Comparison of the expression of Core and Myc module genes in EpiSCs and ESCs.

<div><p>(A) Average gene expression values (log₂) of Core, Myc, and PRC module genes in EpiSCs using values from ESCs as references. Data from 99 Core, 426 Myc, and 474 PRC module genes deposited in GEO under GSE30056 were used for the analyses. Data from 12 Core (111 genes), 77 Myc (503 genes), and 86 PRC (560) module genes are not available in the deposited data sets.</p> <p>(B) Comparison of the expression of individual Core, Myc, and PRC module genes between ESCs and EpiSCs. Left, middle, and right scatter plots show the expression values of individual Core, Myc, and PRC module genes, respectively, in ESCs and EpiSCs. Red and blue spots indicate genes with expression levels that are higher or lower by more than 2-fold in EpiSCs compared with those in ESCs, respectively. Gene symbols corresponding to red and blue are listed in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0083769#pone.0083769.s011" target="_blank">Table S2</a>. The variance value was calculated and is shown for each scatter plot.</p> <p>(C) Left, middle, and right scatter plots show the expression values of the selected Core, Myc, and Core module genes (listed in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0083769#pone.0083769.s012" target="_blank">Table S3</a>), respectively, in ESCs and EpiSCs. Red and blue spots indicate as described in B. The variance value was calculated and is shown for each scatter plot.</p></div

Highly specific activation of Core and Myc modules and repression of the PRC module in pluripotent cells.

<p>Publicly available DNA microarray data for 20 different tissue/somatic cell and stem cell types were obtained from the NCBI GEO database. To compare the same sets of genes used in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0083769#pone-0083769-g001" target="_blank">Figures 1</a> and <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0083769#pone-0083769-g002" target="_blank">2</a>, data obtained using the same DNA microarray platform (Mouse Expression Array 430 platform, Affymetrix) by Hayashi et al. [<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0083769#B29" target="_blank">29</a>] were selected from the database. Average gene expression values (log₂) of Core (upper panel), Myc (meddle panel), and PRC (lower panel) modules in each sample were calculated using those in ESCs as references. The data were aligned in an ordered fashion based on the value of average Myc module gene expression in which a sample showing the highest score, i.e., gPSC, was put at the left end of graph. The accession numbers of the obtained DNA microarray data are listed in the Materials and Methods. Data from germline stem cells and their derivatives, somatic stem cells, tissues, terminally differentiated hematopoietic cells and EpiSCs/EpiLCs are indicated by pink, blue, green, red, and gray bars, respectively, in the graph.</p

Striking Similarity in the Gene Expression Levels of Individual Myc Module Members among ESCs, EpiSCs, and Partial iPSCs

<div><p>Predominant transcriptional subnetworks called Core, Myc, and PRC modules have been shown to participate in preservation of the pluripotency and self-renewality of embryonic stem cells (ESCs). Epiblast stem cells (EpiSCs) are another cell type that possesses pluripotency and self-renewality. However, the roles of these modules in EpiSCs have not been systematically examined to date. Here, we compared the average expression levels of Core, Myc, and PRC module genes between ESCs and EpiSCs. EpiSCs showed substantially higher and lower expression levels of PRC and Core module genes, respectively, compared with those in ESCs, while Myc module members showed almost equivalent levels of average gene expression. Subsequent analyses revealed that the similarity in gene expression levels of the Myc module between these two cell types was not just overall, but striking similarities were evident even when comparing the expression of individual genes. We also observed equivalent levels of similarity in the expression of individual Myc module genes between induced pluripotent stem cells (iPSCs) and partial iPSCs that are an unwanted byproduct generated during iPSC induction. Moreover, our data demonstrate that partial iPSCs depend on a high level of c-Myc expression for their self-renewal properties.</p> </div

Most Myc module members maintain constant levels of expression in naïve and primed human iPSCs.

<div><p>(A) Average gene expression values (log₂) of Core, Myc, and PRC module genes in primed human iPSCs using those in human iPSCs converted to a naïve state as references <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0083769#B33" target="_blank">33</a>. Data from 69 Core, 321 Myc, and 423 PRC module genes deposited in GEO under GSE21222 were used for the analyses. Data from six Core, 34 Myc, and 28 PRC module genes are not available in the deposited data sets.</p> <p>(B) Comparison of the expression of individual Core, Myc, and PRC module genes between naïve and primed human iPSCs. Left, middle, and right scatter plots show the expression values of individual Core, Myc, and PRC module genes, respectively, in naïve and primed human iPSCs. Red and blue spots indicate genes with expression levels that are higher or lower by more than 2-fold in primed human iPSCs compared with those in naïve human iPSCs, respectively. Gene symbols corresponding to red and blue are listed in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0083769#pone.0083769.s014" target="_blank">Table S5</a>. The variance value was calculated and is shown for each scatter plot.</p> <p>(C) Scatter plot analyses of the selected genes from Core (left), Myc (middle), and PRC (right) modules. The same sets of genes (<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0083769#pone.0083769.s012" target="_blank">Table S3</a>) used in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0083769#pone-0083769-g001" target="_blank">Figure 1C</a> were used for the analyses. The data lacked information for 15, 33, and 13 genes of the selected Core (50), Myc (98), and PRC (115) module genes, respectively. Red and blue spots indicate as described in B.</p></div

Stimulation of chromosomal binding of condensin I by OA in interphase extracts

<p><b>Copyright information:</b></p><p>Taken from "Analysis of the role of Aurora B on the chromosomal targeting of condensin I"</p><p></p><p>Nucleic Acids Research 2007;35(7):2403-2412.</p><p>Published online 28 Mar 2007</p><p>PMCID:PMC1874644.</p><p>© 2007 The Author(s)</p> Sperm nuclei were incubated with mitotic extract (lanes 1–3), interphase extract (lanes 4–6), interphase extract supplemented with 1.2 (lanes 7–9), 3.6 (lanes 10–12) or 12 μM (lanes 13–15) of OA at 22°C for 2 h. Chromatin-bound proteins were dissolved with SDS-PAGE sample buffer, and 12.5 (lanes 1, 4, 7, 10 and 13), 25 (lanes 2, 5, 8, 11 and 14) and 50% (lanes 3, 6, 9, 12 and 15) of each sample were separated by SDS–PAGE, and immunoblotted with anti-phospho H3. Samples were prepared as described in (A), and 6.25% (lane 1), 12.5% (lanes 2, 4, 7, 10 and 13), 25% (lanes 3, 5, 8, 11 and 14) and 50% (lanes 6, 9, 12 and 15) of samples were blotted using anti-XCAP-E (upper), and anti-XCAP-G (lower) antibodies. Sperm chromatin was assembled in the mitotic extract (a, d), interphase extract (b, e, g), and interphase extract supplemented with 3.6 μM OA (c, f, h). Samples were fixed and stained with Hoechst (a, b, c; first low), and anti-XCAP-H antibody (d, e, f; second low, short exposure: g, h; third low, long exposure). Bar, 10 μm. () Sperm chromatin was assembled in the mitotic extract (a, c, e) or interphase extract supplemented with 3.6 μM OA (b, d, f). After assembly, the reaction mixtures were supplemented with the indicated extra concentration of KCl at 22°C for 20 min, fixed, and stained with Hoechst. Bar, 10 μm

Requirement of condensin in OA-dependent partial chromosome condensation in the interphase extract

<p><b>Copyright information:</b></p><p>Taken from "Analysis of the role of Aurora B on the chromosomal targeting of condensin I"</p><p></p><p>Nucleic Acids Research 2007;35(7):2403-2412.</p><p>Published online 28 Mar 2007</p><p>PMCID:PMC1874644.</p><p>© 2007 The Author(s)</p> Mitotic (lanes 1–2) and interphase (lanes 3–4) extracts were mock-depleted (lanes 1 and 3) or depleted with a mixture of affinity-purified condensin antibodies (lanes 2 and 4). Equal volumes of these extracts were subjected to SDS-PAGE, blotted, and detected using the indicated antibodies. Sperm chromatin was incubated with mock-depleted mitotic extract (lanes 1–4), condensin-depleted mitotic extract (lane 5), mock-depleted interphase extract (lane 6), mock-depleted interphase extract supplemented with OA (lane 7), condensin-depleted interphase extract (lane 8) or condensin-depleted interphase extract supplemented with OA (lane 9) at 22°C for 2 h. The assembled structures were isolated, and 25 (lane 1), 12.5 (lane 2), 6.3 (lane 3), 3.1 (lane 4) and 100% (lanes 5–9) were analyzed by immunoblotting with the indicated antibodies. Sperm chromatin was incubated with mitotic extract (a), condensin-depleted mitotic extract (b), mock-depleted interphase extract (c), mock-depleted interphase extract with OA (d), condensin-depleted interphase extract (e), or condensin-depleted interphase extract with OA (f) at 22°C for 2 h. After incubation, assembled chromatin structures were fixed and stained with Hoechst. Bar, 10 μm

Requirement of Aurora B in the Cdc2-independent chromosomal targeting of condensin I

<p><b>Copyright information:</b></p><p>Taken from "Analysis of the role of Aurora B on the chromosomal targeting of condensin I"</p><p></p><p>Nucleic Acids Research 2007;35(7):2403-2412.</p><p>Published online 28 Mar 2007</p><p>PMCID:PMC1874644.</p><p>© 2007 The Author(s)</p> Interphase extract was depleted with anti-Aurora B (lane 7), anti-Aurora A (lane 8) or anti-Cdc2 antibodies (lane 9). As a standard, 100% (lane 1) of mitotic extract, 100% (lane 2), 50% (lane 3), 25% (lane 4), 12.5% (lane 5) and 6.25% (lane 6) of interphase extract were loaded in parallel. Efficiency of immunodepletion was measured by quantitative immunoblotting using the antibodies indicated. Sperm nuclei were incubated with mitotic extract (lanes 1–4), or interphase extract (lane 5), OA-treated interphase extract (lane 6), OA-treated interphase extract depleted of Aurora B (lane 7), OA-treated interphase extract depleted of Aurora A (lane 8), and OA-treated interphase extract depleted of Cdc2 (lane 9). Chromatin or chromosomes were isolated, and 100% (lanes 1, 5–9), 50% (lane 2), 25% (lane 3) and 12.5% (lane 4) of the samples were blotted by anti-phospho-H3 antibody (upper), anti-XCAP-C (middle) or anti-XCAP-E (lower) antibodies. In the case of blotting with anti-condensin subunit antibodies, a lower amount of samples was used as a standard, namely, 25% (lane 1), 12.5% (lane 2), 6.3% (lane 3) and 3.1% (lane 4). Sperm chromatin was incubated with mitotic extract (a), interphase extract (b), OA-treated interphase extract (c), OA-treated interphase extract depleted of Aurora B (d), OA-treated interphase extract depleted of Aurora A (e) and OA-treated interphase extract depleted of Cdc2 (f). Samples were fixed and stained with Hoechst

<i>In Vivo</i> Function and Evolution of the Eutherian-Specific Pluripotency Marker UTF1

<div><p>Embryogenesis in placental mammals is sustained by exquisite interplay between the embryo proper and placenta. <i>UTF1</i> is a developmentally regulated gene expressed in both cell lineages. Here, we analyzed the consequence of loss of the <i>UTF1</i> gene during mouse development. We found that homozygous <i>UTF1</i> mutant newborn mice were significantly smaller than wild-type or heterozygous mutant mice, suggesting that placental insufficiency caused by the loss of <i>UTF1</i> expression in extra-embryonic ectodermal cells at least in part contributed to this phenotype. We also found that the effects of loss of <i>UTF1</i> expression in embryonic stem cells on their pluripotency were very subtle. Genome structure and sequence comparisons revealed that the <i>UTF1</i> gene exists only in placental mammals. Our analyses of a family of genes with homology to UTF1 revealed a possible mechanism by which placental mammals have evolved the <i>UTF1</i> genes.</p></div

The <i>UTF1</i> gene is present only in the genomes of eutherian (placental) mammals.

<p>(A) Genomic organizations surrounding the <i>UTF1</i> locus in mammals and their corresponding genomic regions in other organisms. Black boxes indicate regions without available genomic sequences. (B) VISTA Browser (VGB2.0) plot of the 65.5 kb interval (ch10∶134,506,934-134,572,432) containing <i>KNDC1</i>, <i>UTF1</i> and <i>VENTX</i> genes in the human genome. Conservation plots for elephant (top panel) mouse (second panel), opossum (third panel) and wallaby (bottom panel), with respect to human, are shown in the coordinates of the human sequence (horizontal axis). Dark blue boxes indicate portions with unavailable DNA sequences in the database.</p

Role of UTF1 in the placenta.

<p>(A) Immunohistochemical analyses of UTF1 protein expression in wild-type placentas at 12.5 and 14.5 dpc. LB, labyrinth layer. (B) H&E-stained sections of <i>UTF1</i> heterozygous and homozygous mutant placentas. The boundary between the LB region and others is indicated by the dotted line. Each column of bar graph represents the mean of placenta weight with standard deviation (SD) (n = 3). *, p<0.05; **, p<0.01. (C) Cells in the mitotic phase in <i>UTF1</i> homozygous and heterozygous mutant placentas at 12.5 dpc visualized by immunostaining with an anti-phospho-histone H3 (Ser10) antibody. Phospho-histone H3-positive mitotic cells are marked by white arrowheads. Cells were counterstained with 4′,6′ diamidino-2-phenylindole (DAPI). Each column of bar graph represents the mean of number of phosphorylated histone H3 in 0.1 mm square with SD (n = 3). *, p<0.05. (D) Magnified view of H&E-stained sections of placentas. Placentas with the indicated genotypes were sectioned and stained. Dc, deciduas; Gly, glycogen trophoblast; TGC, trophoblast giant cell; Sp, spongiotrophoblast.</p