The endogenous retrovirus ENS-1 provides active binding sites for transcription factors in embryonic stem cells that specify extra embryonic tissue
© Mey et al; licensee BioMed Central Ltd. 2012
Received: 21 July 2011
Accepted: 15 March 2012
Published: 15 March 2012
Long terminal repeats (LTR) from endogenous retroviruses (ERV) are source of binding sites for transcription factors which affect the host regulatory networks in different cell types, including pluripotent cells. The embryonic epiblast is made of pluripotent cells that are subjected to opposite transcriptional regulatory networks to give rise to distinct embryonic and extraembryonic lineages. To assess the transcriptional contribution of ERV to early developmental processes, we have characterized in vitro and in vivo the regulation of ENS-1, a host adopted and developmentally regulated ERV that is expressed in chick embryonic stem cells.
We show that Ens-1 LTR activity is controlled by two transcriptional pathways that drive pluripotent cells to alternative developmental fates. Indeed, both Nanog that maintains pluripotency and Gata4 that induces differentiation toward extraembryonic endoderm independently activate the LTR. Ets coactivators are required to support Gata factors' activity thus preventing inappropriate activation before epigenetic silencing occurs during differentiation. Consistent with their expression patterns during chick embryonic development, Gata4, Nanog and Ets1 are recruited on the LTR in embryonic stem cells; in the epiblast the complementary expression of Nanog and Gata/Ets correlates with the Ens-1 gene expression pattern; and Ens-1 transcripts are also detected in the hypoblast, an extraembryonic tissue expressing Gata4 and Ets2, but not Nanog. Accordingly, over expression of Gata4 in embryos induces an ectopic expression of Ens-1.
Our results show that Ens-1 LTR have co-opted conditions required for the emergence of extraembryonic tissues from pluripotent epiblasts cells. By providing pluripotent cells with intact binding sites for Gata, Nanog, or both, Ens-1 LTR may promote distinct transcriptional networks in embryonic stem cells subpopulations and prime the separation between embryonic and extraembryonic fates.
Long terminal repeats (LTR) from endogenous retroviruses (ERV) are remnants of transposable elements disseminated in the genome that contain promoter activity  and can control nearby genes in different organisms [2–5]. They represent a source of binding sites for transcription factors , and some that are active in embryonic stem (ES) cells have been shown to rewire the Nanog and Oct3/4 transcriptional networks in a species-specific manner . Whether these changes are neutral or reflect species-specific adaptation to conserved developmental processes is not known, but ERV that escape silencing in pluripotent cells have been described in several species [4, 8].
ES cells are isolated from the inner cell mass of very early embryos and can generate all the cells of an organism , a unique property called pluripotency that is supported by Oct3/4 , Sox2  and Nanog  transcription factors. Oct3/4 and Nanog inhibit differentiation toward embryonic and extraembryonic lineages, the latter providing nutrient exchange and inductive signals for the embryo . These functions are well conserved in ES cells from different species, including chicken . In vivo, the emergence of extraembryonic tissues from pluripotent cells represents the first cell fate decision and precedes the differentiation of the embryonic lineages. Notably in different species, Nanog deficiency makes the cells tolerant to differentiation into extraembryonic endoderm lineages [15–17] allowing the action of Gata-6  and Gata-4 [19, 20] transcription factors to drive extraembryonic endoderm formation. However, it is not clear what mechanisms guide pluripotent cells toward embryonic or extraembryonic lineages upon the suppression of the controls exerted by Oct3/4  and Nanog .
To better understand the contribution of LTR to the transcriptional networks available in ES cells, we focused our interest on a developmentally regulated ERV and characterized its transcriptional regulation. The Ens-1 LTR controls the expression of a multigenic family of genes of retroviral origin, ENS (Embryonic Normal Stem cell), present only in Galliform species. The Ens-1 copy presents the most complete coding region and has been maintained in Galliform genomes through negative selection pressure  as observed for host-adopted retrotransposons . Ens-1 also called Erni, is expressed in pluripotent cells of the epiblast and later in the prospective neural plate [24, 25], where it has been demonstrated to delay the expression of Sox2  affecting the timing of emergence of the definitive neural plate and thus embryonic patterning. In vitro, Ens-1 is expressed in chicken ES (cES) cells  and is repressed when ES cells differentiation is induced, mimicking the repression of the Ens-1 LTR as further development occurs . In addition to the coding regions, more than 800 copies of solo-LTR are disseminated and placed in close contact to host genes in sense or in anti-sense orientations  where they might act as alternative promoters . We show here that the Ens-1 LTR is under the control of both Nanog and Gata factors in such a way that may direct the formation of the extraembryonic endoderm when ES cells exit pluripotency.
A cooperation between distinct DNA motifs controls the activity of the Ens-1promoter
Site S2 was separated from site S3 by only three nucleotides suggesting a close contact between factors occupying both sites and a narrow sequence specificity of the inhibiting deletions when compared with other close mutations.
It thus seems that the Ens-1 promoter is controlled by a combination of DNA binding proteins recognizing distinct and specific motifs and acting in a synergistic manner to promote the transcriptional activity.
The active domains are differently involved in the recruitment of ES specific protein complexes on the promoter
To address the role of the DNA active motifs in the recruitment of protein complexes, electrophoretic mobility shift assays (EMSA) were performed with nuclear extracts from cES cells. A 32P end-labelled double stranded oligonucleotide, spanning sites S1 to S3 and called p40, was used as a probe and was compared with the same sequence carrying mutations on sites S1, S2 or S3 (Figure 1A). To compare probes of similar sizes, the mutations were made by substitution. The p40 probe formed three different protein-DNA complexes, x, y and z (Figure 1C), the latest being sometimes resumed to a single band as illustrated in Figure 1D. These complexes were competed off by a 100-fold molar excess of unlabelled probe, but only the complex x resisted to a 100-fold molar excess of an irrelevant unlabelled probe indicating specific binding only for x (Figure 1C). When using nuclear extracts from cES cells induced to differentiate for four days with retinoic acid, no complex was formed on the DNA probe (Figure 1D) indicating that the binding was specific for pluripotent stem cells. As shown in Figure 1C the mutation of the S1 site did not affect complex formation, while mutation of the S3 site inhibited the formation of the complex x. The double mutation in S1 and S3 gave similar results as those obtained with the single S3 mutant version, confirming that S1 was not involved in complex formation. The mutation S2 (Figure 1D) completely inhibited the formation of the complex.
Altogether, these results indicate that a protein complex is specific for undifferentiated cES cells bound to the functional domain of the Ens-1 promoter and that sites S2 and S3 were necessary for the interaction with DNA.
Identification of the transcription factors recruited on the active binding sites
To confirm the recruitment of these transcription factors to the promoter, we performed chromatin immunoprecipitation (ChIP) assays using cES cells expressing exogenous Ets1, Gata4 or Nanog in fusion with a flag tag. Untagged factors and a flag-tagged version of the ubiquitous YY1 transcription factor were used as negative controls. Results shown in Figure 3C confirmed the specific recruitment of all the tagged proteins on the regulatory domain of the Ens-1 promoter when compared with flanking regions. These interactions were significantly higher than those obtained with negative controls. Altogether these data indicate that Nanog, Gata4, and Ets1 expressed in ES cells and repressed upon differentiation are recruited to the Ens-1 promoter in pluripotent cells and are good candidates to support its activity.
Combinations with Ets are required for Gata or Nanog to support the full Ens-1promoter activity
To test whether the active motifs in the Ens-1 promoter that have been characterized in ES cells were also used in differentiated cells, the combinations that fully restored the promoter activity were tested on p455 and on its mutated versions. As expected, the activation mediated by Gata4/Ets1 or by Nanog/Ets1 was fully impaired by mutations affecting either S1 + S3 or S2 + S3, respectively, leading to significantly lower luciferase activities than those obtained in undifferentiated cells with the wild type promoter. None of the single mutations abrogated the activity obtained with combinations of the transcription factors to the same extent. Indeed, with any of the transcription factors combinations tested, luciferase activities of p455 with single mutations were either not significantly different or higher than those observed in undifferentiated cells with p455 (Figure 5E). However, for a given combination of transcription factors, strong differences in the contribution of each binding site were revealed when compared to the activity on p455 in differentiated cells (Figure 5E).
As expected, the mutation in S3 (in an Ets binding site) significantly inhibited the activity mediated by Gata4/Ets1 or by Nanog/Ets1 on the wild type promoter (p < 0.05) while the S1 mutation (in a Gata binding site) only inhibited (p < 0.05) the activity of the Gata4/Ets1 combination (Figure 5E). In contrast, the S2 mutated version (in a Nanog binding site) did not show significant inhibition of the activity (p > 0.05) after ectopic expression of Nanog/Ets1 (Figure 5E) suggesting an indirect effect of Nanog in this combination of exogenous factors. To clarify this result, we evaluated the consequences of the mutations on promoter activity when expressing only Nanog.
Results shown in Figure 5F indicate that any of the single or double mutations significantly impaired the reactivation of the promoter mediated by Nanog, confirming the indirect effect and the requirement for intact S1, S2 and S3 binding sites. Results were different when expressing the other transcription factors. Although Gata4 alone failed to reactivate the p455 construct (Figure 5A and 5F), it reactivated the S2 mutant version to levels comparable to those obtained with the intact promoter in undifferentiated cells (Figure 5F). This was not the case with Nanog alone that restored the promoter activity on wild type p455 only. This indicates that the indirect effect of Nanog on the promoter activity required its interaction with the S2 site, probably releasing another DNA binding protein acting as a repressor. EMSA experiments in human HEK293 cells confirmed the direct interaction of the transfected chicken protein Gata4 with S1 site in non-ES cells (Additional file 3: Figure S3).
In contrast to Gata4, Ets1 was not able to increase the activity of a S2 mutant version of the promoter, indicating that the activity mediated by the combination of Nanog and Ets1 could not be only due to an indirect effect. The 2.5 (Figure 5B) to 4 (Figure 5E) fold increase in promoter activity in differentiated versus undifferentiated cells further illustrates the synergy between Nanog and Ets1.
Altogether these results reveal a functional interplay between Gata4, Nanog and Ets1 that requires intact S1, S2 and S3 binding sites, respectively. They also show the major role played by Ets1 to promote the activity mediated by Gata4 and by Nanog and also that Nanog partly acts in an indirect manner, probably by competition with another DNA binding protein acting as activity repressor on the S2 site.
Gata4 induces the ectopic expression of Ens-1 in the developing embryo and is associated with the expression of Ens-1in extraembryonic tissues
To confirm that Gata and Ets factors can support the activity of the Ens-1 promoter in vivo, Gata4 and Ets1 were overexpessed by electroporation in stage HH3 chick embryos. Interestingly, Gata4 electroporation, but not Ets1, was sufficient to induce Ens-1 ectopic expression (Figure 6C). Since Gata4 could not induce Ens-1 promoter activity when used alone in differentiated cells, these results may be due to the endogenous expression of Ets1 and Ets2 at the electroporation site (see Figure 4) that can cooperate with Gata4. In contrast, Gata factors were not expressed at the electroporation site but rather overlapped with Ens-1 expression (see Figure 4), discarding the possibility of testing the activity of Ets1 ectopically. These results confirmed that Gata4 is an activator of the Ens-1 LTR in vivo acting independently from Nanog. The electroporation of CP2 poorly induced the ectopic expression of Ens-1 confirming that its enhancer activity mainly depends of the control exerted by Nanog that was repressed at that stage (see Figure 4).
These results are in agreement with the existence of an additional level of regulation that involves epigenetic silencing, thereby restricting the accessibility of Ens-1 LTR for the binding of transcription factors. This is likely to occur at developmental stages where Ens-1 is no longer necessary and is in fact not expressed.
Distribution of the active copies of the Ens-1promoter in the chicken genome
This study addresses the question of whether the activity of an ERV LTR at very early developmental stages might be a source of targeted variability in the regulatory pathways operating in pluripotent cells. We show that the balance between the two opposite regulatory pathways controlling the decision between embryonic and extraembryonic tissues is co-opted in the regulation of the Ens-1 LTR promoter and correlates with its pattern of transcriptional activity.
We show that in ES cells, the Ens-1 LTR is controlled by the pluripotency specific transcription factor Nanog as described for other ERV that escape silencing . However, this LTR is also activated by a combination of Gata and Ets transcription factors, two families that are not restricted to pluripotent cells, but whose members were found here to be expressed in ES cells and in the epiblast in agreement with a previous report . At early developmental stages, the expression pattern of Gata and Ets transcription factors is likely to promote that of the ERV gene Ens-1, even in the absence of Nanog, such as in the primitive streak. In agreement with this observation, electroporation of Gata4 induced ectopic expression of Ens-1 in embryonic tissues that expressed Ets1 but not Nanog. In mammals, Gata4 overexpression is sufficient to transform ES cells into the extraembryonic endoderm lineage , and in agreement with this, we found expression of Gata4 in the chick hypoblast along with that of Ets-2. We show here that Ens-1 was also expressed in this extraembryonic tissue. In post-streak embryonic tissues, a good correlation was also observed between Gata4 and Ens-1 expression patterns until the formation of the neural plate (HH6), but Ets factors were not detected anymore suggesting the involvement of additional regulators. Indeed, in differentiated cells the activation domain attributed to Nanog was shown to play an indirect role in the activity mediated by Gata4 in the absence of Ets1. At later developmental stages Ens-1 is repressed in the whole embryo [24, 25] despite the wider expression of Gata [44, 45] and Ets  factors. In accordance with the silencing mechanisms reported for other ERV [4, 8], epigenetic regulations are likely to restrict the promoter accessibility in irrelevant tissues as observed here in differentiated cells where the expression of Ens-1 was strongly induced by treatment with epigenetic modifying drugs but not by the overexpression of Gata/Ets. Our results thus reveal that the Gata/Ets combination plays a role at developmental stages that correlates with the emergence of the hypoblast while distinct mechanisms are likely to occur in the neural plate [24, 47] and later.
Several lines of evidence indicate that both Nanog and Ets/Gata regulations are active in ES cells. First, all were expressed in ES cells; secondly, we found that Nanog, Gata4 and Ets1 were recruited on the Ens-1 promoter active domain in ES cells; thirdly, the suppression of the Nanog binding site only partially suppressed the promoter activity in ES cells and reciprocally with mutations in the Gata or in the Ets binding sites; fourthly, the activity mediated by Nanog is increased by Ets-1. This dual regulation is in agreement with the recent demonstration in the mouse that Nanog is required for the extraembryonic endoderm formation  that relies on the heterogeneity of ES cells populations. Accordingly distinct levels of the pluripotency marker Nanog are found among individual ES cells, Nanog-low cells expressing higher levels of extraembryonic endoderm markers  and being more prone to differentiate . Similarly the epiblast that concentrates pluripotent cells, also contains cellular sub-populations expressing extraembryonic endoderm markers in different species [51, 52]. These cells are likely precursors of the extraembryonic endoderm. Heterogeneity in the expression levels of Nanog, Ets and Gata factors was also observed here in stage XII/XIII chick epiblast where the periphery of the embryo that concentrates Gata factors expressed lower levels of Nanog transcripts. Despite this heterogeneity in the distribution of its regulating transcription factors, the expression level of Ens-1 was maintained in the whole epiblast probably reflecting the ability of both regulation pathways to support the Ens-1 LTR activity in cells with distinct fates. In embryonic tissues, Ens-1 regulates the timing of Sox2 activation and thus the emergence of the definitive neural plate . The present data support an earlier role of Ens-1 or co-regulated sequences in the process that drives the formation of the hypoblast from pluripotent cells. Accordingly, Ens-1 expression was found to be maintained in the hypoblast.
Experiments performed in differentiated cells revealed that Nanog as well as the Gata4/Ets1 combination can restore the promoter activity normally observed in ES cells. However, additional regulations are likely to favor one or the other regulation pathway as illustrated by the transcription factor CP2 that is an enhancer of the Ens-1 promoter activity in ES cells , but was shown here to solely promote the activation mediated by Nanog.
This balance between opposite active binding sites provided by the Ens-1 LTR is thus coherent with the requirements supporting the emergence of the extraembryonic endoderm from pluripotent tissues and may contribute to this progress. Active copies of the Ens-1 LTR may support in pluripotent cells the specific priming of genes involved later in the extraembryonic endoderm or in the neural plate formation. This is illustrated with Ens-1 that is expressed in cES cells but involved later during the neural plate formation . Alternatively the epigenetic silencing of the Ens-1 LTR during differentiation may serve to repress irrelevant genes [53, 54] according to the heterochromatin formation during ES cells differentiation .
Genome-wide studies combined with transcriptome analysis have concluded that LTR promoters may have an impact on tissue specific transcription [56, 57]. We show here that only 26% (227 on 874 ) of the Ens-1 LTR copies in the chicken genome contain an intact activation domain that supports transcriptional activity in the early embryo. Most of them are far from genes, and one third is localized in or at less than 20 kb of host genes, a distance that is compatible with a promoter activity and may direct gene functions in specific tissues. They may also act as enhancers inducing the transcription in both orientations  of non-coding RNA from intergenic loci . Such sequences are known to be important players during development  and may be involved in the guidance of chromatin-modifying complexes on specific targets  as required during ES cells differentiation [61–63]. The presence of active LTR near genes already involved in embryonic or in extraembryonic development as listed here is in favour of relevant species-specific adaptations.
Our results demonstrate that the Ens-1 LTR support gene expression in pluripotent and in extraembryonic tissues thus providing conditions for cell priming compatible with the unclarified emergence of extraembryonic endoderm cells from ES cells. In addition to Ens-1, transcriptome analysis based on active LTR distribution along the genome will serve as a basis to explore their contribution in the regulation of other genes and their role in defining ES cells subpopulations with distinct cell fates.
Cell culture and DNA transfection
The culturing of cES cells and their differentiation by retinoic acid 10-6 M have been previously described . cES cells or cES cells induced to differentiate 48 hours by retinoic acid were transfected using Lipofectamine 2000 reagent (Invitrogen) with p455-Firefly Luciferase reporter construct containing the Ens-1 minimal promoter, the Renilla Luciferase reporter construct, pRL-CMV, to normalize for transfection efficiency and expression vectors for transcription factors used alone or in combinations. Except when mentioned, an equal quantity of each expression vector was used and total DNA quantity between conditions was maintained constant using empty vector. Twenty-four hours after transfection the Firefly and Renilla Luciferase luminescences were successively measured using Dual Luciferase Assay (Promega) as described by the manufacturer. Firefly reporter gene values were normalized to the activity of the Renilla luciferase. Chromatin modifying drugs Trichostatin A (TSA), Valproic acid (VPA) and 5-azacytidine (5-aza) were from Sigma.
HEK (Human Embryonic Kidney) 293 cells were from ATCC (CRL-1573) and cultivated in DMEM (Gibco) supplemented with 10% fetal bovine serum (Perbio) as recommended by the supplier.
DNA binding assays
The preparation of DNA binding assays and nuclear extracts was performed as previously described  using double-stranded DNA probes labelled with 32P-ATP (Amersham). For competition experiments, a 100-fold molar excess of unlabelled double-stranded nucleotide, synthesized by Sigma, was incubated for 10 min with nuclear extract prior to the addition of the labeled double-stranded probe. For supershift experiments in HEK293 cells anti-Flag M2 antibody was from Sigma. Whole IgG purified from mice were from Zymed.
DNA constructs and site directed mutagenesis
The luciferase reporter construct p455-Luc was done using the pGL2 basic vector (Promega) as previously described and includes the LTR sequence from -455 to +83 of the transcription start site . Targeted mutagenesis by deletions was performed using the Quick Change Mutagenesis Kit (Stratagene) following the manufacturer's instructions. The U3-GFP construct expresses a GFP reporter gene placed under the control of to the sequence from -738 to +83 of the transcription start site described before . This largest construct contains the 738 bp of the promoter defined previously  which is present in the U3 region of the LTR of Ens genes . Both p455-Luc and U3-GFP contain 83 bp from the R region 5' end starting downstream the transcription start site .
Site directed mutations were performed by replacements or by deletions of bases as indicated in the figure legends. Large deletions in the constructs p455 del 128-87, del 128-57 del 179-128, del 179-87, del 179-57 and del 237-31 were obtained by ligation of two PCR amplified fragments surrounding the deletion. The transcription factors were cloned in a pCi-Neo expression vector (Promega) modified to introduce a flag tag at the N-terminal part of the protein. Ets-2 (Genbank:X07202), Gata3 (Genbank:XM_417294), Gata4 (Genbank:XM_420041) and Gata5 (Genbank:NM_205421) were amplified from chicken ES cells cDNA. Chicken Ets-1 (p54, Genbank:X13026) was given by Dr B. Wasylyk , Churchill (Genbank:AF238863) was a gift from Dr C. Stern . For over-expression experiments in the embryo, transcription factor coding sequences were placed under the control of the CAG promoter (a chicken b-actin promoter combined with CMV enhancer) to ensure strong expression . The predictions for transcription factor binding sites were carried out using the indicated programs available online (http://www.gene-regulation.com/pub/programs.html).
Real time PCR
Oligonucleotides used for gene expression analysis
ES cells were transfected using Lipofectamine 2000 (Invitrogen) with pCi vectors encoding for the indicated transcription factor in fusion with a Flag tag. The following day, cells were fixed with formaldehyde, collected and lysed in 50 mM Tris-HCl (pH 8.1), 10 mM EDTA, 0.5 mM EGTA, 1% (w/v) SDS, and proteases inhibitor for 5 minutes on ice. The cells were then sonicated to shear chromatin to a final average size of 200-600 base pairs. Sonicated chromatin was diluted 1/10 with the following buffer: 20 mM Tris-HCl (pH 8.1), 1% (v/v) Triton X-100, 150 mM NaCl, 1 mM EDTA and proteases inhibitors. Immunoprecipitation was carried out overnight at 4°C with 50 ml of agarose beads coated with anti-Flag M2 antibody (Sigma). Beads were washed extensively, and bound material was eluted by two incubation rounds of 15 minutes in 1% (w/v) SDS and 0.1 M NaHCO3 at room temperature. Cross-linking was reversed by incubation 4 h at 65°C in 200 mM NaCl and 100 mg/ml proteinase K. The DNA was purified using Mini-Elute columns (Qiagen). Aliquots were used for quantitative real-time PCR as described above. The oligonuclotides used were designed either inside the p455 region (GAGGAACAAGTCCAGGCAAG; GATGGCCATTTTCCTTGAGA), or 1000 bp upstream (CCCACGGTACACAATGAACA; GCTAGGGAGCCCTTTAACCA), or 1000 bp downstream (TGGTGTGGTGTTTGCAGTTT; CCCTTTGTTGAGGAAAGCAC) from the Ens-1 copy on chromosome 5. The region bounded by the primers designed inside the p455 sequence is located between positions -278 and -93 from the transcription start site.
Fertilised chicken eggs were purchased from Granja Santa Isabel, Cordoba, Spain. Eggs were incubated, opened and staged according to Eyal-Giladi and Kochav  for the pre-primitive streak stages and Hamburger and Hamilton  for subsequent stages. They were dissected and fixed overnight in 4% paraformaldehyde in phosphate buffered saline (PBS) at 4°C.
Chicken embryos electroporation
Stage 2-4  chick embryos were explanted, washed in PBS, and placed upside down over an electroporation chamber (NEPAGEN) containing a platinum electrode connected to the negative pole. After visualizing the embryo, a solution containing expression plasmids (2 mg/ml in PBS with 0.1% Fastgreen and 6% sucrose) was injected between the vitelline membrane and the epiblast. An anodal electrode was placed over the hypoblast to cover the injected area and contact was made with PBS. A train of electric pulses (5 pulses, 4 Volts, 50 ms, 0.5 Hz) were applied using an Intracept TSS10 pulse stimulator (Intracell). The embryos were then placed in culture as described  and allowed to develop until they reach the required stage. Embryos were then photographed with a Leica MZFLIII dissecting microscope to record GFP or DsRed expression and fixed overnight in 4% paraformaldehyde (PFA) in PBS at 4°C for subsequent processing.
Whole mount in situ hybridization
Whole-mount in situ hybridization was carried out in chick embryos at various stages of development as previously described . Digoxigenin-labelled probes for ENS1 , CP2 , Ets1, Ets2, Gata2, Gata4, Gata5 and Nanog with digoxigenin-UTP (Roche) were synthesized. After hybridization, embryos were fixed in 4% paraformaldehyde in PBS, washed in PBS, and photographed in whole-mount under a Leica M10 dissecting scope. Subsequently, some embryos were embedded in gelatine and sectioned in a vibratome at 40 μm. These slices were photographed using an Olympus DP70 digital camera mounted on a Leica DMR microscope with Nomarski optics.
Detection and localization of solo-LTR in the chicken genome
Using the sequence of the Ens-1 LTR as a reference, the occurrence of solo-LTR were searched in the latest version of the chicken genome (release galGal3) that was downloaded from the UCSC website (http://hgdownload.cse.ucsc.edu/downloads.html) using blastn . We classified each solo-LTR as active or inactive according to the presence or absence of the motifs identified as being essential to its activity by using the program fuzznuc from the EMBOSS package . We thus obtained 227 active solo-LTR and 916 inactive solo-LTR. Using the Ensembl facilities  (http://www.ensembl.org/index.html), we mapped the distribution of each type of solo-LTR on the chromosomes. By combining the positions of the active solo-LTR and those of the genes, we determined the active solo-LTR inserted close to genes (at less than 20 kb or inside the genes). Genes ontology annotations were retrieved from the Ensembl database using the Biomart tool  (http://www.ensembl.org/index.html).
We thank Dr. B. Wasylyk and Dr. C. Stern for Ets1 and Churchill expression vectors respectively. We thank Dr. F. Lavial and Dr. B. Pain for qPCR primers sequences. This work was supported by grants from the ANR (Agence Nationale pour la Recherche) Genanimal (ANR-06-GANI-007-01) and the ANR Blanc (ANR-09-BLAN-0141) to JS, grants from INRA to AM and grants from the Spanish Ministry of Science and Innovation (BFU2008-01042, CONSOLIDER-INGENIO 2010 CSD2007-00017 and CSD2007-00023) to MAN.
- Brosius J: Genomes were forged by massive bombardments with retroelements and retrosequences. Genetica. 1999, 107: 209-238. 10.1023/A:1004018519722.View ArticlePubMedGoogle Scholar
- Medstrand P, van de Lagemaat LN, Dunn CA, Landry JR, Svenback D, Mager DL: Impact of transposable elements on the evolution of mammalian gene regulation. Cytogenet Genome Res. 2005, 110: 342-352. 10.1159/000084966.View ArticlePubMedGoogle Scholar
- van de Lagemaat LN, Landry JR, Mager DL, Medstrand P: Transposable elements in mammals promote regulatory variation and diversification of genes with specialized functions. Trends Genet. 2003, 19: 530-536. 10.1016/j.tig.2003.08.004.View ArticlePubMedGoogle Scholar
- Peaston AE, Evsikov AV, Graber JH, de Vries WN, Holbrook AE, Solter D, Knowles BB: Retrotransposons regulate host genes in mouse oocytes and preimplantation embryos. Dev Cell. 2004, 7: 597-606. 10.1016/j.devcel.2004.09.004.View ArticlePubMedGoogle Scholar
- Jordan IK, Rogozin IB, Glazko GV, Koonin EV: Origin of a substantial fraction of human regulatory sequences from transposable elements. Trends Genet. 2003, 19: 68-72. 10.1016/S0168-9525(02)00006-9.View ArticlePubMedGoogle Scholar
- Bourque G, Leong B, Vega VB, Chen X, Lee YL, Srinivasan KG, Chew J-L, Ruan Y, Wei C-L, Ng HH, Liu ET: Evolution of the mammalian transcription factor binding repertoire via transposable elements. Genome Res. 2008, 18: 1752-1762. 10.1101/gr.080663.108.PubMed CentralView ArticlePubMedGoogle Scholar
- Kunarso G, Chia N-Y, Jeyakani J, Hwang C, Lu X, Chan Y-S, Ng H-H, Bourque G: Transposable elements have rewired the core regulatory network of human embryonic stem cells. Nat Genet. 2010, 42: 631-634. 10.1038/ng.600.View ArticlePubMedGoogle Scholar
- Rowe HM, Trono D: Dynamic control of endogenous retroviruses during development. Virology. 2011, 411: 273-287. 10.1016/j.virol.2010.12.007.View ArticlePubMedGoogle Scholar
- O'Shea KS: Self-renewal vs. differentiation of mouse embryonic stem cells. Biol Reprod. 2004, 71: 1755-1765. 10.1095/biolreprod.104.028100.View ArticlePubMedGoogle Scholar
- Nichols J, Zevnik B, Anastassiadis K, Niwa H, Klewe-Nebenius D, Chambers I, Scholer H, Smith A: Formation of pluripotent stem cells in the mammalian embryo depends on the POU transcription factor Oct4. Cell. 1998, 95: 379-391. 10.1016/S0092-8674(00)81769-9.View ArticlePubMedGoogle Scholar
- Avilion AA, Nicolis SK, Pevny LH, Perez L, Vivian N, Lovell-Badge R: Multipotent cell lineages in early mouse development depend on SOX2 function. Genes Dev. 2003, 17: 126-140. 10.1101/gad.224503.PubMed CentralView ArticlePubMedGoogle Scholar
- Chambers I, Colby D, Robertson M, Nichols J, Lee S, Tweedie S, Smith A: Functional expression cloning of Nanog, a pluripotency sustaining factor in embryonic stem cells. Cell. 2003, 113: 643-655. 10.1016/S0092-8674(03)00392-1.View ArticlePubMedGoogle Scholar
- Arnold SJ, Robertson EJ: Making a commitment: cell lineage allocation and axis patterning in the early mouse embryo. Nat Rev Mol Cell Biol. 2009, 10: 91-103. 10.1038/nrm2618.View ArticlePubMedGoogle Scholar
- Lavial F, Acloque H, Bertocchini F, Macleod DJ, Boast S, Bachelard E, Montillet G, Thenot S, Sang HM, Stern CD, et al: The Oct4 homologue PouV and Nanog regulate pluripotency in chicken embryonic stem cells. Development. 2007, 134: 3549-3563. 10.1242/dev.006569.View ArticlePubMedGoogle Scholar
- Mitsui K, Tokuzawa Y, Itoh H, Segawa K, Murakami M, Takahashi K, Maruyama M, Maeda M, Yamanaka S: The homeoprotein Nanog is required for maintenance of pluripotency in mouse epiblast and ES cells. Cell. 2003, 113: 631-642. 10.1016/S0092-8674(03)00393-3.View ArticlePubMedGoogle Scholar
- Hyslop L, Stojkovic M, Armstrong L, Walter T, Stojkovic P, Przyborski S, Herbert M, Murdoch A, Strachan T, Lako M: Downregulation of NANOG Induces Differentiation of Human Embryonic Stem Cells to Extraembryonic Lineages. Stem Cells. 2005, 23: 1035-1043. 10.1634/stemcells.2005-0080.View ArticlePubMedGoogle Scholar
- Hough SR, Clements I, Welch PJ, Wiederholt KA: Differentiation of Mouse Embryonic Stem Cells after RNA Interference-Mediated Silencing of OCT4 and Nanog. Stem Cells. 2006, 24: 1467-1475. 10.1634/stemcells.2005-0475.View ArticlePubMedGoogle Scholar
- Koutsourakis M, Langeveld A, Patient R, Beddington R, Grosveld F: The transcription factor GATA6 is essential for early extraembryonic development. Development. 1999, 126: 723-732.Google Scholar
- Soudais C, Bielinska M, Heikinheimo M, MacArthur CA, Narita N, Saffitz JE, Simon MC, Leiden JM, Wilson DB: Targeted mutagenesis of the transcription factor GATA-4 gene in mouse embryonic stem cells disrupts visceral endoderm differentiation in vitro. Development. 1995, 121: 3877-3888.PubMedGoogle Scholar
- Fujikura J, Yamato E, Yonemura S, Hosoda K, Masui S, Nakao K: Miyazaki J-i, Niwa H: Differentiation of embryonic stem cells is induced by GATA factors. Genes Dev. 2002, 16: 784-789. 10.1101/gad.968802.PubMed CentralView ArticlePubMedGoogle Scholar
- Niwa H, Miyazaki J, Smith AG: Quantitative expression of Oct-3/4 defines differentiation, dedifferentiation or self-renewal of ES cells. Nat Genet. 2000, 24: 372-376. 10.1038/74199.View ArticlePubMedGoogle Scholar
- Lerat E, Birot AM, Samarut J, Mey A: Maintenance in the chicken genome of the retroviral-like cENS gene family specifically expressed in early embryos. J Mol Evol. 2007, 65: 215-227. 10.1007/s00239-007-9001-4.View ArticlePubMedGoogle Scholar
- Sekita Y, Wagatsuma H, Nakamura K, Ono R, Kagami M, Wakisaka N, Hino T, Suzuki-Migishima R, Kohda T, Ogura A, et al: Role of retrotransposon-derived imprinted gene, Rtl1, in the feto-maternal interface of mouse placenta. Nat Genet. 2008, 40: 243-248. 10.1038/ng.2007.51.View ArticlePubMedGoogle Scholar
- Streit A, Berliner AJ, Papanayotou C, Sirulnik A, Stern CD: Initiation of neural induction by FGF signalling before gastrulation. Nature. 2000, 406: 74-78. 10.1038/35017617.View ArticlePubMedGoogle Scholar
- Acloque H, Risson V, Birot AM, Kunita R, Pain B, Samarut J: Identification of a new gene family specifically expressed in chicken embryonic stem cells and early embryo. Mech Dev. 2001, 103: 79-91. 10.1016/S0925-4773(01)00336-7.View ArticlePubMedGoogle Scholar
- Papanayotou C, Mey A, Birot AM, Saka Y, Boast S, Smith JC, Samarut J, Stern CD: A mechanism regulating the onset of Sox2 expression in the embryonic neural plate. PLoS Biol. 2008, 6: e2-PubMed CentralView ArticlePubMedGoogle Scholar
- Acloque H, Mey A, Birot AM, Gruffat H, Pain B, Samarut J: Transcription factor cCP2 controls gene expression in chicken embryonic stem cells. Nucleic Acids Res. 2004, 32: 2259-2271. 10.1093/nar/gkh545.PubMed CentralView ArticlePubMedGoogle Scholar
- Cohen CJ, Lock WM, Mager DL: Endogenous retroviral LTRs as promoters for human genes: A critical assessment. Gene. 2009, 448: 105-114. 10.1016/j.gene.2009.06.020.View ArticlePubMedGoogle Scholar
- Merika M, Orkin SH: DNA-binding specificity of GATA family transcription factors. Mol Cell Biol. 1993, 13: 3999-4010.PubMed CentralView ArticlePubMedGoogle Scholar
- Fisher RJ, Mavrothalassitis G, Kondoh A, Papas TS: High-affinity DNA-protein interactions of the cellular ETS1 protein: the determination of the ETS binding motif. Oncogene. 1991, 6: 2249-2254.PubMedGoogle Scholar
- Sheng G, dos Reis M, Stern CD: Churchill, a zinc finger transcriptional activator, regulates the transition between gastrulation and neurulation. Cell. 2003, 115: 603-613. 10.1016/S0092-8674(03)00927-9.View ArticlePubMedGoogle Scholar
- Jauch R, Ng CKL, Saikatendu KS, Stevens RC, Kolatkar PR: Crystal Structure and DNA Binding of the Homeodomain of the Stem Cell Transcription Factor Nanog. J Mol Biol. 2008, 376: 758-770. 10.1016/j.jmb.2007.11.091.View ArticlePubMedGoogle Scholar
- Segal E, Widom J: Poly(dA:dT) tracts: major determinants of nucleosome organization. Curr Opin Struct Biol. 2009, 19: 65-71. 10.1016/j.sbi.2009.01.004.PubMed CentralView ArticlePubMedGoogle Scholar
- Rex M, Orme A, Uwanogho D, Tointon K, Wigmore PM, Sharpe PT, Scotting PJ: Dynamic expression of chicken Sox2 and Sox3 genes in ectoderm induced to form neural tissue. Dev Dyn. 1997, 209: 323-332. 10.1002/(SICI)1097-0177(199707)209:3<323::AID-AJA7>3.0.CO;2-K.View ArticlePubMedGoogle Scholar
- Chazaud C, Yamanaka Y, Pawson T, Rossant J: Early Lineage Segregation between Epiblast and Primitive Endoderm in Mouse Blastocysts through the Grb2-MAPK Pathway. Dev Cell. 2006, 10: 615-624. 10.1016/j.devcel.2006.02.020.View ArticlePubMedGoogle Scholar
- Bertocchini F, Stern CD: The Hypoblast of the Chick Embryo Positions the Primitive Streak by Antagonizing Nodal Signaling. Dev Cell. 2002, 3: 735-744. 10.1016/S1534-5807(02)00318-0.View ArticlePubMedGoogle Scholar
- Haider S, Ballester B, Smedley D, Zhang J, Rice P, Kasprzyk A: BioMart Central Portal‚Äîunified access to biological data. Nucleic Acids Res. 2009, 37: W23-W27. 10.1093/nar/gkp265.PubMed CentralView ArticlePubMedGoogle Scholar
- Lowe CB, Bejerano G, Haussler D: Thousands of human mobile element fragments undergo strong purifying selection near developmental genes. Proc Natl Acad Sci. 2007, 104: 8005-8010. 10.1073/pnas.0611223104.PubMed CentralView ArticlePubMedGoogle Scholar
- Blanchon L, Bocco JL, Gallot D, Gachon A-M, LÈmery D, DÈchelotte P, Dastugue B, Sapin V: Co-localization of KLF6 and KLF4 with pregnancy-specific glycoproteins during human placenta development. Mech Dev. 2001, 105: 185-189. 10.1016/S0925-4773(01)00391-4.View ArticlePubMedGoogle Scholar
- Kenzelmann-Broz D, Tucker RP, Leachman NT, Chiquet-Ehrismann R: The expression of teneurin-4 in the avian embryo: potential roles in patterning of the limb and nervous system. Int J Dev Biol. 2010, 54: 1509-1516.View ArticlePubMedGoogle Scholar
- Lee H-J, Palkovits Ms, Young WS: miR-7b, a microRNA up-regulated in the hypothalamus after chronic hyperosmolar stimulation, inhibits Fos translation. Proc Natl Acad Sci. 2006, 103: 15669-15674. 10.1073/pnas.0605781103.PubMed CentralView ArticlePubMedGoogle Scholar
- Yang D-H, Smith ER, Cai KQ, Xu X-X: c-fos elimination compensates for disabled-2 requirement in mouse extraembryonic endoderm development. Dev Dyn. 2009, 238: 514-523. 10.1002/dvdy.21856.PubMed CentralView ArticlePubMedGoogle Scholar
- Chapman S, Matsumoto K, Cai Q, Schoenwolf G: Specification of germ layer identity in the chick gastrula. BMC Dev Biol. 2007, 7: 91-107. 10.1186/1471-213X-7-91.PubMed CentralView ArticlePubMedGoogle Scholar
- Laverriere AC, MacNeill C, Mueller C, Poelmann RE, Burch JB, Evans T: GATA-4/5/6, a subfamily of three transcription factors transcribed in developing heart and gut. J Biol Chem. 1994, 269: 23177-23184.PubMedGoogle Scholar
- Minko K, Bollerot K, Drevon C, Hallais MF, Jaffredo T: From mesoderm to blood islands: patterns of key molecules during yolk sac erythropoiesis. Gene Expr Patterns. 2003, 3: 261-272. 10.1016/S1567-133X(03)00053-X.View ArticlePubMedGoogle Scholar
- Tahtakran SA, Selleck MAJ: Ets-1 expression is associated with cranial neural crest migration and vasculogenesis in the chick embryo. Gene Expr Patterns. 2003, 3: 455-458. 10.1016/S1567-133X(03)00065-6.View ArticlePubMedGoogle Scholar
- Albazerchi A, Stern CD: A role for the hypoblast (AVE) in the initiation of neural induction, independent of its ability to position the primitive streak. Dev Biol. 2007, 301: 489-503. 10.1016/j.ydbio.2006.08.057.View ArticlePubMedGoogle Scholar
- Messerschmidt DM, Kemler R: Nanog is required for primitive endoderm formation through a non-cell autonomous mechanism. Dev Biol. 2010, 344: 129-137. 10.1016/j.ydbio.2010.04.020.View ArticlePubMedGoogle Scholar
- Singh AM, Hamazaki T, Hankowski KE, Terada N: A Heterogeneous Expression Pattern for Nanog in Embryonic Stem Cells. Stem Cells. 2007, 25: 2534-2542. 10.1634/stemcells.2007-0126.View ArticlePubMedGoogle Scholar
- Chambers I, Silva J, Colby D, Nichols J, Nijmeijer B, Robertson M, Vrana J, Jones K, Grotewold L, Smith A: Nanog safeguards pluripotency and mediates germline development. Nature. 2007, 450: 1230-1234. 10.1038/nature06403.View ArticlePubMedGoogle Scholar
- Canham MA, Sharov AA, Ko MSH, Brickman JM: Functional Heterogeneity of Embryonic Stem Cells Revealed through Translational Amplification of an Early Endodermal Transcript. PLoS Biol. 2010, 8: e1000379-10.1371/journal.pbio.1000379.PubMed CentralView ArticlePubMedGoogle Scholar
- Debeb BG, Galat V, Epple-Farmer J, Iannaccone S, Woodward WA, Bader M, Iannaccone P, Binas B: Isolation of Oct4-Expressing Extraembryonic Endoderm Precursor Cell Lines. PLoS One. 2009, 4: e7216-10.1371/journal.pone.0007216.PubMed CentralView ArticlePubMedGoogle Scholar
- Huda A, Bowen NJ, Conley AB, Jordan IK: Epigenetic regulation of transposable element derived human gene promoters. Gene. 2011, 475: 39-48. 10.1016/j.gene.2010.12.010.View ArticlePubMedGoogle Scholar
- Macfarlan TS, Gifford WD, Agarwal S, Driscoll S, Lettieri K, Wang J, Andrews SE, Franco L, Rosenfeld MG, Ren B, Pfaff SL: Endogenous retroviruses and neighboring genes are coordinately repressed by LSD1/KDM1A. Genes Dev. 2011, 25: 594-607. 10.1101/gad.2008511.PubMed CentralView ArticlePubMedGoogle Scholar
- Meshorer E, Misteli T: Chromatin in pluripotent embryonic stem cells and differentiation. Nat Rev Mol Cell Biol. 2006, 7: 540-546. 10.1038/nrm1938.View ArticlePubMedGoogle Scholar
- Conley AB, Piriyapongsa J, Jordan IK: Retroviral promoters in the human genome. Bioinformatics. 2008, 24: 1563-1567. 10.1093/bioinformatics/btn243.View ArticlePubMedGoogle Scholar
- Faulkner GJ, Kimura Y, Daub CO, Wani S, Plessy C, Irvine KM, Schroder K, Cloonan N, Steptoe AL, Lassmann T, et al: The regulated retrotransposon transcriptome of mammalian cells. Nat Genet. 2009, 41: 563-571. 10.1038/ng.368.View ArticlePubMedGoogle Scholar
- Pi W, Zhu X, Wu M, Wang Y, Fulzele S, Eroglu A, Ling J, Tuan D: Long-range function of an intergenic retrotransposon. Proc Natl Acad Sci. 2010, 107: 12992-12997. 10.1073/pnas.1004139107.PubMed CentralView ArticlePubMedGoogle Scholar
- Pauli A, Rinn JL, Schier AF: Non-coding RNAs as regulators of embryogenesis. Nat Rev Genet. 2011, 12: 136-149.PubMed CentralView ArticlePubMedGoogle Scholar
- Khalil AM, Guttman M, Huarte M, Garber M, Raj A, Rivea Morales D, Thomas K, Presser A, Bernstein BE, van Oudenaarden A, et al: Many human large intergenic noncoding RNAs associate with chromatin-modifying complexes and affect gene expression. Proc Natl Acad Sci. 2009, 106: 11667-11672. 10.1073/pnas.0904715106.PubMed CentralView ArticlePubMedGoogle Scholar
- Fazzio TG, Huff JT, Panning B: An RNAi Screen of Chromatin Proteins Identifies Tip60-p400 as a Regulator of Embryonic Stem Cell Identity. Cell. 2008, 134: 162-174. 10.1016/j.cell.2008.05.031.PubMed CentralView ArticlePubMedGoogle Scholar
- Gaspar-Maia A, Alajem A, Polesso F, Sridharan R, Mason MJ, Heidersbach A, Ramalho-Santos Jo, McManus MT, Plath K, Meshorer E, Ramalho-Santos M: Chd1 regulates open chromatin and pluripotency of embryonic stem cells. Nature. 2009, 460: 863-868.PubMed CentralPubMedGoogle Scholar
- Caillier M, Thenot S, Tribollet V, Birot AM, Samarut J, Mey A: Role of the Epigenetic Regulator HP1gamma in the Control of Embryonic Stem Cell Properties. PLoS One. 2010, 5: e15507-10.1371/journal.pone.0015507.PubMed CentralView ArticlePubMedGoogle Scholar
- Schneikert J, Lutz Y, Wasylyk B: Two independent activation domains in c-Ets-1 and c-Ets-2 located in non-conserved sequences of the ets gene family. Oncogene. 1992, 7: 249-256.PubMedGoogle Scholar
- Niwa H, Yamamura K, Miyazaki J: Efficient Selection for High-Expression Transfectants with a Novel Eukaryotic Vector. Gene. 1991, 108: 193-199. 10.1016/0378-1119(91)90434-D.View ArticlePubMedGoogle Scholar
- Eyal-Giladi H, Kochav S: From cleavage to primitive streak formation: A complementary normal table and a new look at the first stages of the development of the chick: I. General morphology. Developmental Biology. 1976, 49: 321-337.PubMedGoogle Scholar
- Hamburger V, Hamilton H: A series of normal stages in the development of the chick embryo. J Morphol. 1951, 88: 49-92. 10.1002/jmor.1050880104.View ArticlePubMedGoogle Scholar
- Chapman SC, Collignon J, Schoenwolf GC, Lumsden A: Improved method for chick whole-embryo culture using a filter paper carrier. Dev Dyn. 2001, 220: 284-289. 10.1002/1097-0177(20010301)220:3<284::AID-DVDY1102>3.0.CO;2-5.View ArticlePubMedGoogle Scholar
- Acloque H, Wilkinson DG, Nieto MA, Dr. Marianne B-F: Chapter 9 In Situ Hybridization Analysis of Chick Embryos in Whole[hyphen (true graphic)]Mount and Tissue Sections. Methods in Cell Biology. 2008, Academic Press, 87: 169-185.Google Scholar
- Altschul SF, Madden TL, Schäffer AA, Zhang J, Zhang Z, Miller W, Lipman DJ: Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res. 1997, 25: 3389-3402. 10.1093/nar/25.17.3389.PubMed CentralView ArticlePubMedGoogle Scholar
- Rice P, Longden I, Bleasby A: EMBOSS: The European Molecular Biology Open Software Suite. Trends Genet. 2000, 16: 276-277. 10.1016/S0168-9525(00)02024-2.View ArticlePubMedGoogle Scholar
- Flicek P, Amode MR, Barrell D, Beal K, Brent S, Chen Y, Clapham P, Coates G, Fairley S, Fitzgerald S, et al: Ensembl 2011. Nucleic Acids Res. 2011, 39: D800-D806. 10.1093/nar/gkq1064.PubMed CentralView ArticlePubMedGoogle Scholar
This article is published under license to 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.