Sox2 levels regulate the chromatin occupancy of WNT mediators in epiblast progenitors responsible for vertebrate body formation

Abstract

WNT signalling has multiple roles. It maintains pluripotency of embryonic stem cells, assigns posterior identity in the epiblast and induces mesodermal tissue. Here we provide evidence that these distinct functions are conducted by the transcription factor SOX2, which adopts different modes of chromatin interaction and regulatory element selection depending on its level of expression. At high levels, SOX2 displaces nucleosomes from regulatory elements with high-affinity SOX2 binding sites, recruiting the WNT effector TCF/β-catenin and maintaining pluripotent gene expression. Reducing SOX2 levels destabilizes pluripotency and reconfigures SOX2/TCF/β-catenin occupancy to caudal epiblast expressed genes. These contain low-affinity SOX2 sites and are co-occupied by T/Bra and CDX. The loss of SOX2 allows WNT-induced mesodermal differentiation. These findings define a role for Sox2 levels in dictating the chromatin occupancy of TCF/β-catenin and reveal how context-specific responses to a signal are configured by the level of a transcription factor.

Time-resolved analysis of Wnt-signaling reveals β-catenin temporal genomic repositioning and cell type-specific plastic or elastic chromatin responses

“…Time-resolved motif analysis of our datasets indicated that the answer might lie in the promiscuous cooperativity between b-catenin and other transcription factors (Figure 2E). In support to this, a recent report proposed that the stemness factor SOX2 determines b-catenin genomic localization in hESCs (Blassberg et al, 2022). This is consistent with the observed prominent association in our study between b-catenin peaks and motifs of SOX factors, enriched in particular at the early time points after Wnt activation in hESCs.…”

“…We propose that the association with cell-specific transcription factors will explain in part the differential distribution of β-catenin in different models. Whether this fully depends on the distinctive association of β-catenin with tissue specific molecular partners (Blassberg et al, 2022; Zimmerli et al, 2020), by its recruitment to MED1-marked molecular condensates (Zamudio et al, 2019), or a combination of the two, remains to be established.…”

Developmental cell fate choice employs two distinct cis regulatory strategies

“…This is expected as cells adopt neural identity. Consistent with this, SOX2 ChIP-seq from NMPs (Blassberg et al, 2022) is enriched in Cluster 1 “NMP” elements and SOX2 ChIPseq from neural cells (Peterson et al, 2012) is enriched in neural clusters (9, 6, 7, 8, 4 and 5) (Fig 3C).…”

“…Elements ordered by average accessibility. (C) Heatmap of ChIP-seq coverage for the same elements for NKX6.1, OLIG2, NKX2.2 (Nishi et al, 2015) performed in neural embryoid bodies treated with SAG shows binding to both pan-neuronal and cell type specific elements, and SOX2 from either NMP stage (Blassberg et al, 2022) or SAG treated neural embryoid bodies (Peterson et al, 2012) correlates with accessibility in either NMP or neural progenitors, respectively. (D) Footprinting scores (using TOBIAS, see Methods) for motifs with highly variable scores between p0-1, p2 and pMN at days 5 and 6 obtained, and normalized RNA counts for the most correlated TF within the motif archetype.…”

Extensive co-binding and rapid redistribution of NANOG and GATA6 during emergence of divergent lineages

“…Contrarily, less abundant, lower affinity binding sites could lead to only transient occupancy by the TF, not allowing sufficient time for activation, and instead marking them for inactivation by recruitment of histone deacetylases. A related observation was recently made where cells of the caudal epithelium that contain neural and mesodermal progenitors use binding of the same TF (SOX2) at sites of different affinity to elicit opposing regulatory responses in cells differentiating into divergent paths 67 . In our study, we observed that CREs activated during PrE differentiation were bound by GATA6 starting at 2hrs and continued in most cases until 48 h (Fig.…”