Functional Antagonism between OTX2 and NANOG Specifies a Spectrum of Heterogeneous Identities in Embryonic Stem Cells

Acampora, Dario; Giovannantonio, Luca Giovanni Di; Garofalo, Arcomaria; Nigro, Vincenzo; Omodei, Daniela; Lombardi, Alessia; Zhang, Jingchao; Chambers, Ian; Simeone, Antonio

doi:10.1016/j.stemcr.2017.09.019

Cited by 28 publications

(37 citation statements)

References 39 publications

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“…Deep coverage of the proteome, coupled with high temporal-resolution, allowed us to uncover distinct waves of global changes to the proteome that reflect pluripotent state transitions. The initial wave of changes, likely triggered by the loss of LIF/Stat3 signaling and/or activation of ERK signaling, marks the onset of down-regulation of key naïve pluripotency factors Nanog and Tfcp2l1 along with the activation of post-implantation epiblast markers Otx2 and Zic2, consistent with the recently reported functional antagonism between Nanog and Otx2 (Acampora et al, 2017). This is immediately followed by the second wave of changes characterized by down-regulation of other naïve markers (Esrrb, Sox2, Tbx3, Nr0b1, Rex1, and Klf2/4/5) and up-regulation of Dnmt3a/b, setting the stage for rewiring of the gene regulatory network and remodeling of the epigenome (Buecker et al, 2014;Kurimoto et al, 2015;Shirane et al, 2016).…”

Section: Discussionsupporting

confidence: 83%

Multi-Omic Profiling Reveals Dynamics of the Phased Progression of Pluripotency

Yang

Humphrey

Cinghu

et al. 2018

Preprint

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Pluripotency is highly dynamic and progresses through a continuum of pluripotent stem-cell states. The two states that bookend the pluripotency continuum, naïve and primed, are well characterized, but our understanding of the intermediate states and transitions between them remain incomplete. Here, we dissect the dynamics of pluripotent state transitions underlying pre-to post-implantation epiblast differentiation. Through integrative analysis of the proteome, phosphoproteome, transcriptome, and epigenome of embryonic stem cells transitioning from naïve to primed pluripotency, we show that rapid, acute, and widespread changes to the phosphoproteome precede ordered changes to the epigenome, transcriptome, and proteome. Reconstruction of kinase-substrate networks reveals signaling cascades, dynamics, and crosstalk. Distinct waves of global proteomic changes mark discrete phases of pluripotency, characterized by cell surface markers that track pluripotent state transitions. Our data provide new insights into the multi-layered control of the phased progression of pluripotency and a foundation for modeling mechanisms regulating pluripotent state transitions. HIGHLIGHTS • Multi-ome maps of cells transitioning from naïve to primed pluripotency • Phosphoproteome dynamics precede changes to epigenome, transcriptome, and proteome • Kinase-substrate network reconstruction uncovers signaling dynamics and crosstalk • Proteins and cell surface markers that track pluripotent state transitions • Comparative analysis of mouse and human pluripotent states

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Section: Discussionsupporting

confidence: 83%

Multi-Omic Profiling Reveals Dynamics of the Phased Progression of Pluripotency

Yang

Humphrey

Cinghu

et al. 2018

Preprint

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“…S5A). Third, the ectopic expression of Otx2 drives ES cells into differentiation (Buecker et al, 2014;Acampora et al, 2017), even in the presence of LIF, as we show here using our Sun-Tag system targeted to the Otx2 promoter (Fig. S5E, G).…”

Section: Fig 3 Nanog Rewires the Pluripotency Network (A)supporting

confidence: 51%

“…Several lines of evidence point to Otx2 downregulation being an important mediator of Nanog function. First, Otx2 has been already identified as an important negative target of Nanog Acampora et al, 2017); accordingly, we observe its downregulation at the mRNA and protein levels upon Nanog induction (Fig. S5D, E).…”

Section: Fig 3 Nanog Rewires the Pluripotency Network (A)mentioning

confidence: 52%

“…5F). Hence, at the molecular level, Otx2 induction partially compensates the gene expression changes induced by Nanog overexpression in the absence of LIF, underscoring the antagonistic effect of Nanog and Otx2 over a large set of common genes (Acampora et al, 2017), including developmental TFs such as Sox3, Sox11, Id1 and Pou3f1, among others (Table S1), which tend to be expressed in somatic cells and more particularly in neuroectodermal derivatives. In combination with the previous section, these results indicate strongly that Nanog controls H3K27me3 at key nodes in the differentiation network, such as Otx2, to indirectly repress a large set of genes involved with differentiation.…”

Section: Fig 3 Nanog Rewires the Pluripotency Network (A)mentioning

confidence: 98%

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The molecular logic of Nanog-induced self-renewal

Heurtier

Owens

González

et al. 2018

Preprint

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rue du docteur Roux, Paris 75015. a Equal contributionTranscription factor networks, together with histone modifications and signalling pathways, underlie the establishment and maintenance of gene regulatory architectures associated with the molecular identity of each cell type. However, how master transcription factors individually impact the epigenomic landscape and orchestrate the behaviour of regulatory networks under different environmental constraints is only very partially understood. Here, we show that the transcription factor Nanog deploys multiple distinct mechanisms to enhance embryonic stem cell self-renewal. In the presence of LIF, which fosters self-renewal, Nanog rewires the pluripotency network by promoting chromatin accessibility and binding of other pluripotency factors to thousands of enhancers. In the absence of LIF, Nanog blocks differentiation by sustaining H3K27me3, a repressive histone mark, at developmental regulators. Among those, we show that the repression of Otx2 plays a preponderant role. Our results underscore the versatility of master transcription factors, such as Nanog, to globally influence gene regulation during developmental processes.

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“…Similarly, accumulation of OTX2 during exit from naïve pluripotency partially redirects OCT4 to a new enhancer set (Buecker et al , 2014; Yang et al , 2014). Since Otx2 is a direct target gene repressed by NANOG (Festuccia et al , 2012), a strong increase in OTX2 levels would occur only after complete loss of NANOG (Acampora et al , 2013, 2017). The moderate increase in binding by OCT4 in Esrrb‐GFP negative cells that we detect might indeed be a sign of such an accumulation and occur at sites where the effect of lineage‐specific TFs is not yet fully evident, as compared to other studies.…”

Section: Discussionmentioning

confidence: 99%

Esrrb extinction triggers dismantling of naïve pluripotency and marks commitment to differentiation

et al. 2018

Self Cite

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Self‐renewal of embryonic stem cells (ESCs) cultured in LIF/fetal calf serum (FCS) is incomplete with some cells initiating differentiation. While this is reflected in heterogeneous expression of naive pluripotency transcription factors (TFs), the link between TF heterogeneity and differentiation is not fully understood. Here, we purify ESCs with distinct TF expression levels from LIF/FCS cultures to uncover early events during commitment from naïve pluripotency. ESCs carrying fluorescent Nanog and Esrrb reporters show Esrrb downregulation only in Nanoglow cells. Independent Esrrb reporter lines demonstrate that Esrrbnegative ESCs cannot effectively self‐renew. Upon Esrrb loss, pre‐implantation pluripotency gene expression collapses. ChIP‐Seq identifies different regulatory element classes that bind both OCT4 and NANOG in Esrrbpositive cells. Class I elements lose NANOG and OCT4 binding in Esrrbnegative ESCs and associate with genes expressed preferentially in naïve ESCs. In contrast, Class II elements retain OCT4 but not NANOG binding in ESRRB‐negative cells and associate with more broadly expressed genes. Therefore, mechanistic differences in TF function act cumulatively to restrict potency during exit from naïve pluripotency.

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Functional Antagonism between OTX2 and NANOG Specifies a Spectrum of Heterogeneous Identities in Embryonic Stem Cells

Cited by 28 publications

References 39 publications

Multi-Omic Profiling Reveals Dynamics of the Phased Progression of Pluripotency

Multi-Omic Profiling Reveals Dynamics of the Phased Progression of Pluripotency

The molecular logic of Nanog-induced self-renewal

Esrrb extinction triggers dismantling of naïve pluripotency and marks commitment to differentiation

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