Foxd3 Promotes Exit from Naive Pluripotency through Enhancer Decommissioning and Inhibits Germline Specification

Abstract

Summary Following implantation, mouse epiblast cells transit from a naïve to a primed state in which they are competent for both somatic and primordial germ cell (PGC) specification. Using mouse embryonic stem cells (mESC) as an in vitro model to study the transcriptional regulatory principles orchestrating peri-implantation development, here we show that the transcription factor Foxd3 is necessary for exit from naïve pluripotency and progression to a primed pluripotent state. During this transition, Foxd3 acts as a repressor that dismantles a significant fraction of the naïve pluripotency expression program through decommissioning of active enhancers associated with key naïve pluripotency and early germline genes. Subsequently, Foxd3 needs to be silenced in primed pluripotent cells to allow reactivation of relevant genes required for proper PGC specification. Our findings therefore uncover a cycle of activation and deactivation of Foxd3 required for exit from naïve pluripotency and subsequent PGC specification.

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

“…Percentages are the number of overlapping peaks relative to the total number of Class I (top row), Class II (middle row), or all OCT4/NANOG‐bound peaks [bottom row; data from Respuela et al (2016)].Average binding profile of FOXD3 using FLAG (left) and HA (right) antibodies to Class I (green), Class II (orange), or all Nanog‐ and Oct4‐bound (gray dashed line) elements in ESCs [data from Respuela et al (2016)]. Read counts per base pair were normalized by library size and by subtracting the background signal (IgG).…”

“…Percentages are the number of overlapping peaks relative to the total number of Class I (top row), Class II (middle row), or all OCT4/NANOG‐bound peaks [bottom row; data from Respuela et al (2016)].…”

“…Average binding profile of FOXD3 using FLAG (left) and HA (right) antibodies to Class I (green), Class II (orange), or all Nanog‐ and Oct4‐bound (gray dashed line) elements in ESCs [data from Respuela et al (2016)]. Read counts per base pair were normalized by library size and by subtracting the background signal (IgG).…”

“…Recently, it has been reported that FOXD3, a TF expressed in naïve ESCs but upregulated during the transition to EpiSC‐like cells, co‐occupies numerous enhancers that are also bound by pluripotency TFs. However, FOXD3 directly contributes to the inactivation of only a fraction of these elements (Respuela et al , 2016). A similar number of Class I and Class II enhancers are bound by FoxD3 in ESCs (~30%; Fig EV5B) with both Class I and Class II enhancers binding FOXD3 at similar levels (Fig EV5C).…”

The paradox of Foxd3: how does it function in pluripotency and differentiation of embryonic stem cells?

“…While the in vivo and in vitro requirements for Foxd3 in these cell lineages have been established, the mechanisms by which Foxd3 elicits its functions is less clear. Two publications from earlier this year dove deeply into understanding how Foxd3 regulates gene expression during early cell fate transitions of progenitor cells (6,7). While the two publications shared some similarity, they also presented some conflicting results.…”