# A gene expression signature shared by human mature oocytes and embryonic stem cells.

Said Assou, Doris Cerecedo, Sylvie Tondeur, Véronique Pantesco, Outi Hovatta, Bernard Klein, Samir Hamamah, John de Vos

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Said Assou, Doris Cerecedo, Sylvie Tondeur, Véronique Pantesco, Outi Hovatta, et al.. A gene expression signature shared by human mature oocytes and embryonic stem cells.. BMC Genomics, 2009, 10, pp.10. 10.1186/1471-2164-10-10 . inserm-00369777

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Open Access

# A gene expression signature shared by human mature oocytes and embryonic stem cells

Said Assou<sup>1,2,3,4</sup>, Doris Cerecedo<sup>1,2</sup>, Sylvie Tondeur<sup>1,2,3</sup>, Véronique Pantesco<sup>1,2</sup>, Outi Hovatta<sup>5</sup>, Bernard Klein<sup>1,2,3</sup>, Samir Hamamah*<sup>1,2,3,6</sup> and John De Vos*<sup>1,2,3</sup>

Address: <sup>1</sup>CHU Montpellier, Institute for Research in Biotherapy, Hôpital Saint-Eloi, Montpellier, F-34000 France, <sup>2</sup>INSERM, U847, Montpellier, F-34000 France, <sup>3</sup>Université MONTPELLIER1, UFR de médecine, Montpellier, F-34000 France, <sup>4</sup>MacoPharma, Tourcoing, F-59200 France, <sup>5</sup>Department of Obstetrics and Gynecology, CLINTEC, Karolinska Institutet, Karolinska University Hospital, Huddinge, Stockholm, Sweden and <sup>6</sup>CHU Montpellier, Unité biologie clinique d'AMP - DPI, Hôpital Arnaud de Villeneuve, Montpellier, F-34000 France

Email: Said Assou - said.assou@inserm.fr; Doris Cerecedo - dcereced@prodigy.net.mx; Sylvie Tondeur - sylvie.tondeur@inserm.fr; Véronique Pantesco - veronique.pantesco@inserm.fr; Outi Hovatta - outi.hovatta@ki.se; Bernard Klein - bernard.klein@inserm.fr; Samir Hamamah* - s-hamamah@chu-montpellier.fr; John De Vos* - john.devos@inserm.fr

Published: 8 January 2009

Received: 3 June 2008

BMC Genomics 2009, 10:10 doi:10.1186/1471-2164-10-10

Accepted: 8 January 2009

This article is available from: http://www.biomedcentral.com/1471-2164/10/10

© 2009 Assou et al; licensee BioMed Central Ltd.

This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.

## Abstract

**Background:** The first week of human pre-embryo development is characterized by the induction of totipotency and then pluripotency. The understanding of this delicate process will have far reaching implication for in vitro fertilization and regenerative medicine. Human mature MII oocytes and embryonic stem (ES) cells are both able to achieve the feat of cell reprogramming towards pluripotency, either by somatic cell nuclear transfer or by cell fusion, respectively. Comparison of the transcriptome of these two cell types may highlight genes that are involved in pluripotency initiation.

**Results:** Based on a microarray compendium of 205 samples, we compared the gene expression profile of mature MII oocytes and human ES cells (hESC) to that of somatic tissues. We identified a common oocyte/hESC gene expression profile, which included a strong cell cycle signature, genes associated with pluripotency such as *LIN28* and *TDGF1*, a large chromatin remodelling network (*TOP2A*, *DNMT3B*, *JARID2*, *SMARCA5*, *CBX1*, *CBX5*), 18 different zinc finger transcription factors, including *ZNF84*, and several still poorly annotated genes such as *KLHL7*, *MRS2*, or the Selenophosphate synthetase 1 (*SEPHS1*). Interestingly, a large set of genes was also found to code for proteins involved in the ubiquitination and proteasome pathway. Upon hESC differentiation into embryoid bodies, the transcription of this pathway declined. In vitro, we observed a selective sensitivity of hESC to the inhibition of the activity of the proteasome.

**Conclusion:** These results shed light on the gene networks that are concurrently overexpressed by the two human cell types with somatic cell reprogramming properties.

<footnote>* Corresponding authors</footnote>
## Background

Oocytes have the unique ability to remodel the chromatin of the germinal nuclei into a totipotent state. These modifications are particularly striking for the male pro-nuclei: upon fertilization, the sperm chromatin packaging proteins are stripped off and replaced by histones, the DNA is demethylated within 4 hours of fertilization, and the amino terminal tails of histones are modified including methylation of arginin 9 and phosphorylation of serin 10 of histone H3 (H3K9 and PhH3S10, respectively) [1,2]. Remarkably, the reprogramming properties of oocytes are not restricted to the very specialized germinal nuclei. Indisputably, the cloning of Dolly has shown that the oocyte cytoplasm is able to extensively reverse the chromatin modifications associated with a differentiated state [3,4]. Somatic cell nuclear transplantation (SCNT) has since been extended to other species, including human cells, and to many cell types, including terminally differentiated cells such as granulocytes [5,6]. Thus differentiation is not anymore considered as an irreversible process, but rather as modifications of the cellular epigenome and transcriptome, that are amenable to complete reversal. In addition to oocytes, other cell types can reprogram somatic cells towards pluripotency. For example, using cell fusion strategies, it has been shown that hybrid cell clones obtained by fusion of a differentiated cell with either teratocarcinoma cells or embryonic stem cells display features of pluripotent, undifferentiated cells with concomitant loss of the markers associated with differentiation [7,8]. More recently, and quite unexpectedly, Takahashi and Yamanaka have shown that the expression of only four selected transcription factors, *OCT3/4*, *SOX2*, *CMYC* and *KLF4*, is sufficient to drive a mouse fibroblast into an induced pluripotent stem cell (iPS) with all the features of embryonic stem cells, including a high growth rate and the ability to form a variety of tissues from all three germ layers in vitro and in vivo [9]. These results have been confirmed by other studies, extended to human cells, and applied to non-fibroblastic cells such as mesenchymal stem cells (MSCs), gastric epithelial cells or hepatocytes [10-12]. At the center of cellular reprogramming lies the activation of the pluripotency transcriptional regulatory circuitry involving *POU5F1/OCT4*, *NANOG* and *SOX2* [13] and extensive chromatin-remodeling. However, the details of this process, such as the exact mediators of the chromatin modifications, remain ill defined. Data from xenopus egg experiments point to nucleosomal ATPases, but these findings await confirmation using mammalian oocytes [14,15].

As oocytes and ES cells are two cell types able to reprogram a somatic cell such as fibroblasts into pluripotent cells, the comparison of the gene expression program of these two cell types could contribute to the understanding of these cell reprogramming properties. Therefore, we

generated a transcriptome compendium of 205 samples by collecting public microarray data and compared the gene expression profile of oocytes and hESC to that of somatic tissues. We defined a common oocyte/hESC signature, which comprised many cell cycle genes, but also several biological pathways not associated with cell growth. Strikingly, a large set of genes is coding for genes involved in protein ubiquitination and the proteasome pathway. Upon hESC differentiation into embryoid bodies, the transcription of this pathway declines. In agreement with this preferential expression in pluripotent cells, we observed a selective sensitivity of hESC to the pharmacological inhibition of the proteasome activity, suggesting a role for this machinery in the maintenance of pluripotency.

## Results

### Human oocytes and hESC share a common transcriptome signature

To identify a gene expression signature shared by mature oocytes and hESC but not by somatic cells, we confronted 9 oocyte and 29 hESC expression profiles to a transcriptome collection of 167 samples spanning a wide variety of fetal and adult somatic cell samples (see Table 1; see Additional file 1). This microarray compendium quantified the expression of 13 279 unique Refseq transcripts in a total of 205 samples (see Methods and Additional file 2). A non-supervised analysis using principal component analysis (PCA) mapped the samples in a two dimensional space with a differentiation gradient ranging from undifferentiated hESC samples to highly specialized tissues such as hematopoietic cell samples or nervous system tissue samples (Figure 1A). The hESC samples grouped together very tightly, even though the transcriptomes were obtained from six different studies and included 15 different hESC cell lines, in agreement with the low variation between hESC cell lines [16] and the robustness of the Affymetrix microarrays [17]. Strikingly, the human mature oocyte samples were situated in the vicinity of the hESC samples, distantly located from most somatic tissue samples. A hierarchical clustering confirmed these findings, showing that MII oocytes and hESC clustered together, sharing a signature of overexpressed genes, demonstrating a close gene expression (Figure 1B; see Additional file 3). We computed an oocyte and a hESC signature by comparing each of these two categories to somatic cells. Using Significance Analysis of Microarrays (SAM) software with a false discovery rate (FDR) of 0.05% and a ratio between groups of at least 2, we determined that oocytes overexpressed 2622 probesets (PS) (2097 different Refseq transcripts) compared to somatic samples, whereas hESC overexpressed 1792 PS (1436 different Refseq transcripts) (see Additional file 4). The "oocytes signature" comprised *DAZL*, *SOX30*, *ZP2*, *GDF9*, *AURKC*, *PTTG3*, etc. (Figure 1C) which have previously
<table><caption>Table 1: Samples of the microarray compendium</caption><thead><tr><th>Cell type</th><th>Tissue or cell line</th><th>Normal or Malignant</th><th>Number of samples</th><th>References</th></tr></thead><tbody><tr><td colspan="5" style="text-align: center; font-weight: bold;">Normal cell compendium (n = 205)</td></tr><tr><td>Human embryonic stem cells</td><td>Cell line</td><td>Normal</td><td>29</td><td>[38-43]</td></tr><tr><td>Mature oocytes</td><td>Cells</td><td>Normal</td><td>9</td><td>[18,44,45] and this study</td></tr><tr><td>Foreskin fibroblasts</td><td>Cell line</td><td>Normal</td><td>4</td><td>[40]</td></tr><tr><td>Ovary</td><td>Tissue</td><td>Normal</td><td>3</td><td>[46,47]</td></tr><tr><td>Central nervous system</td><td>Tissue</td><td>Normal</td><td>44</td><td>[46,47]</td></tr><tr><td>Peripheral nervous system</td><td>Tissue</td><td>Normal</td><td>18</td><td>[46,47]</td></tr><tr><td>Skin and keratinocytes</td><td>Tissue and cultured primary cells</td><td>Normal</td><td>6</td><td>[39]</td></tr><tr><td>Lung</td><td>Tissue</td><td>Normal</td><td>11</td><td>[46,47]</td></tr><tr><td>Digestive tract</td><td>Tissue</td><td>Normal</td><td>19</td><td>[46,47]</td></tr><tr><td>Thyroid</td><td>Tissue</td><td>Normal</td><td>5</td><td>[46,47]</td></tr><tr><td>Adipocytes</td><td>Tissue</td><td>Normal</td><td>2</td><td>[46,47]</td></tr><tr><td>Kidney and prostate</td><td>Tissue</td><td>Normal</td><td>6</td><td>[46,47]</td></tr><tr><td>Heart and muscle</td><td>Tissue</td><td>Normal</td><td>10</td><td>[46,47]</td></tr><tr><td>Hematopoietic tissues</td><td>Tissue and purified cells</td><td>Normal</td><td>30</td><td>[39,46,47]</td></tr><tr><td>Uterus</td><td>Tissue</td><td>Normal</td><td>6</td><td>[46,47]</td></tr><tr><td>Placenta</td><td>Tissue</td><td>Normal</td><td>3</td><td>[46,47]</td></tr><tr><td colspan="5" style="text-align: center; font-weight: bold;">Highly cycling cells compendium (n = 22)</td></tr><tr><td>Leukemia cell lines</td><td>Cell line</td><td>Malignant</td><td>8</td><td>[47]</td></tr><tr><td>Lymphoma cell lines</td><td>Cell line</td><td>Malignant</td><td>4</td><td>[47]</td></tr><tr><td>Early erythroid cells</td><td>Cultured primary cells</td><td>Normal</td><td>2</td><td>[47]</td></tr><tr><td>Endothelial cells</td><td>Cultured primary cells</td><td>Normal</td><td>2</td><td>[47]</td></tr><tr><td>Hepatocarcinoma cell line</td><td>Cell line</td><td>Malignant</td><td>2</td><td>This study</td></tr><tr><td>Colorectal cancer cell line</td><td>Cell line</td><td>Malignant</td><td>2</td><td>[47]</td></tr><tr><td>Breast cancer cell line</td><td>Cell line</td><td>Malignant</td><td>2</td><td>This study</td></tr></tbody></table>

A summary of the microarray samples used in this study (A full list of samples is found in Additional file 1)
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<figure><img src="image_5.png" /><figcaption>**Figure 1**</figcaption></figure>

**Human mature MII oocytes and hESC display a common transcriptome signature.** Principal component analysis (PCA) (A). A PCA of 9 mature oocytes (MII), 29 hESCs and 167 somatic tissue samples. CNS, central nervous system; PNS, peripheral nervous system. Hierarchical clustering (B). Each horizontal line represents a PS and each column represents a single sample. PS up and down-regulated were colored in red and purple, respectively. In white, PS which were neither over nor under-expressed. Clusters: a: hESCs genes; b: MII oocytes genes; c: the oocytes/hESC signature; d: genes expressed in CNS; e: genes expressed in hematopoietic cells. AD: adipocytes; hFF: human foreskin fibroblasts; SK: skin and keratinocytes; DT: digestive tract; Hemato: hematopoietic cells; PL: placenta; H: heart; LU: lung; TH: thyroid; UT: uterus; OV: ovary; M: muscle. Expression bar charts of selected genes (C). Expression bar charts of three oocytes specific genes (DAZL, SOX30, ZP2), three hESCs specific genes (*POU5F1/OCT4*, *NANOG*, and *DPPA4*), three genes up-regulated in hESC and oocytes MII (*DNMT3B*, *TOP2A* and *ZNF84*) and one ubiquitously expressed gene (*RPL4*) using our on-line expression atlas *Amazonia*! http://amazonia.montp.inserm.fr. Diff: non-specific differentiated hESC; MCF7: breast cancer cell line; HEPG2: hepatocarcinoma cell line. Venn diagram detailing shared and distinct gene expression among hESCs and MII human oocytes (D). The oocyte/hESC signature was defined as the intersection of the hESC signature (genes overexpressed in hESC compared to somatic tissues (ST)) and the MII oocytes signature (genes overexpressed in MII oocytes compared to ST). The oocytes/hESC signature was then further parted into a fraction sharing a cell cycle signature and a non-cell cycle part.

been identified as overexpressed by female germinal cells by our group and others [18,19]. Similarly, the "hESC sig- nature" displayed numerous genes known to be specifi- cally overexpressed in hESC such as *POU5F1/OCT4*, *NANOG*, *DPPA4*, *TDGF1*, *CD24*, *PODXL*, *HELLS*, etc. [20]. These findings validated the biological relevance of our compendium and the signatures specific to oocytes and hESC. We intersected these two lists of genes and established a "oocyte/hESC signature", composed of 652 PS (558 different Refseq transcripts) (Figures 1D; see Additional file 4).

**A strong cell cycle signature**

To get an insight into the oocyte/hESC signature, we searched for overrepresented gene ontology (GO) func- tional annotations. As expected from our previous studies on oocytes transcriptome or hESC transcriptome [18,20], the oocytes/hESC signature was highly enriched in genes associated with intra-cellular localization, DNA and RNA binding, and conversely, it was significantly depleted in genes which encode for secreted proteins or proteins implicated in signal transduction (Figure 2A and 2B). Remarkably, we observed that the biological process
annotations related to cell cycle such as "mitotic cell cycle", "cell cycle progress", "nucleobase, nucleoside, nucleotide synthesis" were among the most highly enriched in the oocyte/hESC signature (P < 1. 10⁻³). These findings were in line with the very short cell cycle duration of primate ESC [21] and with the fact that MII oocytes samples are pure populations of cells undergoing the second meiotic division, which has many features of mitosis. Thus, these two tissue types highly express genes involved in the process of cell division. To delineate more clearly

the cell cycle contribution to the oocyte/hESC signature, we defined a cell cycle signature independently from the oocytes and hESC samples. We compared samples characterized by a high proliferation index to our somatic samples series. Proliferating samples included normal cells such as rapidly dividing CD71+ early erythroid progenitors and CD105+ endothelial cells, as well as cell lines originating from haematological, hepatic, breast and colorectal tumors (See Table 1 and Additional file 1 for the list of additional samples). A SAM analysis with a FDR

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**Figure 2**

**Biological annotations of genes overexpressed in human mature MII oocytes and hESC.** Cellular compartment localisation according to Gene Ontology (GO) annotations (A). Statistical comparison of the distribution of GO annotations in the oocytes/hESC signature with the genes underexpressed in oocytes and hESC (B). Gene Ontology categories which differed significantly (p value ≤ 0.01) between oocytes and hESC are shown. Oocyte/hESC gene networks (C). We computed interaction networks from the oocyte/hESC signature. Genes included in the oocyte/hESC signature are in red (the color intensity is proportional to the oocyte/hESC to somatic samples fold change). Genes not found in the signature are in white. In each network, edge types are indicatives: a plain line indicates direct interaction, a dashed line indicates indirect interaction; a line without arrowhead indicates binding only; a line with an arrowhead indicates "acts on". Node types represent different types of molecules: diamond, enzyme; square, cytokine; triangle, phosphatase; and circle, other. Double line edge represents a group or a complex. Validation of microarray data (D). Gene expression of DNMT3A, SMARCA5, PSMA5, PSMA2 were assayed with quantitative RT-PCR (QRT-PCR). The expression of these four selected genes was compared in mature oocytes, hESC and various somatic samples: human fibroblasts (hFF), human breast adenocarcinoma cell line (MCF7), human hepatocellular liver carcinoma cell line (HepG2), endometrial cells (End7) and T-lymphocyte cells (TL) using QRT-PCR. All measurements were performed in duplicate in two separate runs. The relative levels of gene expression of target mRNA was normalized against GAPDH expression. Fold change values are plotted on a log₁₀ scale.
of 0.05% identified 818 PS (682 different Refseq tran-
scripts) overexpressed in proliferating somatic samples,
composing a "cell cycle signature". Intersection with the
oocyte/hESC signatures revealed that 220 PS (33.7%)
were shared with the cell cycle signature (Figure 1D; see
Additional file 4). This cell cycle part of the oocytes/hESC
signature included enzymes involved in general cell
metabolism (METAP2, SHMT2, etc.), nucleoside synthe-
sis (DHFR, TYMS, RRM2, PPAT, etc.), DNA repair includ-
ing mismatch repair (MSH2 and MSH6) or base excision
repair (UNG, PCNA), main components of the cell cycle
regulatory machinery (CCNB1 and 2, CCNA, CCNE, etc.),
regulator of the topologic state of DNA (TOP1, TOP2A)
and components of the mitotic spindle assembly check-
point (the centromer constituents CENPE, the securin
PTTG1, and MAD2L1, BUB1B, BUB3) (Figure 2C). How-
ever, it must be noted that 36 genes from the oocyte/hESC
signature that are functionally annotated "cell cycle" by
Gene Ontology were not included in the cell cycle signa-
ture. These are cell cycle genes that are preferentially
expressed in mature oocytes and hESC as compared to
other cycling cell types such as malignant cell lines or pro-
liferating primary hematopoietic cells, and included the
spindle checkpoint gene CHEK1, FBXO5/EMI1, the cyclin
dependent kinase-activating kinase CDK7 and a compo-
nent of transcription factor IIH, CDK8.

Human oocytes and hESC share a large chromatin
remodelling network

We focused the second part of our analysis on the non-cell
cycle part of the oocyte/hESC signature. Removing the
220 cell cycles PS led to the definition of a "non-cell cycle
oocyte/hESC signature" that retained 432 PS (384 tran-
scripts). This signature contained many transcripts
involved in DNA and histone modifications. One of these
transcripts was *DNMT3B*, involved in DNA methylation.
The high fold change of *DNMT3B* in hESC and oocytes
compared to somatic samples (43.4 and 9.4, respectively)
suggests a central role of this DNA methyltransferase in
the control of the epigenome of these cells. In addition,
several transcripts, comprising *JARID2*, *SMARCA5*, *CBX5*,
*CHAF1A* and *CBX1*, were involved in histone modifica-
tion processes (Figure 2C). We selected two chromatin
remodelling genes, *DNMT3B* and *SMARCA5*, and vali-
dated by QRT-PCR their preferential expression in oocytes
and hESC compared to somatic samples (Figure 2D).

Zinc finger genes

Mature MII oocytes and hESC overexpressed numerous
zinc finger domain genes. The zinc finger motif is a DNA
binding domain dependent on a zinc ion, frequently
found in transcription factors. The non-cell cycle oocyte/
hESC signature was significantly enriched in zinc finger PS
: 20 (18 Refseq transcripts) out of 432 PS (4.6%) in the
signature compared to 611 out of 22215 PS (2.7%) in the

complete list of PS (P = 0.018) (Table 2). The expression
bar charts for the zinc finger domain gene ZNF84 is
shown in Figure 1C and that of all 18 zinc finger domain
genes from the non-cell cycle oocyte/hESC list is available
as Additional file 5.

Ubiquitination and proteasome

Surprisingly, we found that a highly significant propor-
tion of genes of the non-cycle oocytes/hESC signature was
involved in the protein ubiquitination and proteasome
canonical pathway (P-value ≤ 1.93E-06, using Ingenuity
software) (Figure 3A). Enzymes from the three E1/E2/E3
ubiquitination classes were found significantly overex-
pressed in the functional regulatory network: the E1 ubiq-
uitin-activating enzyme UBE1C, the E2 ubiquitin-
conjugating enzymes UBE2G1, UBE2V1 and UBE2V2, and
the E3 ubiquitin protein ligases UBE3B and breast cancer
1, early onset (BRCA1) (Figure 3A). It was recently showed
that BRCA1 is part of a holoenzyme complex containing
BRCA1, BRCA2, BARD1 and RAD51 which is called the
BRCA1- and BRCA2-containing complex (BRCC) that dis-
plays an ubiquitin E3 ligase activity [22]. We found that
three out of the four components of BRCC, namely
BARD1, BRCA1 and RAD51 are overexpressed in MII
oocytes and hESC whereas BRCA2 is simply expressed.
One key consequence of protein ubiquitination is to tar-
get proteins for degradation by the 26S proteasome. In
line with the biased high expression of ubiquitination
pathway components, we also found many subunits of
the proteasome significantly overexpressed in MII oocytes
and hESC (Figure 3B). As expected for a ubiquitous cell
machinery complex, the expression of most subunits of
the 26S proteasome is detected by microarrays in oocytes
and hESC. Among these, four catalytic alpha proteasome
subunits (PSMA2, PSMA3, PSMA4 and PSMA5) and three
regulatory subunits, the ATPase PSMC6 and the non-
ATPase PSMD10 and PSMD11, are significantly upregu-
lated in MII oocytes and hESC as compared to somatic tis-
sues (P < 0.001 for each cited proteasome subunit) (Figure
3B), in line with the overexpression of the ubiquitin path-
way. In addition, three ubiquitin-specific proteases
(USP1, USP7 and USP9X), that are deubiquitinating
enzymes, were also found highly expressed in the oocytes
and hESC. Remarkably, microarray analysis showed that
upon differentiation, the expression level of proteasome
components that are overexpressed in hESC decreased to
a level similar to that of somatic cells (Figure 3C).

High sensitivity of human embryonic stem cells to
proteasome inhibition

The high expression level of the proteasome machinery in
hESC and its decrease during hESC differentiation sug-
gested that this pathway could play an important role in
pluripotent cells. To determine the consequence of func-
tional blocking of the proteasome activity in hESC, we
<table><caption>Table 2: Genes from the mature oocyte/hESC signature with a Zinc finger domain.</caption><thead><tr><th>Gene Symbol</th><th>Probe Set</th><th>Gene Title</th><th>Chromosomal Location</th><th>Fold change Oocyte MII (a)</th><th>Fold change hESC (b)</th></tr></thead><tbody><tr><td>DPF2</td><td>202116_at</td><td>D4, zinc and double PHD fingers family 2</td><td>chr11q13</td><td>6.1</td><td>2.1</td></tr><tr><td>GATAD2A</td><td>218131_s_at</td><td>GATA zinc finger domain containing 2A</td><td>chr19p13.11</td><td>9.8</td><td>2.8</td></tr><tr><td>LOC730051</td><td>221963_x_at</td><td>Similar to Zinc finger protein 418</td><td>chr19q13.43</td><td>5.9</td><td>2.5</td></tr><tr><td>RCHY1</td><td>214281_s_at</td><td>ring finger and CHY zinc finger domain containing 1</td><td>chr4q21.1</td><td>5.7</td><td>3.3</td></tr><tr><td>ZC3H13</td><td>212402_at</td><td>zinc finger CCCH-type containing 13</td><td>chr13q14.12</td><td>3.2</td><td>2.4</td></tr><tr><td>ZC3H15</td><td>201595_s_at</td><td>zinc finger CCCH-type containing 15</td><td>chr2q32.1</td><td>3.5</td><td>2.3</td></tr><tr><td>ZCCHC8</td><td>218478_s_at</td><td>zinc finger, CCHC domain containing 8</td><td>chr12q24.31</td><td>4.5</td><td>2.6</td></tr><tr><td>ZFAND6</td><td>221613_s_at</td><td>zinc finger, AN1-type domain 6</td><td>chr15q25.1</td><td>13.8</td><td>3.1</td></tr><tr><td>ZMYM2</td><td>202778_s_at</td><td>zinc finger, MYM-type 2</td><td>chr13q11-q12</td><td>33.1</td><td>3.4</td></tr><tr><td>ZNF131</td><td>221842_s_at</td><td>zinc finger protein 131</td><td>chr5p12-p11</td><td>8.8</td><td>2.2</td></tr><tr><td>ZNF281</td><td>218401_s_at</td><td>zinc finger protein 281</td><td>chr1q32.1</td><td>6.5</td><td>3.1</td></tr><tr><td>ZNF3</td><td>212684_at</td><td>zinc finger protein 3</td><td>chr7q22.1</td><td>2.8</td><td>2.1</td></tr><tr><td>ZNF330</td><td>209814_at</td><td>zinc finger protein 330</td><td>chr4q31.1-q31.2</td><td>3.5</td><td>2.4</td></tr><tr><td>ZNF508</td><td>203322_at</td><td>zinc finger protein 508</td><td>chr18q23</td><td>4.5</td><td>3.9</td></tr><tr><td>ZNF588</td><td>205739_x_at</td><td>zinc finger protein 588</td><td>chr7q11.2</td><td>6.4</td><td>2.1</td></tr><tr><td>ZNF84</td><td>204453_at</td><td>zinc finger protein 84</td><td>chr12q24.33</td><td>3.1</td><td>2.5</td></tr><tr><td>ZNF93</td><td>215758_x_at</td><td>zinc finger protein 93</td><td>chr19p12</td><td>10.3</td><td>2.1</td></tr><tr><td>ZZZ3</td><td>212893_at</td><td>zinc finger, ZZ-type containing 3</td><td>chr1p31.1</td><td>2.1</td><td>2.2</td></tr></tbody></table>

List of genes from the oocyte/hESC signature that display a zinc finger domain, with PS number, and fold change (oocyte versus somatic tissues (a) and hESC versus somatic tissues (b)).

tested the effect of MG132, a specific proteasome inhibitor, on embryonic stem cells [23]. Increasing doses of MG132 were added to the culture media of HS181 hES cells. At 250 nM the morphology of the hESC colonies clearly showed large patches of differentiation and at 500 nM no undifferentiated cells remained (Figure 4A). Furthermore, when colonies contained mixed populations of

undifferentiated and differentiated cells, 1 µM of MG132 induced the detachment of the undifferentiated cells whereas the differentiated progeny stayed tightly sticked to the dish. These results were reproduced on two other hES cell lines (HD83 and HD90, data not shown). By contrast, the morphology and adhesion of human foreskin fibroblasts (HFF) were not altered by MG132 at concen-
A

<figure><img src="image_10.png" /></figure>

B

<figure><img src="image_11.png" /></figure>

C

<figure><img src="image_12.png" /><figcaption>**Figure 3**</figcaption></figure>

**Overexpression of the ubiquitination/proteasome pathway.** Interaction network analysis of the ubiquitination/proteasome pathway in the oocytes/hESC signature. (A) The interaction network was generated with the Ingenuity software and shows a high number of genes from this cellular pathway overexpressed (red) or expressed (orange) in the oocytes/hESC signature. Transcripts that were not detected by the microarray are white. Notably, we found elements of the ubiquitin-activating enzyme (UBE), BRCA1- and BRCA2-containing complex (BRCC), the regulatory 19S proteasome, the core proteolytic 20S proteasome and the ubiquitin-specific protease (USP) modules in the oocyte/hESC signature. Gene expression measured by microarrays in 9 genes involved in the ubiquitin and proteasome pathway (B). Box-and-whisker plots comparing the expression level of PSMA2, PSMA3, PSMA4, PSMA5, PSMC6, PSMD10, PSMD11, UBE2G1 and SKP2 in mature oocytes and hESC (38 samples) versus somatic tissues (167 samples). The signal intensity for each gene is shown on the y axis as arbitrary units determined by the GCOS 1.2 software (Affymetrix). (*): *P*-value < 0.0001 using a Mann-Whitney statistical test. Down regulation of the proteasome pathway during hESC differentiation (C). U133A microarray signal values for PSMA2, PSMA4 and PSMA5 in 29 undifferentiated hESC samples (mean value) versus two embryoid bodies (EB) samples (EB day 5 and EB day 14) and 3 non-lineage differentiated hESC samples (mean value).

tration up to 1 µM (Figure 4B). Moreover, we differentiated the HD90 and HS181 hESC into hES-differentiated fibroblasts (dF) that display features characteristic of fibroblasts: flattened cells with elongated nucleus and branching pseudopodia, expression of membrane markers such as P4H, CD13 or CD44. Treatment with MG132 did not induce changes in cell morphology of the hES-dF-HD90 (Figure 4C) and hES-dF-HS181 (data not shown), even at high concentrations. RT-PCR analysis showed that expression of pluripotency markers decreased when hESC were treated with MG132. Whereas the expression of

POU5F1/OCT4, SOX2 and NANOG decreased with the proteasome treatment, GAPDH expression was not modified (Figure 4D). This effect was also substantiated by flow cytometry. We observed decreasing expression of the pluripotency marker TRA-1-60 on HS181 hESC after exposition to MG132 (Figure 4E). However, high concentration of MG132, up to 1 µM, did not affect two different fibroblasts cell surface markers, CD44 and CD13 on hFF, on hES-dF-HS181 or on hES-dF-HD90. Thus, our results showed that pluripotent hESC are highly susceptible to the action of proteasome blockage, whereas somatic cells
<figure><img src="image_13.png" /></figure>

<figure><img src="image_14.png" /></figure>

<figure><img src="image_15.png" /><figcaption>**Figure 4**</figcaption></figure>

**Figure 4**

**Blocking proteasome activity in hESC.** Proteasome inhibition causes differentiation of hESCs (A). HS181 colonies (p56) were grown 4 days on hFF and then treated 40 hours with the proteasome inhibitor MG132. Control HS181 colonies express POU5F1 (scale bar 25 µ) and display a normal karyotype. Upon treatment with MG132, HS181 colonies differentiated. No effect of proteasome inhibition on hFF (B). HFF express the fibroblastic marker P4H and display a normal karyotype. HFF were cultured with MG132 during 40 hours. No morphological alteration was observed. No effect of proteasome inhibition on hES-dF-HD90 (C). The HD90 hESC line was differentiated into fibroblasts like cells (hES-dF) that display morphologic feature of dermal fibroblasts and express P4H: bottom left. An undifferentiated colony of HD90 P4H-, starts to differentiate at the edges into P4H+ hES-dF (upper left). hES-dF-HD90 cells were cultured with MG132 during 40 hours. No morphological alteration was observed. Down regulation of pluripotency transcription factor in hESC by proteasome blockage (D). The expression of POU5F1/OCT4, NANOG and SOX2 was measured by semiquantitative RT-PCR in HS181 hESC after 40 h culture with MG132. GAPDH was used as a control. Flow cytometry analysis after proteasome inhibition (E). HFF, hES-dF-HS181 and HS181 cells were treated 40 hours with MG132, and then the cell surface fibroblastic markers CD13 and CD44, and the pluripotent cell surface marker TRA-1-60 were measured by FACS. Markers for fibroblastic cells were not altered with MG132 treatment, whereas the marker for pluripotency dropped to barely detectable level. Y-axis: percentage of the control (untreated) sample.

such as hFF or the differentiated progeny of hESC such as hES-dF were not affected.

**Discussion**

Early human embryo development results in the reprogramming of highly specialized germinal cells into totipo-

tent and then pluripotent cells that are the progenitors of all the specialized cell types of the human body. This unique biological property has been harnessed to restore pluripotency in human somatic cells by SCNT or cell-fusion using embryonic stem cells [6,7]. hESC share with pluripotent stem cells from the inner cell mass pluripo-
tency transcription factors and multi-lineage differentia-
tion properties, and are considered a good *in vitro* model
for pre-embryo pluripotent stem cells. Though human
oocytes and ESC are developmentally separated by less
than one week, the transcriptome of the oocyte undergoes
rapid changes after fertilization [24,25]. We undertook to
find out a common expression signature to these two cell
types, that share somatic cell reprogramming properties,
by comparing them to a large collection of somatic tissues
samples. A first observation was that the oocytes/hESC
signature was highly enriched in genes involved in cell
cycle. Whereas this was expected because of the cell cycle
status of these two cell types, the expression of a large set
of genes associated with cell division is nevertheless of
interest for cellular reprogramming. As recently reported,
prior mitotic remodeling of the somatic nuclei, involving
topoisomerase II (TOP2)-dependent shortening of chro-
matin loop domains and an increased recruitment of rep-
lication initiation factors onto chromatin, is essential for
reprogramming of differentiated nuclei [26]. Strikingly,
we found that TOP2A was highly up-regulated in both
oocytes and hESC. This observation suggests that TOP2A
could be a major factor in the reprogramming properties
of oocytes and hESC by participating in chromatin
remodeling. Conversely, the identification of a "cell cycle
signature", shared with highly proliferating tissues such as
cancer cell lines, provided a mean to identify by subtrac-
tion a "non-cycle oocytes/hESC" signature of 432 PS. This
signature included transcripts coding for proteins
involved in chromatin structure modifications such as
DNMT3B, JARID2, SMARCA5 or CBX5 that contribute to
the DNA methylation and chromatin remodeling (Figure
2C). Consistent with these observations, hESC display a
distinct, permissive, chromatin structure compared with
other tissues [27]. Expression of DNA methyl-transferases
or several ATP-dependent chromatin remodelling factors
are elevated in murine oocytes or ES cells [28,29]. Thus
our findings show large similarities between murine and
human ES cells, and put forward several genes whose
strong overexpression could contribute to the specific
chromatin state of hESC.

Another lesson from our transcriptomic approach is that
the common oocytes/hESC gene expression profile has a
very low number of genes that are either secreted or mem-
brane bound (Figure 2A). This is in line with our previ-
ously published data that both oocytes and hESC
"specific genes" are significantly depleted in extracellular
signalling components, suggesting that this feature is
indeed a common characteristic shared by oocytes and
hESC and is not simply due to a lack of overlap [18,20].
Hence, genes specifically shared by oocytes and hESC are
largely nuclear proteins. One assumption that can be
inferred from these findings is that determinant of
pluripotency may be mostly intrinsic factors. This obser-

vation converges on a recent model, which proposed that
pluripotency is a ground state that is intrinsically self-
maintained when protected from extrinsic differentiation
stimuli [30].

An unexpected observation was that genes involved in
protein ubiquitination and proteasome pathway were
also overrepresented in the oocytes/hESC signature. This
could be linked to the strong proliferation signature of
hESC and oocytes as this pathway is by many way impli-
cated in the regulating the cell cycle [31]. However, the
overexpression of the ubiquitination/proteasome path-
way was still significant when the cell cycle signature was
subtracted, suggesting that this pathway could have a role
in pluripotent cells in addition to its house keeping or cell
cycle functions. In line with these results, we showed a
selective sensitivity of hESC to the inhibition of the activ-
ity of the proteasome, resulting in loss of pluripotency
and cell growth at doses without any detectable effects on
differentiated but cycling cells such as primary fibroblasts
or hESC derived fibroblast like cells. In addition, it must
be stressed that the dramatic effects on hESC pluripotency
were observed at doses of the proteasome inhibitor
MG132 (0.5 µM) significantly lower than those typically
found in the literature (several µM) or in mice ES cells (20
µM) [23]. This observation is highly interesting in light of
the recent findings of the role of the proteasome in tran-
scription, especially in hESC. The 26S proteasome consists
of a 20S core proteolytic part, capped by a 19S regulatory
complex. Specificity of degradation of proteins is medi-
ated in part by poly-ubiquitination of the substrate bound
for destruction. Based on early work in yeast, the proteas-
ome is known to interact with chromatin and function at
multiple steps in transcription, both through proteolytic
and non-proteolytic activities [32]. Recently, Szutorisz et
al. reported that the 26S proteasome is assembled on
intergenic and intragenic regions in ES cells and act as a
transcriptional silencer by blocking non-specific transcrip-
tion initiation [23]. This mechanism involves the proteo-
lytic activity of the 20S core by degrading non-specific
preinitiation complexes, thereby preventing permissive
transcription and spreading of the modified chromatin.
Our results are consistent with this hypothesis, but final
answer on this issue will require further investigations.

This work has compared human MII oocytes and hESC to
somatic tissues gene expression profiles. One goal was to
provide new hints on the process of nucleus reprogram-
ming which takes place in vivo during early embryo devel-
opment or in vitro during SCNT, and may thus help to
improve the iPS technology. Indeed, since the seminal
work of the team of Shinya Yamanaka, numerous
improvement have been made, including the identifica-
tion of new genes able to replace some of the original ones
in the reprogramming cocktail, the use of small molecules
or the replacement of the retroviral vectors by adenovi-
ruses or plasmids [33-37]. A first observation is that
human mature oocytes do not express the pluripotency
core transcriptional genes POU5F1/OCT4, NANOG and
SOX2 [13], except POU5F1/OCT4 at low level (see Figure
1C and our Amazonia! on-line expression atlas, http://
amazonia.montp.inserm.fr). They neither express KLF4
nor CMYC, which compose, with POU5F1/OCT4 and
SOX2, the four factors that can reprogram somatic cells by
virus-mediated overexpression [11]. From the six "repro-
gramming" factors described to date, only LIN28 was
found in the oocyte/hESC signature. However, POU5F1/
OCT4, NANOG, SOX2, KLF4, LIN28 and CMYC are all
expressed by hESC. Therefore, during early embryo devel-
opment, the expression of these genes is induced. Thus,
two different molecular pathways that can reprogram
adult somatic cells can be envisioned: (i) the process tak-
ing place in the oocyte cytoplasm, able to activate the core
transcriptional genes, or (ii) the overexpression of the core
transcriptional genes themselves together with adjuvant
genes, either by viral overexpression or by fusion with
cells already expressing these genes. It can be speculated
that the factors that lie upstream of the pluripotency core
transcriptional circuitry are expressed as mRNA in mature
MII oocytes and are still present at blastocyst stage from
which hESC are derived. Thus, the oocytes/hESC signature
likely includes these factors, and therefore this informa-
tion could be highly informative for cell reprogramming.
The signature contained numerous transcription factors,
including many zinc finger such as ZNF84, several still
poorly annotated genes such as KLHL7, MRS2, or the
Selenophosphate synthetase 1 (SEPHS1), displayed a
strong cell cycle signature, chromatin modification genes,
and also many actors of the proteasome pathway. All
these genes are candidate genes to improve the efficiency
of iPS generation, especially in the light of the recent
advances that uses non retroviral vectors but at the cost of
lower efficacy.

Conclusion

Human ESC are not only a very promising source of cells
for regenerative medicine, but are also a unique tool to
understand early embryo development that can not easily
be studied on live embryos because of ethical and techni-
cal limits. Our comparison of human mature oocytes and
hESC to a large collection of somatic samples helps to
understand the early embryo development and pluripo-
tency, and is therefore relevant for therapeutics, including
improvement of the pregnancy success rate in IVF and
regenerative medicine applications such as those involv-
ing cell reprogramming.

Methods

Transcriptome compendium

We built an expression compendium by combining
U133A and U133 Plus 2.0 (Affymetrix, Santa Clara, USA)

microarray data from 11 publications and from our labo-
ratory, totalizing 205 samples (Table 1; see Additional file
1) [18,38-47]. Data were analyzed with the GCOS 1.2
software (Affymetrix), using the default analysis settings
and global scaling as first normalization method, with a
trimmed mean target intensity value (TGT) of each array
arbitrarily set to 100. Data was floored at 50, i.e each value
below 50 was set to 50. In order to compare U133A and
U133 Plus 2.0 data, we further normalized the data with
a rank-based normalization method. This method,
"MetaNorm", orders the values of the 22 215 PS of the
Affymetrix U133A microarray and allocates a new value to
each PS according to its rank, using a unique signal value
template (Assou et al., manuscript in preparation). Sam-
ples are listed in Table 1 (see Additional file 1), along with
references, microarray design and, when available, GEO
(Gene Expression Omnibus) dataset number. The dataset
is available as Additional file 2 (signal and p-value) and
each PS can be individually accessed on our website http:/
/amazonia.montp.inserm.fr[20].

Data analysis and visualization

Principle component analysis (PCA) was performed using ArrayAssist® software (Stratagene, La Jolla, CA, USA) to provide a global view of how the various sample groups were related. Hierarchical clustering was carried out with CLUSTER and TREEVIEW software [48]. PCA and clustering were performed on 10,000 PS with the highest coefficient of variation (CV). Gene expression profiles were identified using two-class Significance Analysis of Microarrays (SAM) method [49]http://www-stat.stanford.edu/~tibs/SAM/ which utilizes a Wilcoxon-test statistic and sample-label permutations to evaluate statistical significance. SAM analysis was applied after data filtering retaining only PS with at least 2 samples with a "Present" call. The False Discovery Rate (FDR), an estimate of the fraction of selective genes, was kept below 5% in all statistical analyses. Gene Ontology annotation analysis was carried out using the Fatigo+ tool at the Babelomics website http://babelomics.bioinfo.cipf.es[50]. Only annotations with a false discovery rate-adjusted P-value below 0.05 were considered significant. To uncover functional biological networks, we imported gene expression signatures into the Ingenuity Pathways Analysis (IPA) Software (Ingenuity Systems, Redwood City, CA, USA). Comparison of the frequency of zinc finger domain containing transcript between the non-cell cycle oocytes/hESC signature and the entire U133A microarray was carried out using a Pearson's Chi-squared test with Yates' continuity correction.

Human mature MII oocytes, fibroblasts and malignant cell lines transcriptome

Unfertilized MII oocytes were collected after informed
consent 44 hours post insemination or post microinjec-
tion by ICSI as previously published [18,44]. Briefly, MII
oocytes were from couples referred to our center for cIVF
(tubal infertility) or for ICSI (male infertility). Mature M2 oocytes were pooled: 16 oocytes for Oocyte_M2_16 sample, 21 for Oocyte_M2_21 and 24 for Oocyte_M2_24, from 6, 8 and 8 patients respectively. Human foreskin fibroblasts cell lines were described previously [20]. MCF7 and HEPG2 were from ATCC and cultured in DMEM medium containing 10% fetal calf serum (FCS). Total RNA was isolated using RNeasy mini kits (Qiagen, Courtaboeuf, France) and quantified using a NanoDrop spectrophotometer (Thermo Fischer, Wilmington, Delaware, USA). Total RNA (100 ng) was used to prepare twice amplified labeled cRNA for hybridization to HG-U133 plus 2.0 GeneChip pangenomic oligonucleotide arrays (Affymetrix, Santa Clara, CA, USA) as previously described [18]. The 9 microarray data obtained in our lab are accessible in US National Center for Biotechnology Information, Gene Expression Omnibus (GEO) through the provisional accession numbers GSE11450 (series), and GSM28886, GSM28885, GSM28883, GSM28882, GSM28880, GSM28887, GSM288877, GSM288876, GSM288812 (samples).

## hES cell culture

The HS181 hES cell line was imported from the Karolinska Institute (Stockholm, Sweden). The HD83/D17/FE07-135-L1 and HD90/D18/FE07-142-L1 hES cell lines were derived in our laboratory from a normal embryo and an embryo that carried an abnormal VHL gene according to preimplantation genetic diagnostic, respectively (De Vos et al. manuscript in preparation). Briefly, derivation of HD83 and HD90 was carried out using mechanical dissociation of the inner cell mass [51]. The culture medium used for hESCs derivation and culture consisted of 80% KO-DMEM, 20% knockout SR, 2 mM L-glutamine, 1% nonessential amino acids, 0.5 mM β-mercaptoethanol (all from Gibco Invitrogen, Cergy-Pontoise, France) and 10 ng/mL of bFGF (Abcys, Paris, France). Passaging was performed mechanically by cutting the colony using a #15 scalpel under the microscope. Human foreskin fibroblasts (HFF), mitotically inactivated using irradiation (40 Gy),

were used as feeder cells. HFF cells were cultured in 85% DMEM, 15% FBS. All hESC expressed POU5F1/OCT4, NANOG and TRA-1-60, and were able to differentiate into embryoid bodies that expressed differentiation markers. For proteasome inhibition experiments, hESC were incubated 40 h with various concentration of MG132 (Sigma), with medium renewal at 24 h.

## Production of hES-derived fibroblasts

Briefly, hES cells were mechanically isolated and plated on laminin precoated 6-wells culture dishes (Becton Dickinson, San Jose, CA, USA) in hESC culture medium renewed every day. After 5 days, bFGF was removed, and after three additional days, medium was switched to HFF medium. In these conditions, hES cells differentiated into flattened cells with elongated nucleus and branching pseudopodia forming hESC-derived fibroblasts (hES-dF). The hES-dF were then mechanically isolated and transferred to feeder free 6-wells culture dishes. Subsequent passages were carried out using 0.05% trypsin-EDTA (Invitrogen) every 6 days and cultures upscaled into T75 flasks.

## RT-PCR and quantitative PCR (QRT-PCR)

RT-PCR was carried out on total RNA isolated from hESCs grown in the absence or presence of increasing concentration of MG132. PCR conditions and sequence for each primer are shown in Table 3. PCR products were separated on a 1% agarose gel. Expression of the housekeeping gene GAPDH was used to normalise PCR reactions. For QRT-PCR, approximately 1 µg of linear-amplified, biotin-labelled cDNA was mixed with Assays-on-Demand primers and probes and TaqMan Universal Master Mix according to the manufacturer's instructions (Applied Biosystems, Courtaboeuf, France). Real-time QRT-PCR was performed using the ABI Prism 7000 sequence detection system (Applied Biosystems) and normalized to GAPDH for each sample using the following formula in which Ct is cycle threshold: $100/2^{\Delta\Delta Ct}$, where $\Delta\Delta Ct = \Delta Ct$ unknown $-\Delta Ct$ positive control.

<table><caption>Table 3: Primer sequences and conditions used for RT-PCR</caption><thead><tr><th>Gene</th><th>Primer sequences (Forward, Reverse)</th><th>Cycles</th><th>MgCl2 (mM)</th><th>Annealing Tm (°C)</th><th>Product size (bp)</th></tr></thead><tbody><tr><td>NANOG</td><td>F: CAAAGGCAAACAACCCACTT<br>R: CTGGATGTTCTGG GTCTGGT</td><td>30</td><td>1.5</td><td>62</td><td>426</td></tr><tr><td>POU5F1/OCT4</td><td>F: GACAACAATGAGAACCTTCA<br>R: TTCTGGCGCCGGTTACAGAA</td><td>30</td><td>1.5</td><td>62</td><td>218</td></tr><tr><td>SOX2</td><td>F: ATGGACAGTTACGCGCACAT<br>R: GACTTGACCACCGAACCCAT</td><td>30</td><td>1.5</td><td>62</td><td>268</td></tr><tr><td>GAPDH</td><td>F: AGCCACATCGCTCAGACACC<br>R: GTACTCAGCGGCCAGCATCG</td><td>30</td><td>1.5</td><td>62</td><td>238</td></tr></tbody></table>
## Immunofluorescence and cytometry flow

Cells were fixed with PBS containing 4% paraformaldehyde for 20 minutes at room temperature and blocked with PBS containing 5% normal donkey serum for 30 minutes at room temperature. After blocking, cells were incubated with the appropriate primary antibody against POU5F1/OCT4 (sc-9081, Santa Cruz Biotechnology, Santa Cruz, CA; 1:300) or against proline 4-hydroxylase (P4H) (Dako, Trappes, France; 1:50) for 1 hour at room temperature. Cells were washed three times in PBS and incubated for 1 hour at room temperature with Alexa Fluor® 488 donkey anti-Rabbit (A-11034; Molecular Probes; 1:1000) and Alexa Fluor® 568 goat anti-mouse antibody (A11019, Invitrogen; 1:400) secondary antibodies for POU5F1/OCT4 and P4H respectively. Hoechst staining was added to first wash (Sigma, 5 µg/ml).

For flow cytometry, cells were harvested by treatment with 0.05% trypsin- EDTA (Invitrogen) and were resuspended in culture media. Cell aliquots were incubated on ice with anti-CD13 MAb conjugated to phycoerythrin (PE) (A07762, Beckman-Coulter, 1:50), anti-CD44 MAb conjugated to fluorescein isothiocyanate (FITC) (clone J-173, Immunotech; 1:50) and Tra-1-60 (90232, Chemicon) or conjugated isotypic controls. Flow cytometry was performed on a fluorescence-activated cell sorter (FACS Scan, Becton Dickinson), and data were analyzed with the CelQuest software (Becton Dickinson).

## Authors' contributions

SA: conception and design, collection and assembly of data, data analysis and interpretation, manuscript writing; DC, ST, VP: collection and assembly of data; OH: provision of study material; BK: design; SH: conception and design, provision of study material, manuscript writing; JDV: conception and design, provision of study material, data analysis and interpretation, manuscript writing, final approval of manuscript. All authors read and approved the final manuscript.

## Additional material

### Additional file 1

Table S1. Detailed sample list

Click here for file
[http://www.biomedcentral.com/content/supplementary/1471-2164-10-10-S1.xls]

### Additional file 2

Table S2. Transcriptome compendium. A compendium of 205 transcriptomes (signal and detection call).

Click here for file
[http://www.biomedcentral.com/content/supplementary/1471-2164-10-10-S2.rar]

### Additional file 3

Table S3. Hierarchical clustering gene lists. Transcripts lists from gene clusters a, b & c from Figure 1B.

Click here for file
[http://www.biomedcentral.com/content/supplementary/1471-2164-10-10-S3.zip]

### Additional file 4

Table S4. Main transcript signatures. Transcripts lists from the signatures analyzed in the manuscript: non-cell cycle MII oocytes/hESC signature (1), MII oocytes/hESC signature (2), MII oocyte signature (3), hESC signature (4), cell cycle MII oocytes/hESC signature (5) (Exel file). These lists can be found and datamined on our website Amazonia! http://amazonia.montp.inserm.fr using the "gene list" Amazonia! tool.

Click here for file
[http://www.biomedcentral.com/content/supplementary/1471-2164-10-10-S4.zip]

### Additional file 5

Figure S1. Expression bar charts for zinc finger domain containing genes. Expression bar charts for 18 transcripts overexpressed in oocytes and hESC and containing a zinc finger domain. These charts have been generated on our online gene expression Atlas Amazonia! http://amazonia.montp.inserm.fr. Abbreviations as in Figure 1C.

Click here for file
[http://www.biomedcentral.com/content/supplementary/1471-2164-10-10-S5.tif]

## Acknowledgements

We are grateful to the various labs that gave free access to their complete transcriptome data, in agreement with the MIAME recommendations [52]. We thank Isabelle Rodde-Astier and Bruno Delorme (MacoPharma) for their support, Laure Nadal for excellent technical work, Marc Piechaczyc et Isabelle Jariel for helpful discussions on the proteasome and for providing reagents and Marilyne Dijon for critical reviewing of the manuscript. Supported by the University Hospital of Montpellier, the Association Française contre les Myopathies (AFM), Ferring and Organon pharmaceuticals compagnies.

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