Exploring the time dependent structural rearrangements of SOX2 locus - - PowerPoint PPT Presentation

Marc A. Marti-Renom

Structural Genomics Group (ICREA, CNAG-CRG)

http://marciuslab.org http://3DGenomes.org http://cnag.crg.eu

Exploring the time dependent structural rearrangements of SOX2 locus during transdifferentiation

Resolution Gap

Marti-Renom, M. A. & Mirny, L. A. PLoS Comput Biol 7, e1002125 (2011)

μ 10 10 10 Resolution s Time 10 10 10 10 10 10 10 10 μm Volume 10 10 10 10 10 DNA length nt 10 10 10 10

Knowledge

IDM INM

Experiments Computation

A B C D Chr.18

• Pg

Hybrid Method

Baù, D. & Marti-Renom, M. A. Methods 58, 300—306 (2012).

Chromosome Conformation Capture

Dekker, J., Rippe, K., Dekker, M., & Kleckner, N. (2002). Science, 295(5558), 1306—1311. Lieberman-Aiden, E., et al. (2009). Science, 326(5950), 289—293.

Biomolecular structure determination 2D-NOESY data

Restraint-based Modeling

Baù, D. & Marti-Renom, M. A. Methods 58, 300—306 (2012).

Chromosome structure determination 3C-based data

• Pg

i i+2 i+1 i+n

FastQ files to Maps Map analysis Model building Model analysis

http://3DGenomes.org

Serra, F., Baù, D. et al. PLOS CB (2017)

Baù, D. et al. Nat Struct Mol Biol (2011) Umbarger, M. A. et al. Mol Cell (2011) Le Dily, F. et al. Genes & Dev (2014) Trussart M. et al. Nature Communication (2017) Cattoni et al. Nature Communication (2017)

previous applications...

Interplay: topology, gene expression & chromatin

Stadhouders, R., Vidal, E. et al. (2017) Nature Genetics, in press.

iPS cells

C/EBPa

Transcription factors dictate cell fate

Graf & Enver (2009) Nature

Transcription factors (TFs) determine cell identity through gene regulation Normal ‘forward’ differentiation Cell fates can be converted by enforced TF expression Transdifferentiation or reprogramming

Interplay: topology, gene expression & chromatin

Stadhouders, R., Vidal, E. et al. (2017) Nature Genetics, in press.

Reprogramming from B to PSC

Stadhouders, R., Vidal, E. et al. (2017) Nature Genetics, in press.

Bα

18h

PSC

C/EBPα

D2 D4 D6 D8 B cell

OSKM

GFP OSKM rtTA

Rosa26

TetO Oct4

+β-est. +Doxy.

expression (log2)

somatic

D2 D4 D6 D8 PSC Bα B D2 D4 D6 D8 PSC Bα B

Oct4 Nanog Sox2

4 8 4 8

Ebf1 0.2 0.4 0.6 0.8 1 1.2

D2 D4 D6 D8 PSC Bα B

expression (PSC=1)

Oct4 Nanog Sox2 B iPS

Gene expression (log2)

Birth of a TAD border upstream of Sox2

Stadhouders, R., Vidal, E. et al. (2017) Nature Genetics, in press.

Border strength

Sox2 overall topological changes

Stadhouders et al. Nature Genetics, in press

TADbit modeling of SOX2 from B cells Hi-C

Optimal IMP parameters lowfreq=0 , upfreq=1 , maxdist=200nm, dcutoff=125nm, particle size=50nm (5kb)

SOX2 SE

Hi-C maps of reprogramming from B to PSC

The SOX2 locus

Bα PSC D2 B cell D4 D6 D8

0.2 0.4 0.6 0.8 1 1.2

D2 D4 D6 D8 PSC Bα B

expression (PSC=1)

Oct4 Nanog Sox2

Hi-C maps of reprogramming from B to PSC

The SOX2 locus

How does these structural rearrangements interplay with the transcription activity? What are the main drivers of structural transitions?

Bα PSC D2 B cell D4 D6 D8

Models of reprogramming from B to PSC

The SOX2 locus

Bα PSC D2 B cell D4 D6 D8

Model assessment

Correlation Hi-C int Contacts

0.55 0.65

Spearman correlation between contact maps

0.5 0.55 0.6 0.65 0.7 0.75 0.8 B Bα D2 D4 D6 D8 ES

Cell stage

Models of B

Try to use reproducibility score! IN HiC-Spector! compare the first 20 eigenvectros

Model assessment

Correlation Hi-C int Contacts

0.5 0.55 0.6 0.65 0.7 0.75 0.8 B Bα D2 D4 D6 D8 ES

Cell stage

Models of B Models of Ba Models of D2 Models of D4 Models of D6 Models of D8 Models of ES 0.55 0.65

Spearman correlation between contact maps

Model assessment

Correlation Hi-C int Contacts

0.5 0.55 0.6 0.65 0.7 0.75 0.8 B Bα D2 D4 D6 D8 ES

Cell stage

Models of B Models of Ba Models of D2 Models of D4 Models of D6 Models of D8 Models of ES 0.55 0.65

Spearman correlation between contact maps

Model assessment

Correlation Hi-C int Contacts

0.5 0.55 0.6 0.65 0.7 0.75 0.8 B Bα D2 D4 D6 D8 ES

Cell stage

Models of B Models of Ba Models of D2 Models of D4 Models of D6 Models of D8 Models of ES

Hi-C interactions Models contacts

0.55 0.65

Spearman correlation between contact maps

TADdyn: from time-series Hi-C maps to dynamic restraints

The SOX2 locus

Bα PSC D2 B cell D4 D6 D8

Bα PSC D2 B cell D4 D6 D8

Harmonic HarmonicLowerBound

TADdyn: from time-series Hi-C maps to dynamic restraints

The SOX2 locus

Bα PSC D2 B cell D4 D6 D8

Harmonic HarmonicLowerBound

Transition Stable Vanishing Raising B -> B𝛽 18,612 6,984 7,290 B𝛽 -> D2 18,512 7,390 6,687 D2 -> D4 18,369 6,830 6,893 D4 -> D6 18,971 6,291 7,289 D6 -> D8 20,167 6,093 6,250 D8 -> ES 20,679 5,738 6,173

TADdyn: from time-series Hi-C maps to dynamic restraints

The SOX2 locus

SOX2 locus structural changes from B to PSC

Contacts

SOX2 SE

SOX2 locus structural changes from B to PSC

Contacts

SOX2 SE

34.00 34.25 34.50 34.75 35.00 35.25

Genomic coordinates (Mb)

• 1.2
• 1
• 0.8
• 0.6
• 0.4
• 0.2

0.2

Signifjcant insulation score

SOX2 locus structural changes from B to PSC

TAD borders

CTCF

34.00 34.25 34.50 34.75 35.00 35.25

Genomic coordinates (Mb)

• 1.2
• 1
• 0.8
• 0.6
• 0.4
• 0.2

0.2

Signifjcant insulation score

SOX2 locus structural changes from B to PSC

TAD borders

CTCF

34.00 34.25 34.50 34.75 35.00 35.25

Genomic coordinates (Mb)

50 100 150 200

Distance to Sox2 locus (nm)

SOX2 locus structural changes from B to PSC

Distance to regulatory elements

ATAC-Seq

34.00 34.25 34.50 34.75 35.00 35.25

Genomic coordinates (Mb)

50 100 150 200

Distance to Sox2 locus (nm)

SOX2 locus structural changes from B to PSC

Distance to regulatory elements

ATAC-Seq

0.2 0.4 0.6 0.8 1

Accessibility of Sox2 particle (a.u.)

SOX2 locus structural changes from B to PSC

Structural exposure

Exposure of Sox2 particle (a.u.)

0.2 0.4 0.6 0.8 1

Accessibility of Sox2 particle (a.u.)

SOX2 locus structural changes from B to PSC

Structural exposure

Exposure of Sox2 particle (a.u.)

SOX2 locus dynamics changes from B to PSC

SOX2 displacement

SOX2 locus dynamics changes from B to PSC

SOX2 displacement

SOX2 locus dynamics changes from B to PSC

SOX2 displacement

Two dimensional trajectories and area explored over 50s of the CCND1 locus recored before -E2 and after +E2 activation.

Germier ,T., et al, BIophys J. 113, 1383—1394 (2017).

A “cage” model for transcriptional activation

The Sox2 transcriptional activation is preceded by major structural rearrangements involving the formation of a small “cage” domain.

http://marciuslab.org http://3DGenomes.org http://cnag.crg.eu

Marco Di Stefano David Castillo Yasmina Cuartero Irene Farabella Silvia Galan Mike Goodstadt Francesca Mugianesi Julen Mendieta Juan Rodriguez François Serra Paula Soler Aleksandra Sparavier Yannick Spill

In collaboration with Ralph Stadhouders (Erasmus MC) and Thomas Graf (CRG)

.: Our current sponsors :.