 16600 16800 17000 Position on chr2L (kb)
Functional COLORs Hou et al. (2012). Molecular Cell, 48(3), 471–484. 50 ~1Mb regions 10 for each color
Structural properties 50 1Mb regions. 10 enriched for each color. Accessibility (%) Density (bp/nm) Interactions Angle
Structural COLORs
Interactions Accessibility (%) 10 20 30 40 0 20 40 60 80 100 *** *** Structural COLORs Density (bp/nm) abs(angle) 80 100 120 140 40 80 120 160 * *** ** *** *** *** ** ***
Structural COLORs A Position on chr2L (kb) 16000 16200 16400 16600 16800 17000 MRG15 SU(VAR)3 − 7 SU(VAR)3 − 9 HP6 HP1 LHR CAF1 ASF1 MUS209 TOP1 RPII18 SIR2 RPD3 type CDK7 DSP1 DF31 MAX PCAF ASH2 53 chromatin proteins HP1c CtBP JRA BRM ECR BCD MED31 SU(VAR)2 − 10 LOLAL GAF CG31367 ACT5C TIP60 MNT SIN3A TBP DWG PHOL PROD BEAF32b SU(HW) LAM D1 H1 SUUR EFF IAL GRO PHO CTCF PC E(Z) PCL SCE
http://3DGenomes.org
Shameless promotion… November 23th-27th, Lisbon http://gtpb.igc.gulbenkian.pt
TADkit v1.0 will be released before summer • Genome track annotation. • Cluster selection. • BED formatted tracks (upload/fetch). • HiC (parallel) track. • Restraints (parallel) track. • Variability representation. • New renderings. • Project and user manager. • Modularity. • TADbit front-end.
Acknowledgments Mike Goodstadt François Serra Davide Baù François le Dily Yasmina Cuartero Yannick Spill Marco di Stefano Francisco Martínez-Jiménez David Dufour Gireesh Bogu 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
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