DOI:.38/nc393 Nnog DAPI Nnog/DAPI c-jun DAPI c-jun/dapi c e Reltive expression to Gpdh mescs ( Feeder free) mescs ( Feeder) MEFs.5 MEFs ipscs ESCs..5 p=.24 p=.483 p=.22. JunB JunD Fos Fr Fr2 ATF2 ATF3 p=.78 d f Reltive expression to Gpdh.2 Nnog.5 c-jun..5. Reltive expression to Gpdh.6 JunB Fos Fr.4 Fr2.2..2. 4 6 8 2 4 2 3 4 5 6 ESCs: -LIF+RA (Dy).6 JunB Fos Fr.4 Fr2 4 6 8 2 4 mescs-->eb Formtion(Dy) g Reltive expression to Gpdh.5 c-jun.2.9.6.3.5h h 2h 4h 6h 2h Emryo development of Zer fish h Reltive expression to Gpdh%.2..8.6.4.2 c-jun 3 6 9 2 hescs(h)-->eb Formtion(Dy) Reltive expression to WT ESCs 2.5.5 Nnog c-jun +/+ ES Sox2 c-jun +/- ES# c-jun +/- ES2# Rex Esrr Sll4 c-jun -/- ES# c-jun -/- ES2# Dpp5 Dnmt3l Reltive expression to Gpdh..8.6.4.2. c-jun +/+ ES c-jun +/- ES# c-jun +/- ES2# c-jun -/- ES# c-jun -/- ES2# Nestin Sox Gt4 Gt6 Sox7 T Flk ESCs-->EB Formtion Dy6 Supplementry Figure Reltive expression of AP- fmily genes on ESCs nd somtic cells. () Immunostining of c-jun nd NANOG in MEFs nd ESCs. ESCs were cultured in feeder free (up pnel) or feeder (middle pnel) condition, respectively. Scre rs, μm. () Reltive expression of AP- fmily memers in MEFs, ipscs nd ESCs(Men±s.e.m., Twotiled, unpired t-test; n=3 independent experiments, Jun P=24, Fr P=.483, Fr P=.2). (c) Time course nlysis of AP- fmily memers during RA induced ESCs differentition y RT-qPCR. Mouse ESCs were cultured in mes+ra (μm). (Men±s.d., n=3 independent experiments). (d) Time course nlysis of the pluripotent genes nd AP- fmily memers during EB formtion y RT-qPCR (Men±s.d., n=3 independent experiments). (e-f) Time course nlysis of c-jun expression during emryo development of Zer fish (e), nd EB formtion of humn ESCs (f)(e-f, n=2 independent experiments). (g) Reltive expression of the pluripotent genes in WT nd Jun-deficient ESCs. Cells were culture in 2i+LIF medium (n=2 independent experiments). (h) Reltive expression of germ lyer mrkers during the EB genertion in WT nd Jun-deficient ESCs (Men±s.d., n=3 independent experiments). For source dt, see Supplementry Tle 3. WWW.NATURE.COM/NATURECELLBIOLOGY
OKS+Ctrl OKS+c-Jun OKSM+Ctrl OKSM+c-Jun /GFP Phse d Dys of Dox Tretment -GFP colonies + 3 Dy Dy6 OKSM+Ctrl OKSM+c-Jun 2 -Dox 6-8 4-8 2-8 -8-6 -4-2 -Dox mes+vc OKS+ c-jun TetOn icd 2 3 4 + -GFP colonies(dy2) c -GFP colonies(dy2) + 3 OKS mes+vc medium n=7 n=7 n=6 2 n=6 n=6 n=7 n=7 n=7 Mock VectorJunB Fos Fr Fr2 Atf2 Atf3 Supplementry Figure 2 The function of AP- fmily memers on somtic reprogrmming. () Phse nd GFP imges of ipsc colonies generted with OKS+Ctrl, OKS+c-Jun, OKSM+Ctrl, nd OKSM+c-Jun. Cells were culture in icd medium. Scle rs, 25 μm. () c-jun inhiit OKSM induced reprogrmming (Men±s.d., Two-tiled, unpired t-test, n=9 wells from 3 independent experiments,p<.) (c) The effect of AP- fmily memers to OKS induced reprogrmming in mes+vc medium (Men±s.d., Two-tiled, unpired t-test; n=7 wells (Mock, Vector, Fos, Fr, Fr2) or 6 wells (JunB, ATF2, ATF3) from 3 independent experiment, Vector-Fos p<., Vector-Fr2 P<., Vector-Fr P<.). (d) The effect of c-jun on reprogrmming t different time windows. OKS, Retrovirus; c-jun TetOn, lenti-virus crrying n inducile c-jun code sequence under the control of TetOn promoter. Reprogrmming cells were cultured in icd medium, Doxycycline (2μg/ml) ws dministrted t different time windows s indicted (n=4 wells from 2 independent experiments). The initil cell numer for reprogrmming is 2x 4 /well (p2) for OKS protocol, or.5x 4 /well (p2) for OKSM protocol. For source dt, see Supplementry Tle. 2 WWW.NATURE.COM/NATURECELLBIOLOGY
Reltive expression to Gpdh%.2.5..5. +Dox(h) Ets 4 8 2 24.5..5. Smd3 Tgf2.3.2.. 4 8 2 24 4 8 2 24 Reltive expression to Gpdh.6.4.2. +Dox(h) q=4.922 4 8 2 24..8.6.4.2. Rex q=6.844.2.5..5 Sll4 q=7.3. 4 8 2 24 4 8 2 24 Supplementry Figure 3 c-jun suppresses pluripotent genes nd ctives EMT reltive genes. () Time course nlysis the expression of EMT reltive genes Ets, Smd3 nd Tgf2 y RT-qPCR (men±s.d., Two-tiled, unpired t-test; n=3 independent experiments, Ets P=.4, Smd3 P=.6, Tgf2 P=.2). () Time course nlysis the expression of pluripotent relted genes, Rex nd Sll4 y RT-qPCR. c-jun TetOn ESCs were cultured in 2i+LIF medium with doxycycline (2μg/ml) tretment (men±s.d., One-wy ANOVA, Dunnett s multiple comprisons test; n=4 independent experiments, q=4.922, Rex q=6.844, Sll4 q=7.3). For source dt, see Supplementry Tle 6. WWW.NATURE.COM/NATURECELLBIOLOGY 3
4k 4k 4k Primers: Fold enrichment 4 3 2 Primers: IgG c-jun 2 3 4 5 6 7 8 9 4 Rex 3 2 2 3 4 5 6 7 8 9 4 3 2 Sll4 2 3 4 5 6 7 8 9 c-jun Input 5k 5k Ze2 2k 5 2k Dusp5 5k 5 5 5 5k Smd3 5k 5 5 5 c-jun Input Thy 5 Ets 5 Tgf2 5 Supplementry Figure 4 c-jun ctives EMT reltive genes directly. () The indings of c-jun on the, Rex nd Sll4 loci were determined y ChIP- PCR. Arrows indicte the predicted inding site contining the conserved AP inding motif (men±s.d., n=3 independent experiments). () ChIP-seq result of c-jun t EMT relted genes Ze2, Dusp5, Smd3, Thy, Ets nd Tgf2. For source dt, see Supplementry Tle 6. 4 WWW.NATURE.COM/NATURECELLBIOLOGY
c-jun 3 OKS-induced reprogrmming(mes+vc) c. -3. -256. 75-3. 7-3. 254-3. 274-3. 7-282 Bsic Motif Trnsctivtion domin Leucine-Zipper d. -3 q=2.35. -256. 75-3. 7-3 q=7.3. 254-3 q=3.9. 274-3. 7-282 Ctrl 2 4 6 8 -GFP + colonies(dy2). -63. 94-63. 77-63. 77-4. 5-63. 25-63. -4. -. -8 JDP2 63 Bsic Motif Leucine-Zipper OKS-induced reprogrmming(mes+vc). -63 q=7.9. 94-63. 77-63. 77-4. 5-63 q=.29. 25-63 q=8.639. -4. -. -8 Ctrl 2 4 6 + -GFP colonies(dy2) Supplementry Figure 5 c-jundn nd enhnce reprogrmming efficiency. () The construction of different c-jun mutnts. Bsic motif, Leucine-Zipper nd Trnsctivtion domin were shown s yellow rectngle, light green rectngle nd Red rectngle, respectively. () Effect of vrious c-jun mutnts on reprogrmming (men±s.d., One-wy ANOVA, Dunnett s multiple comprisons test; n=6 wells pooled from 3 independent experiments,.-3 q=2.35,.7-3 q=7.3,.254-3 q=3.9). (c) The construction of different mutnts. (d) Effect of vrious mutnts on reprogrmming (men±s.d., One-wy ANOVA, Dunnett s multiple comprisons test; n=6 wells pooled from 3 independent experiments,.-63 q=7.9,.5-63 q=.29,.5-63 q=8.639). For ipsc genertion, the initil cell numer ws 2x 4 /well (p2), -GFP + colonies were quntified t post-infection Dy2 in mes+vc medium. For source dt, see Supplementry Tle 6. WWW.NATURE.COM/NATURECELLBIOLOGY 5
Supplementry Figure 6 KSM/c-JunDN-iPSCs KS/c-JunDN-iPSCs NANOG DAPI REX DAPI 2 3 4 5 6 7 8 9 2 3 4 5 6 7 8 9 KSM/c-JunDN 2 3 4 5 6 7 8 9 X Y KSM/-iPSCs 2 3 4 5 2 3 4 5 6 7 8 9 X Y KS/-iPSCs 2 3 4 5 KS/c-JunDN KSM/ 6 7 8 9 2 3 4 5 6 7 8 9 X Y 6 7 8 9 2 3 4 5 6 7 8 9 X Y KS/ c Nnog MEFs ESCs KSM/c-JunDN KSM/ d Sox2 Klf4 c-myc Gpdh KSM/-Chimer Mice Brin Eyes Hert Bone Pncres Stomch C57 ES plsmid Ctrl H2O e KSM/c-Jun shrna-ipscs 2 3 4 5 6 7 8 9 2 3 4 5 6 7 8 9 X Y Supplementry Figure 6 c-jun ntgonists cn replce in somtic reprogrmming. () Norml kryotypes of representtive KSM/c-JunDN, KS/c-JunDN, KSM/, KSM/ ipscs colonies. () Immunofluorescence nlysis the expression of pluripotent mrkers of indicted ipscs colonies. Scre rs, μm. (c) Bisulfite genomic sequencing of the Nnog nd promoter regions in indicted ipscs colonies. (d) PCR nlysis show the KSM- ipsc colonies contriuted to ll three germ lyer in chimeric mice. (e) Norml kryotypes of representtive KSM/c-Jun shrna ipscs colonies. 6 WWW.NATURE.COM/NATURECELLBIOLOGY
regulted genes(fold chnge>2) n=284-2 2 Log2(fold chnge) Ctrl c-jundn 4 Cell numer( ) 5 4 3 2 Ctrl c-junwt c-jundn D D2 D3 D4 D5 Supplementry Figure 7 c-jun ntgonists regulted different genes with in MEFs. () Hetmp for RNA-seq dt from MEFs infected with control,,c-jundn nd. MEFs, cultured in %FBS for 72 hours fter virus infection,were hrvested for nlysis. () c-junwt promotes, ut c-jundn, nd inhiit, the prolifertion of MEFs. Cells were cultured in %FBS (men±s.d., n=3 wells, this experiment were repeted twice, one of the represented experiment ws showed). For source dt, see Supplementry Tle 5 () nd Supplementry Tle 6 (). WWW.NATURE.COM/NATURECELLBIOLOGY 7
c d GFP+ ips colonies 8 6 4 2 Sox2 Klf4 c-myc JhdmB Id Sll4 Glis Lrh icd icd+bmp Ctrl Id Id3 /Sox2 OKSM OKS OK OS 6F- 6F-2 ESCs MEFs H2O e O/S/Id O/Jhdm/Id 6F-iPSCs 2 3 4 5 6 7 8 9 2 3 4 5 6 7 8 9 X Y f GFP+ ips colonies Sox2 Klf4 c-myc Glis Lrh Id Gpdh 3 25 2 5 5 6F-Chimer Mice Brin Eyes Hert Bone +Id+Jhdm+ Ctrl Klf4 Sox2 Lrh Nnog Glis Sll4 Pncres Lung C57 ES Positive Ctrl H2O Supplementry Figure 8 non-ymnk fctors reprogrmming. () Id nd Id3 enhnce OS induced reprogrmming in icd or icd+bmp medium. The initil cell numer ws 2x 4 per well (p2), cells were cultured in icd or icd+bmp4 (ng/ml) medium. -GFP + colonies were quntitted t post-infection Dy6 (men±s.d., n=4 wells pooled from 2 independent experiments). () Phse nd GFP imges of ipsc colonies generted with /Sox2/Id nd /Jhdm/Id. Scle rs, 25 μm. (c) The replcement of y indicted genes. The initil cell numer ws 2x 4 per well (p2). Cells were cultured in icd medium. -GFP + colonies were quntitted t post-infection Dy6 (men±s.d., n=6 wells pooled from 2 independent experiments). (d) Retrovirl integrtions of 6F-iPSCs nlyzed y PCR with genomic DNA. (e) Norml kryotypes of representtive 6F ipscs. (f) Retrovirl integrtions of 6F-iPSCs nlyzed y PCR with genomic DNA. For source dt, see Supplementry Tle 3. 8 WWW.NATURE.COM/NATURECELLBIOLOGY
Originl uncropped western lots Figure c Figure e c-jun c-jun OCT4 GAPDH GAPDH Figure g Figure 2 Figure 5f c-jun 72 c-jun 72 c-jun 72 GAPDH GAPDH 72 GAPDH Supplementry Figure 9 Uncropped western lot imges WWW.NATURE.COM/NATURECELLBIOLOGY 9
Supplementry Tle legends Supplementry Tle List of the primers in this reserch. The primers of AP- fmily genes, pluripotent genes, MET reltive genes, germ lyer genes, c-jun trget genes, nd other primers for ChIP-PCR. Supplementry Tle 2 c-jun shrna. Sequence for constructing 3 c-jun shrna Supplementry Tle 3 Relted to Figure 3. Showing gene list in which gene hs low expression level in ESC nd high level in MEF, nd ws up regulted when overexpression Jun in ESCc, nd vice vers. Supplementry Tle 4 Relted to Figure 7. Showing gene list in which gene ws regulted on dy 3 during SKM + reprogrmming system, nd their expression pttern in SKM + JunDN nd SKM + reprogrmming systems. Supplementry Tle 5 Relted to Supplementry Figure 7. Showing gene list in which gene ws regulted when overexpression in MEF, nd their expression pttern when overexpression JunDN or in MEF. Supplementry Tle 6 Sttistics souse dt. WWW.NATURE.COM/NATURECELLBIOLOGY