Posts Tagged ‘epigenomics’

9:20AM 11/12/2014 – 10th Annual Personalized Medicine Conference at the Harvard Medical School, Boston

REAL TIME Coverage of this Conference by Dr. Aviva Lev-Ari, PhD, RN – Director and Founder of LEADERS in PHARMACEUTICAL BUSINESS INTELLIGENCE, Boston

9:20 a.m. Panel Discussion – Genomic Technologies

Genomic Technologies

The greatest impetus for personalized medicine is the initial sequencing of the human genome at the beginning of this Century. As we began to recognize the importance of genetic factors in human health and disease, efforts to understand genetic variation and its impact on health have accelerated. It was estimated that it cost more than two billion dollars to sequence the first human genome and reduction in the cost of sequence became an imperative to apply this technology to many facets of risk assessment, diagnosis, prognosis and therapeutic intervention. This panel will take a brief historical look back at how the technologies have evolved over the last 15 years and what the future holds and how these technologies are being applied to patient care.

Genomic Technologies

Opening Speaker and Moderator:

George Church, Ph.D.
Professor of Genetics, Harvard Medical School; Director, Personal Genomics

Genomic Technologies and Sequencing

  • highly predictive, preventative
  • non predictive

Shareable Human Genomes Omics Standards

$800 Human Genome Sequence – Moore’s Law does not account for the rapid decrease in cost of Genome Sequencing

Genome Technologies and Applications

  • Genia nanopore – battery operated device
  • RNA & protein traffic
  • Molecular Stratification Methods – more than one read, sequence ties
  • Brain Atlas  – transcriptome of mouse brains
  • Multigenics – 700 genes: hGH therapies


  • vaccine
  • hygiene
  • age

~1970 Gene Therapy in Clinical Trials

Is Omic technologies — a Commodity?

  • Some practices will have protocols
  • other will never become a commodity



Sam Hanash, M.D., Ph.D. @MDAndersonNews

Director, Red & Charline McCombs Institute for Early Detection & Treatment of Cancer MD Anderson Cancer Center

Heterogeneity among Cancer cells. Data analysis and interpretation is very difficult, back up technology

Proteins and Peptides before analysis with spectrometry:

  • PM  – Immunotherapy approaches need be combined with other techniques
  • How modification in protein type affects disease
  • amplification of an aberrant protein – when that happens cancer developed. Modeling on a CHip of peptide synthesizer

Mark Stevenson @servingscience

Executive Vice President and President, Life Sciences Solutions
Thermo Fisher Scientific

Issues of a Diagnostics Developer:

  • FDA regulation, need to test on several tissues
  • computational environment
  • PCR, qPCR – cost effective
  • BGI – competitiveness

Robert Green, MD @BrighamWomens

Partners, Health Care Personalized Medicine — >>Disclosure: Illumina and three Pharmas

Innovative Clinical Trial: Alzheimer’s Disease, integration of sequencing with drug development

  • Population based screening with diagnosis
  • Cancer predisposition: Cost, Value, BRCA
  • epigenomics technologies to be integrated
  • Real-time diagnostics
  • Screening makes assumption on Predisposition
  • Public Health view: Phenotypes in the Framingham Studies: 64% pathogenic genes were prevalent – complication based in sequencing.

Questions from the Podium:

  • Variants analysis
  • Metastasis different than solid tumor itself – Genomics will not answer issues related to tumor in special tissues variability





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Jmjd3 and Cardiovascular Differentiation of Embryonic Stem Cells

Author and Curator: Larry H Bernstein, MD, FCAP


Curator: Aviva Lev-Ari, PhD, RN

This article is a presentation of recently published work on the basis for control of mesodermal and cardiovascular differentiation of embryonic stem cells, which has taken on increasing importance in the treatment of cardiovascular disease, with particular application to heart failure due to any cause, but with particular relevance to significant loss of myocardium, as may occur with acute myocardial infarction with more than 60% occlusion of the left anterior descending artery, near the osteum, with or without adjacent artery involvement, resulting in major loss of cardiac contractile force and insufficient ejection fraction. The article is of high interest and makes the following points:

  1. Ablation of Jmjd3 in mouse embryonic stem cells does not affect the maintenance of pluripotency and self-renewal
  2. Ablation of Jmjd3 in mouse embryonic stem cells compromised mesoderm and subsequent endothelial and cardiac differentiation 
  3. Jmjd3 reduces H3K27me3 marks at the Brachyury promoter and facilitates the recruitment of β-catenin
  4. β-catenin s critical for Wnt signal–induced mesoderm differentiation. 

Jmjd3 Controls Mesodermal and Cardiovascular Differentiation of Embryonic Stem Cells

K Ohtani, C Zhao, G Dobreva, Y Manavski, B Kluge, T Braun, MA Rieger, AM Zeiher and S Dimmeler

I The Institute of Cardiovascular Regeneration, Centre for Molecular Medicine, University of Frankfurt, Frankfurt, Germany (K.O., C.Z., Y.M., B.K., S.D.); Max-Planck-Institute for Heart and Lung Research, Bad Nauheim, Germany (G.D., T.B.); Department of Hematology/Oncology, Internal Medicine
II LOEWE Center for Cell and Gene Therapy, University of Frankfurt, Frankfurt, Germany (M.A.R.); and Department of Cardiology, Internal Medicine
III University of Frankfurt, Frankfurt, Germany (A.M.Z.).
This manuscript was sent to Benoit Bruneau, Consulting Editor, for review by expert referees, editorial decision, and final disposition.
Correspondence to Stefanie Dimmeler,  Institute of Cardiovascular Regeneration, Centre for Molecular Medicine, University of Frankfurt, Frankfurt, Germany. E-mail
 Circ Res. 2013;113:856-862;  


Rationale: The developmental role of the H3K27 demethylases Jmjd3, especially its epigenetic regulation at target genes in response to upstream developmental signaling, is unclear.

Objective: To determine the role of Jmjd3 during mesoderm and cardiovascular lineage commitment.

Methods and Results: Ablation of Jmjd3 in mouse embryonic stem cells does not affect the maintenance of pluripotency and self-renewal but compromised mesoderm and subsequent endothelial and cardiac differentiation. Jmjd3 reduces H3K27me3 marks at the Brachyury promoter and facilitates the recruitment of β-catenin, which is critical for Wnt signal–induced mesoderm differentiation.

Conclusions: These data demonstrate that Jmjd3 is required for mesoderm differentiation and cardiovascular lineage commitment. (Circ Res. 2013;113:856-862.)

  • Key Words: Brachyury protein ■ embryonic stem cells ■ epigenomics ■ Jmjd3 protein, mouse ■ mesodermn  –  Wnt signaling pathway


Post-translational modifications of histone proteins represent essential epigenetic control mechanisms that can either allow or repress gene expression.1 Trimethylation of H3K27 is mediated by Polycomb group proteins and represses gene expression.2 The JmjC domain–containing proteins, UTX (ubiquitously transcribed tetratricopeptide repeat, X chromosome) and Jmjd3 (jumonji domain–containing protein 3, Kdm6b), not only act as demethylases to remove the repressive H3K27me3 marks, but also exhibit additional demethylase-independent functions.3–6 Jmjd3 is induced and participates in Hox gene expression during development,7 neuronal differentiation,8,9 and inflammation,5,10–12 and recent data suggest that Jmjd3 inhibits reprogramming by inducing cellular senescence.13 Because previous studies suggest that H3K27me3 regulates endothelial gene expression in adult proangiogenic cells,14 we addressed the function of Jmjd3 in cardiovascular lineage differentiation of embryonic stem cells (ESCs).


A detailed description of the experimental procedure is provided in the Online Data Supplement.  The online-only Data Supplement is available with this article at 113.302035/-/DC1.

Cell Culture

Plasmid Construction and Stable Transfection

The full-length Jmjd3, the mutants, and Brachyury were cloned into pEF1 vector (Invitrogen). The linearized plasmids were transfected in Jmjd3−/− ESCs using the Amaxa nucleofection system (Lonza).

Chromatin Immunoprecipitation

Nonstandard Abbreviations and Acronyms

EB                       embryoid body

ESC                    embryonic stem cell

WI                        wild type


Jmjd3 knockout ESCs were generated by 2 rounds of gene targeting (Online Figure IA and IB). We obtained 7 Jmjd3−/− ESC clones, which lacked Jmjd3 mRNA and protein expression. All of the clones showed slightly increased global H3K27me3, but the expression of pluripotency genes, the morphology, the growth kinetic, and survival was indistinguishable from wild-type (WT) ESCs (Figure 1A–1C; Online Figure IC–IF). No significant changes of repressive H3K27me3 marks at the promoters of pluripotency genes were detected in Jmjd3−/− compared with WT ESCs (Online Figure IH). When

  • spontaneous differentiation was induced by leukemia inhibitory factor withdrawal,
  • Jmjd3 expression increased in WT ESCs (Figure 1D).
  • EBs derived from Jmjd3−/− ESCs were slightly smaller in size compared with WT EBs (Figure 1E).

mRNA expression profiling of Jmjd3−/− and WT ESC clones at day 4 after induction of differentiation showed

  • a distinct expression pattern of lineage-specific genes (Online Figure IIA).

Gene ontology functional analyses revealed a significant repression of genes that are involved in mesoderm development (Figure 1F; Online Figure IIB). Moreover,

  • repressed gene sets in Jmjd3−/− EBs were shown to be related to cardiac and vascular development,
  • consistent with impaired mesoderm differentiation (Figure 1F; Online Figure IIB).

Validation of the microarray results showed a similar reduction of pluripotency gene expression after leukemia inhibitory factor withdrawal in Jmjd3−/− compared with WT ESCs (Figure 1G). However, depletion of Jmjd3 substantially compromised the induction of mesodermal genes (Figure 1G). Especially, the pan-mesoderm marker, Brachyury, and the early mesoendoderm marker, Mixl1, were profoundly increased at day 4 of differentiation in WT ESCs, but not in Jmjd3−/− ESCs (Figure 1G). Moreover, the mesoendodermal marker, Eomes, and endodermal markers, such as Sox17 and FoxA2, were significantly suppressed, which is consistent with a very recent study showing that Jmjd3 is required for endoderm differentiation.19 Ectodermal markers were not significantly changed in Jmjd3−/− ESCs when using the spontaneous differentiation protocol (Figure 1G).

Because Jmjd3−/− ESCs showed a prominent inhibition of mesodermal markers after leukemia inhibitory factor withdrawal, we next questioned whether this phenotype can also be observed when directing differentiation of mesoderm using 2 different protocols. Consistent with our findings,

  • Jmjd3−/− ESCs showed a reduced expression of mesodermal marker genes when using the protocol for mesoderm differentiation described by Gadue et al20 (data not shown). Moreover,
  • mesoderm differentiation was significantly suppressed when Jmjd3−/− ESCs were cultured on OP9 stromal cells, which support mesodermal differentiation21 (Figure 2A).

Whereas WT ESCs showed the typical time-dependent increase in Brachyury+ cells, Jmjd3−/− ESCs generated significantly less Brachyury+ mesodermal cells (Figure 2B). Moreover, fluorescence activated cell sorting analysis revealed that fetal liver kinase (Flk)1+ vascular endothelial-cadherin−mesodermal cells were generated in WT ESCs but were reduced when Jmjd3−/− ESCs were used (Figure 2C). Interestingly, the formation of vascular endothelial-cadherin+ Flk+ cells was also significantly reduced by 96±1% and 88±3% in the 2 Jmjd3−/− ESC clones compared with WT ESCs (P<0.01), prompting us to explore the role of Jmjd3 in vascular differentiation further.
Endothelial differentiation was induced by a cytokine cocktail18 and was associated with a significant upregulation of Jmjd3 expression (Online Figure IIIA). Jmjd3−/− ESCs showed a marked reduction of endothelial differentiation as evidenced by

  • significantly reduced mRNA levels of the endothelial marker vascular endothelial-cadherin and endothelial-specific receptor tyrosine kinase Tie2 (Figure 3A).
  • The formation of endothelial marker expressing vascular structures after induction of endothelial differentiation was abolished in Jmjd3−/− ESCs (Figure 3B; Online Figure IIIB).
  • The impaired endothelial differentiation of Jmjd3−/− cells was partially rescued by the overexpression of Brachyury (Online Figure IIIC and IIID), suggesting that the inhibition of mesoderm formation, at least in part, contributes to the impaired endothelial commitment.

Because genes involved in heart development and morphogenesis were significantly downregulated in Jmjd3−/− ESCs on differentiation (Figure 1F; Online Figure II), we additionally determined the capacity of Jmjd3−/− ESCs to generate cardio-myocytes by inducing cardiac differentiation.17

  • Expression of cardiac progenitor cell markers, Mesp1 and Pdgfra, was inhibited in Jmjd3−/− ESCs compared with WT ESCs (Figure 3C).

Moreover, after plating on gelatin-coated dishes,

  • the Jmjd3−/− ESCs showed an impaired formation of EBs and
  • only 20% of EBs were contracting (Figure 3D).

Consistently, expression of the cardiac transcription factor Mef2c, the marker of working myocardium Nppa, and cardiac structural proteins TnT2 and α-myosin heavy chain were downregulated in Jmjd3−/− ESCs (Figure 3E and 3F; Online Figure IIIE).

  • Next, we addressed whether the impaired mesoderm differentiation observed in Jmjd3−/− ESCs might be mediated by an increase of repressive H3K27me3 marks at the promoters of developmental regulators. Of the various promoters studied, only Brachyury and Mixl1 showed a significant augmentation of H3K27me3 marks in Jmjd3−/− ESCs on differentiation (Figure 4A; Online Figure IVA). Consistently, the recruitment of RNA polymerase II to the transcription start sites of the promoters of Brachyury and Mixl1 was also significantly reduced (Online Figure IVC). In addition, Jmjd3 deficiency repressed polymerase II recruitment to the Flk1 and Mesp1 promoter but the inactivation of these promoters was not associated with changes in H3K27me3 marks (Figure IVA and IVC). These data were confirmed using protocols
  • that induce mesoderm differentiation by addition of Wnt3a (data not shown).20 Under these conditions,
  • Jmjd3−/− ESCs showed a 1.81±0.23-fold (P<0.05) enrichment of H3K27me3 marks at the Brachyury promoter compared with WT ESCs.

To determine whether the demethylase activity of Jmjd3 controls Brachyury expression by reducing repressive H3K27me3 marks during differentiation, we overexpressed full-length Jmjd3, the carboxyl-terminal part, including the JmjC-domain (cJmjd3: amino acids, 1141–1641), and a carboxyl-terminal mutant construct, which includes a point mutation (cJmjd3H1388A) to inactivate demethylase activity. Overexpression of full-length Jmjd3 and the carboxyl-terminal part of Jmjd3 in Jmjd3−/− ESCs partially rescued the expression of Brachyury on differentiation (Figure 4B and 4C). Howver, the inactive carboxyl-terminal part of Jmjd3 failed to rescue the impaired Brachyury expression in Jmjd3−/− ESCs (Figure 4C), suggesting that

  • the demethylase activity of Jmjd3 is required for the activation of the Brachyury promoter.

Because canonical Wnt signaling regulates the expression of Brachyury during development22,23 and Wnt/B-catenin–dependent genes were suppressed in Jmjd3−/− EBs compared with WT EBs (Online Figure V), we further explored whether Jmjd3 might interact with B-catenin signaling. Indeed,

  • B-catenin recruitment to the Brachyury promoter was significantly suppressed in Jmjd3−/− ESCs (Figure 4D) and
  • was rescued by Jmjd3 overexpression (Figure 4E).

Similar results were obtained when using the protocol for direct mesoderm differentiation described by Gadue et al20 (data not shown). To determine whether Jmjd3 might interact with B-catenin, we performed coimmunoprecipitation studies and showed that

  • Jmjd3 interacts with B-catenin in human embryonic kidney 293 cell and differentiated EBs (Figure 4F; Online Figure VI).

To assess a direct effect of Jmjd3 on B-catenin responsive promoter activity, we used a luciferase reporter assay. Coexpression of lymphoid enhancer binding factor 1 and the constitutive active form of B-catenin harboring a nuclear localization signal resulted in the activation of lymphoid enhancer binding factor 1 luciferase reporter activity in WT ESCs, but

  • this transcriptional activation was markedly impaired in Jmjd3−/− ESCs (Figure 4G).


The data of the present study demonstrate that

  • deletion of Jmjd3 in ESCs does not affect self-renewal but
  • significantly impairs the formation of mesoderm on induction of differentiation.

The findings that Jmjd3 is not required for ESC maintenance are consistent with the dispensability of the Polycomb complex and the related demethylase UTX for self-renewal.1

  • The requirement of Jmjd3 for mesoderm differentiation was shown in spontaneous differentiation, as well as
  • when more specifically inducing mesoderm differentiation by the OP9 coculture system or under serum-free conditions followed by Wnt3a stimulation.
  • Jmjd3 deficiency profoundly suppressed the expression of Brachury, which is essential for mesoderm differentiation.

In the absence of Jmjd3,

  • repressive H3K27me3 marks at the Brachyury promoter are significantly increased, and
  • the recruitment of B-catenin, which is a prerequisite for Wnt-induced mesoderm differentiation, is impaired.
  • In addition, Jmjd3 is interacting with B-catenin and is contributing to B-catenin– dependent promoter activation.

This is consistent with the recent findings that cofactors can form a complex with B-catenin/ lymphoid enhancer binding factor 1

  • at Tcf/lymphoid enhancer binding factor 1 binding sites
  • at B-catenin–dependent promoters and
  • synergize with canonical Wnt signaling.24

Interestingly, a demethylase-independent regulation of B-catenin–dependent gene expression was recently described for UTX.25 However, our data provide evidence that

  • Brachyury expression in Jmjd3−/− ESCs is only rescued by catalytically active Jmjd3, which has maintained the demethylase activity.

On the basis of these findings, we propose a model in which Jmjd3 is recruited to the Brachury promoter to remove repressive H3K27me3 marks and on Wnt stimulation additionally promotes B-catenin–dependent promoter activation (Figure 4H). Such a model is similar to the recently described function of Jmjd3 in endoderm differentiation, whereby Jmjd3 associates with Tbx3 and is recruited to the poised promoter of Eomes, to mediate chromatin remodeling allowing subsequent induction of endoderm differentiation induced by activin A.19 The present study additionally demonstrates that

  • Jmjd3 contributes to endothelial and cardiac differentiation.
  • endothelial differentiation was profoundly impaired,

a finding that is consistent with previous findings in adult progenitor cells, showing a high H3K27me3 at endothelial genes.14 The relatively modest inhibition of cardiomyocyte differentiation in Jmjd3−/−  ESCs may be, in part, explained by a compensatory effect of UTX which was shown to regulate cardiac development.26 Together, our study provides first evidence for the regulation of B-catenin–dependent Wnt target genes by Jmjd3 during differentiation of ESCs.  However, the in vivo relevance of the findings is still unclear. The Jmjd3−/− mice that we have generated out of the ESCs, used in the present study, showed embryonic lethality before E6.5, suggesting a crucial role of Jmjd3 in early embryonic development.


Novelty and Significance

What Is Known?

•            Cell fate decisions require well-controlled changes in gene expression that are tightly controlled by epigenetic modulators.

•            The post-transcriptional modifications of histone proteins epigeneti-cally regulate gene expression.

•            Trimethylation of lysine 27 at histone K3 (H3K27me3) silences gene expression and can be reversed by the demethylase Jmjd3.

What New Information Does This Article Contribute?

•            The histone demethylase Jmjd3 is required for mesoderm differentiation and cardiovascular lineage commitment of mouse embryonic stem cells.

•            This effect is partially mediated by a silencing of the mesodermal regulator Brachyury.

•            Ablation of Jmjd3 further reduces β-catenin recruitment to the Brachyury promoter, which interferes with Wnt signaling that is required for proper mesoderm differentiation.

The differentiation of stem cells to specific lineages requires a well-defined modulation of gene expression programs, which is often controlled by epigenetic mechanisms. Although several epi-genetically active enzymes and complexes have been described, the function of the histone demethylase Jmjd3 for cardiovascu¬lar lineage commitment was unknown. Using mouse embryonic stem cells as a model, we now show that the demethylase Jmjd3 is required for mesoderm differentiation and for the differentia¬tion of embryonic stem cells to the vascular and cardiac lineage. We further identified the mechanism and showed that ablation of Jmjd3 resulted in a silencing of the Brachyury promoter that is associated with an increase in H3K27me3 marks. In addition, Jmjd3 was shown to facilitate the recruitment of β-catenin to the Brachyury promoter, which contributes to the Wnt-dependent ac-tivation of mesoderm differentiation. Together these data describe a novel epigenetic mechanism that controls cell fate decision.

Supplemental Methods

Generation of Jmjd3 knockout ES cell lines

Mouse genomic DNA encompassing the murine Jmjd3 gene region were isolated by PCR amplification and used to generate short (1.6kb) and long (6.2kb) arms of homology. The targeting vectors were constructed by inserting a loxP site together with an FRT flanked neomycin selection cassette within the intron 5 and a single distal loxP within the intron 3. This targeting strategy results in the deletion of 600bp coding sequences encoding for the ATG methionine codon and produces a frame shift of JmjC domain existing exon 19-21 required for Jmjd3 demethylase activity. The targeting vector was electroporated in 129Sv ES cells. G418 resistant ES cell clones were screened for homologous recombination by PCR analysis and targeting was verified by Southern blot analysis. Homozygous Jmjd3lox/lox ES cells were generated by electroporation of heterozygous Jmjd3lox/+ ES cells with the same targeting vector as above except that the neomycin resistance gene was replaced by puromycin gene using the Nucleofector (Lonza). Double-allele-recombined ES cells were selected for puromycin (1.3µg/mL, Invitrogen). Correct targeting of homozygous Jmjd3lox/lox ES clones were determined by PCR. To obtain Jmjd3-/- ES cells, Jmjd3lox/lox ES cells were electroporated with Cre-recombinase plasmid vector and loss of targeting cassettes was evaluated by loss of resistance of G418 and puromycin. Correct targeting of homozygous Jmjd3-/- ES cells was determined by PCR.

Reporter gene assays

3xLEF1 reporter plasmid, LEF1 expression construct and NLS-13-catenin were kind gifts from Rudolf Grosschedl. Mouse ES cells were seeded (5×104) on gelatin coated 24-well. After 24 hours of plating, 3xLEF1 reporter plasmid, LEF1, and NLS-13-catenin plasmids were transiently transfected with FugeneHD (Promega). 13-galactosidase plasmid was co-transfected for normalization of transfection efficiency. Each group was transfected in triplicates. 48 hours after transfection, cells were harvested. Cell lysis and luciferase assay were performed following the protocol of Luciferase Reporter Assay System (Promega). 13-galactosidase assays were performed using CPRG (Sigma) as substrate and the absorbance at 600nm was measured. Luciferase activity was normalized to 13-galactosidase activity.

Manuscript References

  1. Shen, X. et al. EZH1 mediates methylation on histone H3 lysine 27 and complements EZH2 in maintaining stem cell identity and executing pluripotency. Mol Cell 32, 491-502 (2008).
  2. Sargent, C.Y., Berguig, G.Y. & McDevitt, T.C. Cardiomyogenic differentiation of embryoid bodies is promoted by rotary orbital suspension culture. Tissue engineering. Part A 15, 331­342 (2009).
  3. Gadue, P., Huber, T.L., Paddison, P.J. & Keller, G.M. Wnt and TGF-beta signaling are required for the induction of an in vitro model of primitive streak formation using embryonic stem cells. Proc Natl Acad Sci U S A 103, 16806-16811 (2006).
  4. Ohtani, K. et al. Epigenetic regulation of endothelial lineage committed genes in pro-angiogenic hematopoietic and endothelial progenitor cells. Circ Res 109, 1219-1229 (2011).
  5. Yamaguchi, T.P., Takada, S., Yoshikawa, Y., Wu, N. & McMahon, A.P. T (Brachyury) is a direct target of Wnt3a during paraxial mesoderm specification. Genes Dev 13, 3185-3190 (1999).

Selected Figures   (Figure may not be shown)

Figure 1. Aberrant differentiation of Jmjd3−/− embryonic stem cells (ESCs). A, Quantitative polymerase chain reaction analysis of Jmjd3 in wild-type (WT) and Jmjd3−/− ESCs. B, Western blot analysis of Jmjd3 and Histone marks in WT and Jmjd3−/− ESCs. Histone H3 is used as a loading control. Quantification is shown in the right (n=3–5). C, Top, Morphology of WT and Jmjd3−/− ESCs on feeder cells. Bottom, Alkaline phosphatase staining of undifferentiated WT and Jmjd3−/− ESCs. D, Western blot analysis of Jmjd3 and Oct4 in WT ESCs during differentiation. α-Tubulin is used as a loading control. E, Bright field image of embryoid bodies at day 5. Scale bar, 200 μm. F, Gene ontology analysis for >2-fold repressed genes in Jmjd3−/− ESCs compared with WT ESCs 4 days after differentiation. The most highly represented categories are presented with ontology terms on the y-axis and P values for the significance of enrichment are shown on the x-axis. G, Gene expression changes of pluripotency and lineage-specific markers in WT and Jmjd3−/− ESCs after spontaneous differentiation by leukemia inhibitory factor withdrawal (n=4). Flk indicates fetal liver kinase.

Figure 2. Jmjd3−/− embryonic stem cells (ESCs) show an impaired ability to differentiate into mesoderm. A, Schematic illustration of the experimental protocol. Differentiation of ESCs (wild-type [WT] and 2 Jmjd3−/− ESCs clones) on OP9 feeder cells was analyzed. B, Left, Representative fluorescence activated cell sorting (FACS) plots showing Brachyury expression of ESC-derived cells. Right, Quantification of FACS analyses (n=3). C, Left, Representative FACS plots showing fetal liver kinase 1 (Flk1) and vascular endothelial-cadherin expression on ESC-derived cells. Right, Quantification of FACS analyses in Flk1+ cells (n=3).

Figure 3. Jmjd3 is required for embryonic stem cells (ESCs) differentiation to the endothelial and cardiac lineage. A, mRNA expression of endothelial markers at day 7 of endothelial differentiation (n=3). B, Platelet endothelial cell adhesion molecule (Pecam)-1 staining of wild-type (WT) and Jmjd3−/− ESCs at day 8 of endothelial differentiation. Phalloidin is used to stain F-actin. Nuclei are stained with 4′,6-diamidino-2-phenylindole (blue). Scale bar, 20 pm. C, Gene expression of cardiac progenitor markers at day 3 of cardiac differentiation. D, Number of beating embryoid bodies (EBs) at day 10 of cardiac differentiation (n=8). E, Gene expression of cardiac markers at day 7 of cardiac differentiation (n=6). F, α-Myosin heavy chain staining of WT and Jmjd3−/− ESCs at day 9 of cardiac differentiation. Nuclei are stained with Hoechst (blue). Scale bar, 20 pm. *P<0.05, **P<0.01, and ***P<0.001

Online Figure I. Generation and characterization of Jmjd3 ESCs  (A) Targeting strategy to generate Jmjd3 mutant ESCs by homologous recombination. Primers used for PCR are shown. (B) Genotyping of Jmjd3 ESCs by using 2 different primers. (C) Oct4 and Nanog staining in WT and Jmjd3−’− ESCs. Scale bar indicates 10µm. (D) Expression of Oct4 and Nanog in WT and Jmjd3 ESCs. Data are presented as fold changes compared with day 0 WT ESCs. N=6. (E) Tunel staining (green) of WT and Jmjd3 ESCs. Nuclei are stained with Hoechst (blue). Scale bar indicates 20µm. (F) Growth curves of WT and Jmjd3 ESCs. N=6-8. (G) H3K27me3 staining in WT and Jmjd3 ESCs. Nuclei are stained with Hoechst (blue). Scale bar indicates 20µm. (H) ChIP assay of undifferentiated WT and Jmjd3 ESCs for H3K27me3. ChIP enrichments are normalized to Histone H3 density and represented as fold change relative to WT. N=3. Data represent mean ± SEM

Online Figure II. Jmjd3 ESCs show an impaired mesoderm differentiation. (A) Microarray gene expression heat map depicting expression of representative pluripotency and lineage markers 4 days after differentiation in Jmjd3 ESCs versus WI ESCs. Coloring illustrates log2 fold changes between Jmjd3 ESCs and WI ESCs. Green and red colors represent down-regulation and up-regulation, respectively. (B) Gene ontology analysis for more than 2-fold altered genes in Jmjd3 ESCs compared to WI ESCs 4 days after differentiation. Red and green colors represent down-regulation and up-regulation, respectively.

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