Sox17 and β-catenin co-occupy Wnt-responsive enhancers to govern the endoderm gene regulatory network

Abstract

Lineage specification is governed by gene regulatory networks (GRNs) that integrate the activity of signaling effectors and transcription factors (TFs) on enhancers. Sox17 is a key transcriptional regulator of definitive endoderm development, and yet, its genomic targets remain largely uncharacterized. Here, using genomic approaches and epistasis experiments, we define the Sox17-governed endoderm GRN in Xenopus gastrulae. We show that Sox17 functionally interacts with the canonical Wnt pathway to specify and pattern the endoderm while repressing alternative mesectoderm fates. Sox17 and β-catenin co-occupy hundreds of key enhancers. In some cases, Sox17 and β-catenin synergistically activate transcription apparently independent of Tcfs, whereas on other enhancers, Sox17 represses β-catenin/Tcf-mediated transcription to spatially restrict gene expression domains. Our findings establish Sox17 as a tissue-specific modifier of Wnt responses and point to a novel paradigm where genomic specificity of Wnt/β-catenin transcription is determined through functional interactions between lineage-specific Sox TFs and β-catenin/Tcf transcriptional complexes. Given the ubiquitous nature of Sox TFs and Wnt signaling, this mechanism has important implications across a diverse range of developmental and disease contexts.

A natural transdifferentiation event involving mitosis is empowered by integrating signaling inputs with conserved plasticity factors

“…Alternatively, through co-occupancy at those sites, SOX-2 could negatively impact on POP-1 activity directly or by sequestering co-factors such as β-catenin. Such model is consistent with studies in vertebrates, where SOX factors have been shown to interact with TCF/β-catenin factors in several ways: at the DNA via interaction with β-catenin and/or TCF, or by impacting β-catenin stability (Akiyama, 2004; Kormish et al, 2010; Mukherjee et al, 2020). The negative interactions between SOX-2 and the Wnt signaling could further be reinforced by CEH-6/POU, as mOct4 has been shown to inhibit Tcf/β-catenin stability and transcriptional activity in mES cells and Xenopus (Cao et al, 2007; Abu-Remaileh et al, 2010).…”

SOX Transcription Factors as Important Regulators of Neuronal and Glial Differentiation During Nervous System Development and Adult Neurogenesis

“…Wnt and SOX interplay and mutual control led to a hypothesis pointing out that interactions between lineage-specific SOX TFs and β-catenin/TCF govern specificity of Wnt/β-catenin dependent transcription ( Mukherjee et al, 2020 ). This idea is supported by the study conducted by Hagey and Muhr (2014) .…”

Uncovering the mesendoderm gene regulatory network through multi-omic data integration

“…Our SOM results suggest that such an interaction may be more wide-spread during Xenopus mesendoderm specification. Additionally, the binding of mesodermal regulator Tbxt (Smith et al, 1991) at stage 12 and the endodermal regulator Sox17 (Hudson et al, 1997; Mukherjee et al, 2020) at stage 10.5 correlated with each other, more so than with the binding of other TFs (Figure S1E, Figure S3). This finding is interesting as Sox17 is generally considered to be an endodermally expressed gene, whereas Tbxt is mesodermally expressed.…”

“…Numerous genomic analyses of individual TFs have been used to understand early Xenopus development (Yoon et al, 2011; Gentsch et al, 2013; Chiu et al, 2014; Yasuoka et al, 2014; Nakamura et al, 2016; Kjolby and Harland, 2017; Charney et al, 2017b; Paraiso et al, 2019; Gentsch et al, 2019; Mukherjee et al, 2020; Afouda et al, 2020). In these experiments, combining a single, or a few, ChIP-seq dataset(s) and RNA-seq datasets in wild type and perturbed states have been used to identify direct transcriptional targets of TFs.…”

“…Published RNA-seq datasets for different embryonic tissues and experimental conditions were obtained from NCBI’s Gene Expression Omnibus (see Key Resources Table). For the MO experiments, 2ng/embryo of ctnnb1 MO (Mukherjee et al, 2020), 20 ng/embryo foxh1 MO (Chiu et al, 2014; Charney et al, 2017), 10 ng/embryo each of two sox17 MOs (targeting sox17a and sox17b1/2) or 4 ng/embryo tcf7l1 MO (Liu et al, 2005) were used. For the knockdown of receptor-mediated Smad2/3 phosphorylation, embryos were treated with SB4315422 at 100uM as previously described (Chiu et al, 2014; Charney et al, 2017).…”