Global identification of SMAD2 target genes reveals a role for multiple co-regulatory factors in zebrafish early gastrulas.

Nodal and Smad2/3 signals play pivotal roles in mesendoderm induction and axis determination during late blastulation and early gastrulation in vertebrate embryos. However, Smad2/3 direct target genes during those critical developmental stages have not been systematically identified. Here, through ChIP-chip assay, we show that the promoter/enhancer regions of 679 genes are bound by Smad2 in the zebrafish early gastrulas. Expression analyses confirm that a significant proportion of Smad2 targets are indeed subjected to Nodal/Smad2 regulation at the onset of gastrulation. The co-existence of DNA-binding sites of other transcription factors in the Smad2-bound regions allows the identification of well known Smad2-binding partners, such as FoxH1 and Lef1/ß-catenin, as well as many previously unknown Smad2 partners, including Oct1 and Gata6, during embryogenesis. We demonstrate that Oct1 physically associates with and enhances the transcription and mesendodermal induction activity of Smad2, whereas Gata6 exerts an inhibitory role in Smad2 signaling and mesendodermal induction. Thus, our study systemically uncovers a large number of Smad2 targets in early gastrulas and suggests cooperative roles of Smad2 and other transcription factors in controlling target gene transcription, which will be valuable for studying regulatory cascades during germ layer formation and patterning of vertebrate embryos.

Ptc, Smo, Sufu, and the Hedgehog signaling pathway in amphioxus.

The Hedgehog (Hh) signaling pathway regulates many developmental processes both in vertebrates and in invertebrates. However, little is known about this pathway in the cephalochordate amphioxus. In this paper, we focus on the Ptc, Smo, and Sufu homologs in amphioxus, which are the key members of the Hh signaling pathway. Their genomic structures show their comparability with homologs in vertebrates. In situ hybridization reveals that amphioxus Ptc, Smo, and Sufu have similar expression patterns in embryogenesis. They are expressed in the neural plate at early neurula stage, and then down-regulated in dorsal neural ectoderm. During development, their transcripts appear and persist in the notochord, the wall of the head cavity, the epithelium of the pharynx, and the gut. The data show that the expression patterns of these three genes are overlapping with Hh and Gli during the embryonic development in amphioxus. Moreover, injection of amphioxus Hh RNA into zebrafish-fertilized eggs can expand the expression domains of Ptc1 and Nk2.2a, the target genes of the Hh signaling pathway, which is similar to the injection of zebrafish Sonic hh a (zShha) and Sonic hh b (zShhb). Our results suggest that amphioxus may possess a conserved and functional Hh signaling pathway similar to that of vertebrates.

Characterization of the immune defense related tissues, cells, and genes in amphioxus.

Amphioxus is an important animal model for phylogenetic analysis, including comparative immunology. Exploring the immune system in amphioxus contributes to our understanding of the origin and evolution of the vertebrate immune system. We investigated the amphioxus immune system using ultrastructural examination and in situ hybridization. The expression patterns of TLR1 (toll-like receptor 1), C1Q (complement component 1, q subcomponent), ECSIT (evolutionarily conserved signaling intermediate in Toll pathways), SoxC, DDAHa (Dimethylarginine dimethylaminohydrolase a), and NOS (nitric oxide synthase) show that these genes play key roles in amphioxus immunity. Our results suggest that the epidermis and alimentary canal epithelium may play important roles in immune defense, while macrophages located in the coelom and so-called lymph spaces may also be crucial immune cells.