Does color have structure? Modeling 3D domains of the fly genome. - - PowerPoint PPT Presentation

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does color have structure modeling 3d domains of the fly
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Does color have structure? Modeling 3D domains of the fly genome. - - PowerPoint PPT Presentation

Mar 02, 2024 182 likes •330 views

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

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SLIDE 1

Does color have structure? Modeling 3D domains of the fly genome.

Marc A. Marti-Renom

Genome Biology Group (CNAG) Structural Genomics Group (CRG)

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SLIDE 2

http://3DGenomes.org

i i+2 i+1 i+n

FastQ files to Maps Map analysis Model building Model analysis

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SLIDE 3

Structuring the COLORs of chromatin

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Fly Chromatin COLORs

Filion et al. (2010). Cell, 143(2), 212–224.

A C B

Principal component analysis Hidden Markov model

53 chromatin proteins

16000 16200 16400 16600 16800 17000

Position on chr2L (kb)

PC1 PC2 PC3

type

16000 16200 16400 16600 16800 17000

Position on chr2L (kb)

MRG15 SU(VAR)3−7 SU(VAR)3−9 HP6 HP1 LHR CAF1 ASF1 MUS209 TOP1 RPII18 SIR2 RPD3 CDK7 DSP1 DF31 MAX PCAF ASH2 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

Genes

+
  • −20
−10 10 20

PC1

−15 −10 −5 5 10 15

PC2

−15 −10 −5 5 10 15 −15 −10 −5 5 10

PC2 PC3

drawing by Guillaume Filion

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SLIDE 5

Functional COLORs

Hou et al. (2012). Molecular Cell, 48(3), 471–484. 50 ~1Mb regions 10 for each color

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SLIDE 6

Structural properties

50 1Mb regions. 10 enriched for each color. Accessibility (%) Density (bp/nm) Interactions Angle

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SLIDE 7

Structural COLORs

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Structural COLORs

*** *** *** *** **

Density (bp/nm) 80 100 120 140

***

Interactions 10 20 30 40 abs(angle) 40 80 120 160

** *** *

Accessibility (%) 20 40 60 80 100

***

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SLIDE 9

Structural COLORs

A

53 chromatin proteins

16000 16200 16400 16600 16800 17000

Position on chr2L (kb)

MRG15 SU(VAR)3−7 SU(VAR)3−9 HP6 HP1 LHR CAF1 ASF1 MUS209 TOP1 RPII18 SIR2 RPD3 CDK7 DSP1 DF31 MAX PCAF ASH2 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

type

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SLIDE 10

http://3DGenomes.org

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SLIDE 11
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SLIDE 12

http://gtpb.igc.gulbenkian.pt

November 23th-27th, Lisbon

Shameless promotion…

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SLIDE 13

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.
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SLIDE 14

Acknowledgments

Mike Goodstadt François Serra Davide Baù


 François le Dily Yasmina Cuartero Yannick Spill Marco di Stefano Francisco Martínez-Jiménez David Dufour Gireesh Bogu

http://marciuslab.org http://3DGenomes.org http://cnag.cat · http://crg.cat

Job Dekker

Program in Systems Biology Department of Biochemistry and Molecular Pharmacology University of Massachusetts Medical School Worcester, MA, USA

Kerstin Bystricky

Chromatin and gene expression Laboratoire de Biologie Moléculaire Eucaryote - CNRS Toulouse, France

Miguel Beato & Guillaume Filion

Gene Regulation, Stem Cells and Cancer Centre de Regulació Genòmica Barcelona, Spain