XB-ART-53584
Semin Cell Dev Biol
2017 Jun 01;66:12-24. doi: 10.1016/j.semcdb.2017.03.003.
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A gene regulatory program controlling early Xenopus mesendoderm formation: Network conservation and motifs.
Charney RM
,
Paraiso KD
,
Blitz IL
,
Cho KWY
.
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Germ layer formation is among the earliest differentiation events in metazoan embryos. In triploblasts, three germ layers are formed, among which the endoderm gives rise to the epithelial lining of the gut tube and associated organs including the liver, pancreas and lungs. In frogs (Xenopus), where early germ layer formation has been studied extensively, the process of endoderm specification involves the interplay of dozens of transcription factors. Here, we review the interactions between these factors, summarized in a transcriptional gene regulatory network (GRN). We highlight regulatory connections conserved between frog, fish, mouse, and human endodermal lineages. Especially prominent is the conserved role and regulatory targets of the Nodal signaling pathway and the T-box transcription factors, Vegt and Eomes. Additionally, we highlight network topologies and motifs, and speculate on their possible roles in development.
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R01 HD073179 NICHD NIH HHS
Species referenced: Xenopus
Genes referenced: bix1.1 bmp2 bmp4 bmp7.1 cer1 ctnnb1 eomes foxa1 foxa2 foxa4 foxh1 gata2 gata4 gata5 gata6 gdf1 gdf3 grn gsc hhex hnf1b lhx1 mix1 mixer nodal nodal1 nodal2 nodal5 nodal6 osr2 otx1 otx2 pitx2 sebox sia1 sia2 smad1 smad2 smad3 snai1 sox17a sox17b.1 sox7 tbxt vegt ventx1 ventx2.2 wnt11b wnt8a zic2
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Fig. 1. Xenopus mesendoderm gene regulatory network from fertilization through early-gastrula. The network is comprised of 35 TFs and 12 growth factors. Maternal proteins are represented as diamonds, and signaling ligands as circles. Connections are drawn from the transcriptional regulator to the cis-regulatory region of the target gene, and direct connections are indicated as solid lines and putative connections as dashed lines. Connections from secreted ligands pass through a chevron and are mediated by their respective intracellular TFs (e.g. Smad2/3, Ctnnb1/β-catenin). Approximate spatiotemporal information is provided from top to bottom (egg through early-gastrula) and from right to left (dorsal to ventral), with some exceptions (e.g. t/bra). The activation time of zygotic sox7 (boxed) is unknown. All direct connections are annotated for TF binding (blue diamond), reporter assay (pink diamond), and TF binding plus functional validation (maroon diamond). For additional connection details, including experimental evidence and references, see Table 1 and Table S2. ZGA, zygotic genome activation. |
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Fig. 2. Network motifs found in the Xenopus mesendoderm GRN. (A) Autoregulatory loop, for example by Nodal signaling. (B) Positive feedback loop, for example between Nodal and Wnt signaling. (C) Coherent and incoherent feedforward loops and their regulatory structure. (D) The type I feedforward loop, which appears to be the most common feedforward loop in the GRN, frequently appears in the structure such that X is a maternal factor, Y is an early zygotic gene, and Z is either an early or late zygotic gene. |
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