Foxh1/Nodal Defines Context-Specific Direct Maternal Wnt/β-Catenin Target Gene Regulation in Early Development

Abstract

Summary Although Wnt/β-catenin signaling is generally conserved and well understood, the regulatory mechanisms controlling context-specific direct Wnt target gene expression in development and disease are still unclear. The onset of zygotic gene transcription in early embryogenesis represents an ideal, accessible experimental system to investigate context-specific direct Wnt target gene regulation. We combine transcriptomics using RNA-seq with genome-wide β-catenin association using ChIP-seq to identify stage-specific direct Wnt target genes. We propose coherent feedforward regulation involving two distinct classes of direct maternal Wnt target genes, which differ both in expression and persistence of β-catenin association. We discover that genomic β-catenin association overlaps with Foxh1-associated regulatory sequences and demonstrate that direct maternal Wnt target gene expression requires Foxh1 function and Nodal/Tgfβ signaling. Our results support a new paradigm for direct Wnt target gene co-regulation with context-specific mechanisms that will inform future studies of embryonic development and more widely stem cell-mediated homeostasis and human disease.

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

“…In support of the latter, the expression patterns of Tbxt and Sox17 are also mutually exclusive in mice (Lolas et al, 2014), indicating that may represent a conserved mutual exclusion mechanism regulating mesoderm and endoderm development. Lastly, at early gastrula stage 10, the binding of dorsal mesendoderm factors Ctnnb1 (β-catenin; Wnt signaling transducer) (Nakamura et al, 2016; Heasman et al, 1994) and Foxh1 (Nodal signaling cofactor) (Chen et al, 1996) clusters with the ventral specifying TF Smad1 (Bmp signaling transducer) (Graff et al, 1996; Afouda et al, 2020) (Figure S1F, Figure S3). Some of these CRMs that show interactions with Wnt, Bmp, and Nodal signaling pathways may represent the nodes critical in controlling the formation of the dorsal-ventral axis during early embryogenesis.…”

“…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.…”

Regulation of Wnt Signaling by FOX Transcription Factors in Cancer

“…It therefore appears likely that FOXG1 has a distinct mode of action in Wnt transcriptional activation. Finally, FOXH1 promotes the transcription of β-catenin target genes during early Xenopus development [ 68 ]. Afouda et al observed that a substantial number of genomic loci were co-occupied by β-catenin and FOXH1 in zygotes.…”

“…Given that both β-catenin and FOX proteins can be traced back to early metazoan ancestors [ 145 , 146 ], it is conceivable that the reciprocal regulation of FOX and Wnt arose during the evolution of multicellular organisms, and that it is conserved throughout the animal kingdom. Support for this hypothesis comes from the observation that the functions of some FOX transcription factors in the Wnt pathway are shared between mammals and lower organisms, such as the Wnt inhibitory role of FOXO proteins in nematodes [ 106 ], or the activation of β-catenin target genes by FOXH1 in frogs [ 68 , 69 ]. These examples also illustrate that both positive and negative regulation of Wnt signaling by FOX proteins have likely appeared early in evolution.…”

T-Cell Factors as Transcriptional Inhibitors: Activities and Regulations in Vertebrate Head Development

“…Analysis performed on the Xenopus siamois (sia) promoter demonstrated that Tcf/Lefbinding sites mediate both basal repression and β-catenindependent activation at the W-CRM (Brannon et al, 1997;Fan et al, 1998). More recently, large-scale analysis demonstrates that in the dorsal blastomeres, Gro/TLE binds to the same W-CRM as β-catenin (Yasuoka et al, 2014;Nakamura and Hoppler, 2017;Afouda et al, 2020). In this context a few lines of evidence indicate that β-catenin activates Wnt-responsive genes by displacing the whole Tcf7l1/Gro repressor complex and replacing it with an activator complex, containing β-catenin in association with Tcf7 (Chambers et al, 2017) (reviewed in Sokol, 2011;Ramakrishnan et al, 2018) In conclusion, the mechanisms by which Gro/TLE mediate transcriptional repression in the presence and/or absence of TCF/ LEF are still not fully understood.…”