High-throughput functional screen of mouse gastrula cDNA libraries reveals new components of endoderm and mesoderm specification

Role of GATA factors in development, differentiation, and homeostasis of the small intestinal epithelium

The small intestinal epithelium develops from embryonic endoderm into a highly specialized layer of cells perfectly suited for the digestion and absorption of nutrients. The development, differentiation, and regeneration of the small intestinal epithelium require complex gene regulatory networks involving multiple context-specific transcription factors. The evolutionarily conserved GATA family of transcription factors, well known for its role in hematopoiesis, is essential for the development of endoderm during embryogenesis and the renewal of the differentiated epithelium in the mature gut. We review the role of GATA factors in the evolution and development of endoderm and summarize our current understanding of the function of GATA factors in the mature small intestine. We offer perspective on the application of epigenetics approaches to define the mechanisms underlying context-specific GATA gene regulation during intestinal development.

Optimized RNA ISH, RNA FISH and protein-RNA double labeling (IF/FISH) in Drosophila ovaries

In situ hybridization (ISH) is a powerful technique for detecting nucleic acids in cells and tissues. Here we describe three ISH procedures that are optimized for Drosophila ovaries: whole-mount, digoxigenin-labeled RNA ISH; RNA fluorescent ISH (FISH); and protein immunofluorescence (IF)-RNA FISH double labeling (IF/FISH). Each procedure balances conflicting requirements for permeabilization, fixation and preservation of antigenicity to detect RNA and protein expression with high resolution and sensitivity. The ISH protocol uses alkaline phosphatase-conjugated digoxigenin antibodies followed by a color reaction, whereas FISH detection involves tyramide signal amplification (TSA). To simultaneously preserve antigens for protein detection and enable RNA probe penetration for IF/FISH, we perform IF before FISH and use xylenes and detergents to permeabilize the tissue rather than proteinase K, which can damage the antigens. ISH and FISH take 3 d to perform, whereas IF/FISH takes 5 d. Probe generation takes 1 or 2 d to perform.

The bilaterian head patterning gene six3/6 controls aboral domain development in a cnidarian

The origin of the bilaterian head is a fundamental question for the evolution of animal body plans. The head of bilaterians develops at the anterior end of their primary body axis and is the site where the brain is located. Cnidarians, the sister group to bilaterians, lack brain-like structures and it is not clear whether the oral, the aboral, or none of the ends of the cnidarian primary body axis corresponds to the anterior domain of bilaterians. In order to understand the evolutionary origin of head development, we analysed the function of conserved genetic regulators of bilaterian anterior development in the sea anemone Nematostella vectensis. We show that orthologs of the bilaterian anterior developmental genes six3/6, foxQ2, and irx have dynamic expression patterns in the aboral region of Nematostella. Functional analyses reveal that NvSix3/6 acts upstream of NvFoxQ2a as a key regulator of the development of a broad aboral territory in Nematostella. NvSix3/6 initiates an autoregulatory feedback loop involving positive and negative regulators of FGF signalling, which subsequently results in the downregulation of NvSix3/6 and NvFoxQ2a in a small domain at the aboral pole, from which the apical organ develops. We show that signalling by NvFGFa1 is specifically required for the development of the apical organ, whereas NvSix3/6 has an earlier and broader function in the specification of the aboral territory. Our functional and gene expression data suggest that the head-forming region of bilaterians is derived from the aboral domain of the cnidarian-bilaterian ancestor.

An evolutionarily conserved kernel of gata5, gata6, otx2 and prdm1a operates in the formation of endoderm in zebrafish

An evolutionarily conserved subcircuit (kernel) dedicated to a specific developmental function is found at the top of the gene regulatory networks (GRNs) hierarchy. Here we comprehensively demonstrate that a pan-deuterostome endoderm specification kernel exists in zebrafish. We analyzed interactions among gata5, gata6, otx2 and prdm1a using specific morpholino knockdowns and measured the gene expression profiles by quantitative real-time RT-PCR and in situ hybridization. The mRNA rescue experiment validated the specificity of the morpholino knockdown. We found that the interactions among gata5, gata6, otx2 and prdm1a determine the initial specification of the zebrafish endoderm. Although otx2 can activate both gata5 and gata6, and the prdm1a/krox homologue also activates some endoderm transcription factors, a feedback loop from Gata to otx2 and prdm1a is missing. Furthermore, we found the positive regulation between gata5 and gata6 to further lock-on the mesendoderm specification by the Gata family. Chromatin immunoprecipitation was used to further validate the recruitment of Otx2 to the gata5 and gata6 loci. Functional assays revealed that module B of gata6 and the basal promoter of gata5 drive the gene at the mesendoderm, and mutational analysis demonstrated that Otx2 and Gata5/6 contribute to reporter gene activation. This is the first direct evidence for evolutionarily conserved endoderm specification across echinoderms and vertebrates.

Developmental expression patterns of candidate cofactors for vertebrate six family transcription factors

Six family transcription factors play important roles in craniofacial development. Their transcriptional activity can be modified by cofactor proteins. Two Six genes and one cofactor gene (Eya1) are involved in the human Branchio-otic (BO) and Branchio-otic-renal (BOR) syndromes. However, mutations in Six and Eya genes only account for approximately half of these patients. To discover potential new causative genes, we searched the Xenopus genome for orthologues of Drosophila cofactor proteins that interact with the fly Six-related factor, SO. We identified 33 Xenopus genes with high sequence identity to 20 of the 25 fly SO-interacting proteins. We provide the developmental expression patterns of the Xenopus orthologues for 11 of the fly genes, and demonstrate that all are expressed in developing craniofacial tissues with at least partial overlap with Six1/Six2. We speculate that these genes may function as Six-interacting partners with important roles in vertebrate craniofacial development and perhaps congenital syndromes.

Sox17 facilitates the differentiation of mouse embryonic stem cells into primitive and definitive endoderm in vitro

The Sox family of HMG (high mobility group)-box transcription factors are highly conserved in vertebrates. Sox members are involved in various developmental processes. Among them Sox17 has been demonstrated to function as an endoderm determinant in zebrafish and Xenopus, respectively. However, little is known about the role of Sox17 in mouse embryonic stem cell (ESC) differentiation. In our research, we investigated the effect of Sox17 on mouse ESC and embryoid body (EB) differentiation. The results demonstrated that Sox17 overexpression upregulated a set of endoderm-specific gene markers, suggesting that Sox17 overexpression induced an ESC differentiation program towards both primitive and definitive endoderm. We believe this finding brings new insights into the understanding of ESC differentiation and the organogenesis of endodermal derivatives.

Genomic organization, gene structure, and developmental expression of three clustered otx genes in the sea anemone Nematostella vectensis

Otx homeodomain transcription factors have been studied in a variety of eumetazoan animals where they have roles in anterior neural development, endomesoderm formation, and the formation of larval ciliated fields. Here, we describe the gene structure and developmental expression of three Otx loci in the starlet sea anemone, Nematostella vectensis (phylum Cnidaria; class Anthozoa). Nematostella's three Otx genes (OtxA, OtxB, and OtxC) are located in a compact genomic cluster spanning 63.6 kb. The homeodomains of all three Otx genes are highly similar to their bilaterian counterparts, but only OtxB exhibits the conserved WSP motif that is located downstream of the homeodomain in many Otx proteins. The genomic organization, in concert with phylogenetic analyses, indicates that two tandem duplications occurred in the lineage leading to Nematostella some time after the Cnidaria diverged from the Bilateria. In situ hybridization reveals that otx is initially expressed by invaginating mesendodermal cells in the gastrula. Later, each of the three otx paralogs is expressed in three discrete larval body regions: in the endoderm of the foot or physa, in an endodermal ring surrounding the pharynx, and in the ectoderm of the tentacles. These data suggest that a single otx locus had already acquired diverse developmental functions in the cnidarian-bilaterian ancestor. Furthermore, following two gene duplications in the line leading to Nematostella, there have been only minor alterations in the spatiotemporal expression of the three Otx paralogs. However, the absence of a conserved protein domain in OtxA and OtxC suggests functional evolution of the protein itself.

HeOtx expression in an indirectly developing polychaete correlates with gastrulation by invagination

The expression of an Otx homolog in the indirectly developing polychaete Hydroides elegans was characterized during embryo, trochophore, and feeding-larva stages. In the animal hemisphere, HeOtx is first expressed in 1q(12) blastomeres and their immediate descendants. Such discrete embryonic animal hemisphere Otx expression perhaps relates to cell-type specification functions of the larva. During feeding stages, transcripts are detected in adult cerebral ganglia precursors and putative adult eye precursors, where it may have adult brain regionalization functions. HeOtx is not expressed in primary trochoblast precursors, but it is expressed in cells adjacent to the ciliary band. HeOtx is also expressed in a group of cells in the dorsal midline of the early trochophore larva in putative posterior sensory organ precursors. The vegetal hemisphere expression starts in oral and lateral sides of the blastopore and later expands to central blastomeres that lead the gastrulation movements. During late gastrulation stages, the expression declines in foregut precursors, but it is maintained in midgut precursors, suggesting its involvement in tripartite gut subdivision functions. HeOtx broader and earlier endoderm expression correlates with gastrulation by invagination associated with the formation of the feeding trochophore, in contrast with a later and orally restricted Otx expression found in a polychaete that gastrulates by epiboly and forms a non-feeding trochophore. The endoderm expression and functional roles in other bilaterians suggest an ancestral role of Otx related to gastrulation by invagination.

Interrogating genomes with combinatorial artificial transcription factor libraries: asking zinc finger questions

Artificial transcription factors (ATFs) are proteins designed to specifically bind and regulate genes. Because of their DNA-binding selectivity and modular organization, arrays of zinc finger (ZF) domains have traditionally been used to build the ATF's DNA-binding domains. ATFs have been designed and constructed to regulate a variety of therapeutic targets. Recently, novel combinatorial technologies have been developed to induce expression of any gene of interest or to modify cellular phenotypes. Large repertoires of ATFs have been generated by recombination of all available sequence-specific ZF lexicons. These libraries comprise millions of ATFs with unique DNA-binding specificities. The ATFs are produced by combinatorial assembly of three- and six-ZF building blocks and are linked to activator or repressor domains. Upon delivery into a cell population, any gene in the human genome can potentially be regulated. ATF library members generate genome-wide, experimental perturbations of gene expression, resulting in a phenotypically diverse population, or cellular library. A variety of phenotypic screenings can be applied to select for cells exhibiting a phenotype of interest. The ATFs are then used as genetic probes to identify the targeted genes responsible for the phenotypic switch. In this review we will summarize several applications of ATF library screenings in gene discovery, biotechnology, and disease therapeutics.

Genomic profiling of mixer and Sox17beta targets during Xenopus endoderm development

The transcription factors Mixer and Sox17beta have well-characterized roles in endoderm specification during Xenopus embryogenesis. In order to more thoroughly understand the mechanisms by which these endodermal regulators act, we expressed Mixer and Sox17beta in naïve ectodermal tissue and, using oligonucleotide-based microarrays, compared their genomic transcriptional profile to that of unaffected tissue. Using this approach, we identified 71 transcripts that are upregulated by Mixer or Sox17beta, 63 of which have previously uncharacterized roles in endoderm development. Furthermore, an in situ hybridization screen using antisense probes for several of these clones identified six targets of Mixer and/or Sox17beta that are expressed in the endoderm during gastrula stages, providing new and regional markers of the endoderm. Our results contribute further insight into the functions of Mixer and Sox17beta and bring us closer to understanding at the molecular level the pathways that regulate endoderm development.