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

Exploring the time dependent structural rearrangements of SOX2 locus during transdifferentiation Marc A. Marti-Renom Structural Genomics Group (ICREA, CNAG-CRG) http://marciuslab.org http://3DGenomes.org http://cnag.crg.eu

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 A Chr.18 -Pg B C D Computation

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.

Restraint-based Modeling Baù, D. & Marti-Renom, M. A. Methods 58, 300—306 (2012). Chromosome structure determination 3C-based data -Pg Biomolecular structure determination 2D-NOESY data

http://3DGenomes.org Serra, F., Baù, D. et al. PLOS CB (2017) FastQ files to Maps Map analysis i+1 i i+2 Model building i+n Model analysis

previous applications... 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)

Interplay: topology, gene expression & chromatin Stadhouders, R., Vidal, E. et al. (2017) Nature Genetics, in press.

Transcription factors dictate cell fate Graf & Enver (2009) Nature iPS cells C/EBPa 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. Oct4 GFP + β -est. +Doxy. OSKM TetO C/EBP α OSKM rtTA Rosa26 18h B cell B α D2 D4 D6 D8 PSC somatic B iPS Nanog Sox2 Oct4 1.2 Gene expression (log2) Ebf1 expression (PSC=1) expression (log2) 1 8 8 Sox2 0.8 Nanog 0.6 4 4 0.4 Oct4 0.2 0 0 0 B B α D2 D4 D6 D8 PSC B B α D2 D4 D6 D8 PSC B B α D2 D4 D6 D8 PSC

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 SE SOX2 Optimal IMP parameters lowfreq=0 , upfreq=1 , maxdist=200nm, dcutoff=125nm, particle size=50nm (5kb)

Hi-C maps of reprogramming from B to PSC The SOX2 locus Nanog Sox2 Oct4 1.2 expression (PSC=1) 1 0.8 0.6 0.4 0.2 0 B B α D2 D4 D6 D8 PSC B cell B α D2 D4 D6 D8 PSC

Hi-C maps of reprogramming from B to PSC The SOX2 locus B cell B α D2 D4 D6 D8 PSC How does these structural rearrangements interplay with the transcription activity? What are the main drivers of structural transitions?

Models of reprogramming from B to PSC The SOX2 locus B cell B α D2 D4 D6 D8 PSC

Model assessment Hi-C int Correlation Spearman correlation between contact maps Contacts 0.8 Try to use reproducibility score! 0.75 IN HiC-Spector! compare the first 20 0.65 eigenvectros 0.7 0.65 0.55 0.6 0.55 Models of B 0.5 B B α D2 D4 D6 D8 ES Cell stage

Model assessment Hi-C int Correlation Spearman correlation between contact maps Contacts 0.8 0.75 0.65 0.7 0.65 0.55 0.6 Models of B Models of Ba 0.55 Models of D2 Models of D4 Models of D6 Models of D8 Models of ES 0.5 B B α D2 D4 D6 D8 ES Cell stage

Model assessment Hi-C int Correlation Spearman correlation between contact maps Contacts 0.8 0.75 0.65 0.7 0.65 0.55 0.6 Models of B Models of Ba 0.55 Models of D2 Models of D4 Models of D6 Models of D8 Models of ES 0.5 B B α D2 D4 D6 D8 ES Cell stage

Model assessment Hi-C int Correlation Spearman correlation between contact maps Contacts Hi-C interactions 0.8 0.75 0.65 0.7 Models contacts 0.65 0.55 0.6 Models of B Models of Ba 0.55 Models of D2 Models of D4 Models of D6 Models of D8 Models of ES 0.5 B B α D2 D4 D6 D8 ES Cell stage

TADdyn: from time-series Hi-C maps to dynamic restraints The SOX2 locus B cell B α D2 D4 D6 D8 PSC

TADdyn: from time-series Hi-C maps to dynamic restraints The SOX2 locus B cell B α D2 D4 D6 D8 PSC Harmonic HarmonicLowerBound

TADdyn: from time-series Hi-C maps to dynamic restraints The SOX2 locus B cell B α D2 D4 D6 D8 PSC Harmonic HarmonicLowerBound Transition Stable Vanishing Raising B -> B 𝛽 18,612 6,984 7,290 B 𝛽 -> 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

SOX2 locus structural changes from B to PSC Contacts SE SOX2

SOX2 locus structural changes from B to PSC Contacts SE SOX2

SOX2 locus structural changes from B to PSC TAD borders CTCF 0.2 35.25 0 Signi fj cant insulation score -0.2 Genomic coordinates (Mb) -0.4 35.00 -0.6 -0.8 34.75 -1 -1.2 34.50 34.25 34.00

SOX2 locus structural changes from B to PSC TAD borders CTCF 0.2 35.25 0 Signi fj cant insulation score -0.2 Genomic coordinates (Mb) -0.4 35.00 -0.6 -0.8 34.75 -1 -1.2 34.50 34.25 34.00

SOX2 locus structural changes from B to PSC Distance to regulatory elements ATAC-Seq 200 35.25 Distance to Sox2 locus (nm) 150 Genomic coordinates (Mb) 35.00 100 34.75 50 0 34.50 34.25 34.00

SOX2 locus structural changes from B to PSC Distance to regulatory elements ATAC-Seq 200 35.25 Distance to Sox2 locus (nm) 150 Genomic coordinates (Mb) 35.00 100 34.75 50 0 34.50 34.25 34.00

SOX2 locus structural changes from B to PSC Structural exposure 1 Accessibility of Sox2 particle (a.u.) Exposure of Sox2 particle (a.u.) 0.8 0.6 0.4 0.2 0

SOX2 locus structural changes from B to PSC Structural exposure 1 Exposure of Sox2 particle (a.u.) Accessibility of Sox2 particle (a.u.) 0.8 0.6 0.4 0.2 0

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.

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