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Dynamics of gene activation
Nature Genetics (2018) 50 238—249 & unpublished
Photo by David Oliete - www.davidoliete.com
Marc A. Marti-Renom
CNAG-CRG · ICREA
Marco di Stefano CNAG-CRG Ralph Stadhouders, Enrique Vidal & Thomas Graf CRG
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 - - PowerPoint PPT Presentation
Dynamics of gene activation Marc A. Marti-Renom CNAG-CRG ICREA Nature Genetics (2018) 50 238249 & unpublished Photo by David Oliete - www.davidoliete.com Marco di Stefano Ralph Stadhouders, Enrique Vidal & Thomas Graf CNAG-CRG
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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
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Interplay: topology, gene expression & chromatin
Graf & Enver (2009) Nature Stadhouders, R., Vidal, E. et al. (2018) Nature Genetics
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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
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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
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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
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Models of reprogramming from B to PSC
The SOX2 locus
Bα PSC D2 B cell D4 D6 D8
http://3DGenomes.org
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TADdyn: from time-series Hi-C maps to dynamic restraints
The SOX2 locus
Bα PSC D2 B cell D4 D6 D8
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Bα PSC D2 B cell D4 D6 D8
Harmonic HarmonicLowerBound
TADdyn: from time-series Hi-C maps to dynamic restraints
The SOX2 locus
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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
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SOX2 locus structural changes from B to PSC
Contacts
SOX2 SE
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SOX2 locus structural changes from B to PSC
Contacts
SOX2 SE
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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
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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
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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
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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
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SOX2 locus structural changes from B to PSC
Chromatin Activity
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
B B D2 D4 D6 D8 ES 34.00 34.25 34.50 34.75 35.00 35.25
Genomic coordinates (Mb)
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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.)
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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.)
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SOX2 locus dynamics changes from B to PSC
SOX2 displacement
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SOX2 locus dynamics changes from B to PSC
SOX2 displacement
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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, (2017) BIophys J.
∆ t (s) 400 800 1,200 3D MSD (µm2) 0.2 0.4 0.6 0.8 1 Red-OFF Red-ON λ control dx (µm) 1 –1 –1 dy (µm) 1 1 –1 dz (µm) dx (µm) 1 –1 –1 dy (µm) 1 1 –1 dz (µm)
Transcription affects the 3D topology of the enhancer-promoted enhancing its temporal stability and is associated with further spatial compaction. Chen ,T., et al, (2018) Nat. Genetics
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Structural changes from B to PSC
Other 21 loci
Bα PSC D2 B cell D4 D6 D8 Bα PSC D2 B cell D4 D6 D8
CEBPa Ebf1 Mmp3 Mmp12 Tet2 Rad23b Rad23a Nanog Lmo7 Nos1ap
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Dynamics of gene activation
Trends in 21 loci
Dist to border (nm) Num AP
r=0.26 p= 0.003 r=0.31 p= 0.000 r=0.70 p= 0.000
log(RPKM+1) Num APD log(RPKM+1) Dist to TSS (nm) Embedding Convex vol Num A
r=-0.16 p= 0.070 r=-0.14 p= 0.121 r=0.03 p= 0.757 r=0.08 p= 0.397
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Dist to border (nm) Num AP
r=0.26 p= 0.003 r=0.31 p= 0.000 r=0.70 p= 0.000
log(RPKM+1) Num APD
Dynamics of gene activation
Trends in ~20 loci
Time and expression levels
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http://marciuslab.org http://3DGenomes.org @marciuslab @mamartirenom
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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.
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