Reorganization of Enhancer Patterns in Transition from Naive to Primed Pluripotency

Abstract

Summary Naïve and primed pluripotency is characterized by distinct signaling requirements, transcriptomes and developmental properties, but both cellular states share key transcriptional regulators, Oct4, Sox2 and Nanog. Here we demonstrate that transition between these two pluripotent states is associated with widespread Oct4 relocalization, mirrored by global rearrangement of enhancer chromatin landscapes. Our genomic and biochemical analyses identified candidate mediators of primed state-specific Oct4 binding, including Otx2 and Zic2/3. Even when differentiation cues are blocked, premature Otx2 overexpression is sufficient to exit the naïve state, induce transcription of a substantial subset of primed pluripotency-associated genes and redirect Oct4 to previously inaccessible enhancer sites. However, ability of Otx2 to engage new enhancer regions is determined by its levels, cis-encoded properties of the sites and signaling environment. Our results illuminate regulatory mechanisms underlying pluripotency and suggest that capacity of transcription factors such as Otx2 and Oct4 to pioneer new enhancer sites is highly context-dependent.

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

“…The central line plot summarizes the average fold change per cell population compared to Esrrb Hi cells (log2 scale) with the color coding indicated below the heat map. Previously identified NANOG and ESRRB (Festuccia et al , 2012) targets are indicated on the right.Pearson correlation coefficients of the gene expression profiles of Esrrb Hi (H), Esrrb Med (M), Esrrb Neg (Neg) E‐GFPd1 ESCs, and embryo‐derived (late bud stage) TNG E‐2a‐tdT EpiSCs (EpiSC) compared to those of naïve ESC and EpiLC from Buecker et al (2014). …”

“…Pearson correlation coefficients of the gene expression profiles of Esrrb Hi (H), Esrrb Med (M), Esrrb Neg (Neg) E‐GFPd1 ESCs, and embryo‐derived (late bud stage) TNG E‐2a‐tdT EpiSCs (EpiSC) compared to those of naïve ESC and EpiLC from Buecker et al (2014). …”

“…The relative occupancies of NANOG and OCT4 at Tet2 or Sall1 (positions highlighted by hatched boxes) alongside expression levels of Tet2 and Sall1 mRNAs in Esrrb Hi (EH), Esrrb Med (EM), or Esrrb Neg (EN) GFPd1 ESCs and EpiSC (Epi) are shown at the bottom. OCT4‐binding data from EpiSC are from Buecker et al (2014). …”

“…Among genes linked to sites losing binding of NANOG and OCT4 (Class I), important regulators of the naïve pluripotent state were identified, for instance, Tet2, which is silenced during the Esrrb‐GFP high to Esrrb‐GFP negative transition (Fig 5H). Other pluripotency factors, such as Sall1, which are expressed in both Esrrb‐GFP high and Esrrb‐GFP negative ESCs or EpiSC, maintained OCT4 binding in all populations, including EpiLC (Buecker et al , 2014; Fig 5I).…”

“…Read counts per base pair were normalized by library size and by subtracting the background (IgG) signal.Average FAIRE profile or ChIP‐Seq profiles for H3K27ac, OCT4, Ep300, or OTX2 in ESCs or EpiLC for Class I and Class II elements [data from Buecker et al (2014)].Results of a differential motif analysis (Thomas‐Chollier et al , 2011) in Class I and Class II peaks. …”