Dynamics of gene activation Marc A. Marti-Renom CNAG-CRG ICREA - PowerPoint PPT Presentation

Dynamics of gene activation Marc A. Marti-Renom CNAG-CRG · ICREA Nature Genetics (2018) 50 238—249 & unpublished Photo by David Oliete - www.davidoliete.com

Marco di Stefano Ralph Stadhouders, Enrique Vidal & Thomas Graf CNAG-CRG CRG

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 Graf & Enver (2009) Nature Stadhouders, R., Vidal, E. et al. (2018) Nature Genetics

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?

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)

Models of reprogramming from B to PSC The SOX2 locus http://3DGenomes.org 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

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 Chromatin Activity 35.25 Genomic coordinates (Mb) 35.00 34.75 34.50 34.25 34.00 B B D2 D4 D6 D8 ES B Ba D2 D4 D6 D8 PSC A 9 6 7 13 13 22 48 AP 4 1 4 4 4 13 23 APD 3 1 1 1 4 10 15

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 Accessibility of Sox2 particle (a.u.) Exposure 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 Red-OFF Red-ON λ control 1 3D MSD ( µ m 2 ) 0.8 1 dz ( µ m) 1 0 dz ( µ m) 0 –1 0.6 –1 1 1 dy ( µ m) 0 0 1 –1 1 –1 dx ( µ m) 0 dy ( µ m) 0.4 0 –1 dx ( µ m) –1 0.2 0 400 800 1,200 ∆ t (s) Two dimensional trajectories and area Transcription affects the 3D topology of explored over 50s of the CCND1 the enhancer-promoted enhancing its locus recored before -E2 and after +E2 temporal stability and is associated activation. with further spatial compaction. Germier ,T., et al, (2017) BIophys J. Chen ,T., et al, (2018) Nat. Genetics

Structural changes from B to PSC Other 21 loci B cell B α B cell B α D2 D4 D6 D8 PSC D2 D4 D6 D8 PSC Nanog CEBPa Lmo7 Ebf1 Nos1ap Rad23a Rad23b Mmp3 Mmp12 Tet2

Dynamics of gene activation Trends in 21 loci r=0.70 p= 0.000 r=0.31 p= 0.000 r=0.26 p= 0.003 log(RPKM+1) Num APD Num AP Dist to border (nm) r=0.08 p= 0.397 r=0.03 p= 0.757 r=-0.14 p= 0.121 r=-0.16 p= 0.070 log(RPKM+1) Num A Convex vol Embedding Dist to TSS (nm)

Dynamics of gene activation Trends in ~20 loci r=0.70 p= 0.000 r=0.31 p= 0.000 r=0.26 p= 0.003 log(RPKM+1) Num APD Num AP Dist to border (nm) Time and expression levels

http://marciuslab.org @marciuslab http://3DGenomes.org @mamartirenom David Castillo Yasmina Cuartero Marco Di Stefano Irene Farabella Silvia Galan Mike Goodstadt Rodrigo Jara Maria Marti-Marimon Francesca Mugianesi Julen Mendieta Juan Rodriguez Paula Soler Aleksandra Sparavier In collaboration with Ralph Stadhouders, Enrique Vidal, and Thomas Graf. .: Our current sponsors :.

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