Ultimately, the cell’s pluripotent state reflects the action of multiple signalling cues on the downstream gene expression programs. Transcription factors (TF) are the key mediators in this process, which will coordinate the activation, repression or even priming of transcription, trough recruitment of multi-protein complexes and alteration of the chromatin environments. Gene function studies in ESCs have allowed thus far the identification of a critical network of TFs that robustly confer their unique pluripotent identity.
1.5.2.1 Core transcription factors
The triad Oct4-Sox2-Nanog is at the core of the transcriptional regulation in ESCs as revealed by their co-binding to the same genome-wide DNA target sites (Kim et al., 2008). Oct4 is a member of the Pit-Oct-Unc (POU) family, and is encoded by the Pou5f1 gene. It was one of the first transcription factors identified as crucial in early embryo development. It is expressed from the 8-cell stage and its expression becomes restricted to the pluripotent ICM prior to implantation, and remains on in the epiblast after implantation before being confined to the posterior epiblast and PGCs (Osorno et al., 2012; Radzisheuskaya et al., 2013; Scholer, 1991). Concordantly, Oct4 is highly expressed in embryo-derived ESCs, EpiSCs and EGs, and its expression is reduced when cells are induced to lose their pluripotent identity (Nichols et al., 1998). Fine-tuning of Oct4 levels is an essential requirement for the pluripotent state in ESCs, as reduction of Oct4 expression is sufficient to trigger differentiation into TS-like cells, by lack of Oct4-depentend inhibition of the
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TE markers Cdx2 (Niwa et al., 2000; Niwa et al., 2005). Conversely, its over-expression induces differentiation of ESCs into primitive endoderm and mesoderm fates (Niwa et al., 2000), proposing that Oct4 may function in a dynamic context-dependent manner.
Oct4 regulates the expression of a broad range of genes through direct DNA binding. In particular, it has been found to recognise an octamer-sox motif (Oct-Sox) in the DNA, where it cooperates with Sox2 in regulating gene activation (Tomioka et al., 2002). Evidence for Oct4 versatility comes from the identification of novel cell state-dependent protein partners. Upon induction of a PrE-like state in ESCs by enforced Sox17 expression, Oct4 is re-distributed into regulatory sites of endodermal genes, switching interaction between Sox2 to Sox17 (Aksoy et al., 2013). Similarly, upon exit of the naïve ESC state into a primed EpiSC-like state, Oct4 binding is also re-distributed into Otx2 or Zic motifs, at regulatory regions of genes associated with the post- implantation epiblast (Buecker et al., 2014; Yang et al., 2014). Notably, some level of Oct4 binding is already present at a selection of post-implantation genes in the naïve state such as Fgf5 or Brachyury, possibly associated with lineage priming functions.
In addition to Sox2, genome-wide Oct4 binding sites in ESCs encompass motif sequences for other pluripotency factors (Buecker et al., 2014), which integrate the so-called “Oct4-centric module”. The definition of such module was based on the chromatin co-occupancy of proteins at target chromatin sites, encompassing factors such as Nanog, Sox2, Esrrb, Klf4, Smad1, Stat3, Dax1 or Tcfp2l1 (Chen et al., 2008; Kim et al., 2008). This analysis further uncovered a second module centred on c-Myc (“Myc-centric module”), which involves factors such as n‑Myc, E2f1, Zfx and Rex1, and appears to control different sets of genes that are associated with protein metabolism and cell cycle (Chen et al., 2008; Hu et al., 2009). Furthermore, Oct4 physically interacts with a set of pluripotency factors, consistent with their identified co-binding in the DNA. Since abolishing Oct4 strikingly impairs the recruitment of these factors, it has been proposed to play a pioneer role in the assembly of multi-protein complexes at the chromatin (van den Berg et al., 2010).
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Sox2 [SRY (sex determining region Y)-box 2] is a member of the Sox family of transcription factors that, like Oct4, is detected in the pluripotent ICM, where it cooperates with Oct4 in TE/ICM segregation (Avilion et al., 2003; Masui et al., 2007). However, after implantation the expression of Oct4 and Sox2 become oppositely restricted to the posterior (mesoderm, endoderm) and anterior (ectoderm) epiblast, respectively. Concordantly, Sox2 is expressed in ESCs, EpiSCs, PGCs/EGs, and embryonic and adult neural stem cells (D'Amour and Gage, 2003; Ellis et al., 2004).
As mentioned above, Oct4 and Sox2 co-regulate pluripotency genes through binding to a common Oct–Sox motif at regulatory regions. Similarly to Oct4, upon induction of neuronal fates, Sox2 was found to switch partners to activate neuronal genes. Specifically, it has been found to co-occupy neuronal-specific regulatory sites with another member of the POU family – Brn2 (Pou3f2). However, unlike Oct4, Sox2 recognises the same DNA sequence in different cell states, suggesting that the re-distribution of binding at target sites is driven by its specific co-partners in a context-dependent manner (Lodato et al., 2013) .
Nanog is a homeobox transcription factor that, alongside Oct4 and Sox2, is expressed in the pluripotent ICM, but becomes restricted to the epiblast progenitor blastomeres in late blastocysts by counteracting Gata6-driven PrE specification (Chazaud et al., 2006). Nanog expression is down-regulated before implantation and is re-activated in the posterior primitive-streak until early somitogenesis (Osorno et al., 2012). Similarly to Oct4 and Sox2, it is expressed in ESCs, EpiSCs and PGCs/EGs, having an essential role in the maintenance of pluripotency as highlighted by the loss of ESC self-renewal upon conditional depletion, and the acquisition of LIF- independence upon over-expression (Chambers et al., 2003; Mitsui et al., 2003). Based on this property the gene was named after the legendary Tir na n’Og - the Celtic land of the ever young. Nanog inhibits the expression of the PrE markers Gata4 and Gata6, while promoting the expression of many pluripotency genes in the Oct4-centric module (Chen et al., 2008; Kim et al., 2008). Unlike Oct4, the expression levels of Nanog (and Sox2) diminish in the post-implantation epiblast and in EpiSCs. Concordantly, forced expression of Nanog in EpiSCs can revert them back
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to an ESC state, whereas over-expressing in ESCs prevents differentiation (Osorno and Chambers, 2011).
Similarly, the expression of a set of naïve pluripotency markers such as Esrrb, Klf4, Klf5, Tbx3 and Rex1 also become down-regulated in EpiSCs (Festuccia et al., 2012; Osorno and Chambers, 2011). Given the equal dynamics of Nanog, reduction of this set of pluripotency markers may be a consequence of Nanog decrease. In agreement, metastable culture conditions (Serum/LIF) stimulate high heterogeneity of Nanog expression, promoted by auto-regulatory loop of Nanog (Navarro et al., 2012). Heterogeneous expression of the downstream targets Esrrb, Klf4 and Tbx3 is also detected in such conditions, suggesting that these fluctuations are directly influenced by Nanog expression itself (Osorno and Chambers, 2011). Notably, over-expression of these Nanog’s gene targets (Klf4, Tbx3 and Esrrb) is sufficient to confer LIF-independence bypassing the requirement for Nanog (Festuccia et al., 2012; Niwa et al., 2009). In particular, LIF-independency mediated by enforced Esrrb expression was found to strictly require the recruitment of its essential co-activator Ncoa3 in ESCs (Percharde et al., 2012). Additionally, forced expression of Esrrb or Klf4 also enables reversion of EpiSCs into an ESC-like state (Festuccia et al., 2012; Guo et al., 2009).
LIF-independency studies furthermore highlighted key connections between LIF/STAT3 signalling and the core transcriptional machinery. Notably, LIF was found to activate a parallel circuitry where the JAK-STAT3 branch activates the expression of Klf4, and the Pi3K–AKT pathway preferentially induces the expression of Tbx3. Klf4 and Tbx3 stimulate Sox2 and Nanog, and contribute to the maintenance of Oct4 (Niwa et al., 2009). Moreover, Esrrb is a key downstream target of the canonical WNT signalling pathway and stimulates the expression of Oct4, Nanog, Klf4 and Esrrb itself, though recognition of ERRE motifs at these loci (Martello et al., 2012; Percharde et al., 2012). In turn, the transcription of Esrrb, Tbx3 and Klf4 is positively regulated by the core Oct4-Sox2-Nanog transcription factors, which may altogether reinforce the stability of the pluripotent state. In post-implantation, the lower expression of Nanog is instead
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regulated by the Nodal signalling pathway and directly sustained by Oct4 and Smad2 (Sun et al., 2014). Altogether, the core network of transcription factors functions in the auto-regulation of their expression via an interconnected regulatory loop and by activating expression of genes required for the ESC self-renewal, while expressing differentiation-associated genes.
1.5.2.2 Transcription factor clusters at “enhanceosomes”
Transcription factors (TF) bind proximal DNA elements, usually associated with promoter regions in the vicinity of a gene, but also bind to distal regions that can be located up to several kb away from the gene itself. These distal elements are typically involved in potentiating gene expression and are termed enhancers. Pioneer mapping of TF binding sites through chromatin- immunoprecipitation techniques, coupled with high-throughput sequencing (ChIP-seq) uncovered that multiple TFs tend to bind to the same DNA regions, termed multiple transcription factor-binding loci (MTL) (Kim et al., 2008; Chen et al., 2008). Moreover, most of these MTLs comprise enhancer regions that are co-occupied by transcriptional co-factors such as p300 and Mediator complexes, and furthermore display enhancer activity when cloned into luciferase reporters (Chen et al., 2008; Kagey et al., 2010). Thus, MTL regions are often referred as to “enhanceosomes” where higher order multi-protein complexes are assembled, being able to modify the chromatin environment and hence allowing the recruitment of the basal transcriptional machinery.
Enhancer activity implies the coordinated recruitment of co-factors by TFs. These molecules do not necessarily have a DNA-binding ability, but are able to further recruit chromatin modifiers. In particular, the p300 and Mediator co-activator complexes are large multi-subunit complexes that are able to simultaneously interact with several TFs (Malik and Roeder, 2005). Of relevance, p300 possesses chromatin modifying activity, being able to acetylate the lysine 27 of histone 3 - a modification associated with permissive chromatin environment for TF binding (Tie et al., 2009). Moreover, the Mediator complex has a key role in mammalian transcription and associates
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with Cohesin-loading factor Nipbl at Oct4-Sox2-Nanog bound sites. In turn, Nipbl loads cohesin ring proteins at enhancer sites contributing to DNA-DNA interactions between enhancer and promoters (Kagey et al., 2010). Cohesin is a multi-meric complex that has been firstly identified for its role in sister chromatid cohesion, but has later been found to promote DNA double-strand break repair and to regulate gene expression in a manner that involves enclosing the DNA within its ring-shaped structure (Nasmyth and Haering, 2009).
The recruitment of given factors at enhancers regions occurs in a cell type specific manner. In ESCs, a subset of large enhancers regions are densely occupied by Oct4, Sox2, Nanog, Klf4, Esrrb and by Mediator, and potentiate the strong expression of pluripotency and self-renewal- associated genes. These regions were recently termed “super” enhancers, and differ from “typical” enhancers that are typically smaller and less densely occupied by TFs. Super enhancers are sensitive to the reduction levels of subunits of the Mediator complex, similarly to a reduction of Oct4, highlighting this TF as a key component of the enhanceosome and cell identity (Kagey et al., 2010). Thus, robust assembly of enhancer complexes is a crucial factor in the maintenance of a cell’s identity due to their roles in bridging enhancers and promoters, shaping the chromatin landscape and allowing the recruitment of the transcriptional machinery for proper expression.