Compact intergenic regions of the pufferfish genome facilitate isolation of gene promoters: characterization ofFugu3′-phosphoadenosine 5′-phosphosulfate synthase 2 (fPapss2) gene promoter function in transgenicXenopus

Regulation of protocadherin gene expression by multiple neuron-restrictive silencer elements scattered in the gene cluster

The clustered protocadherins are a subfamily of neuronal cell adhesion molecules that play an important role in development of the nervous systems in vertebrates. The clustered protocadherin genes exhibit complex expression patterns in the central nervous system. In this study, we have investigated the molecular mechanism underlying neuronal expression of protocadherin genes using the protocadherin gene cluster in fugu as a model. By in silico prediction, we identified multiple neuron-restrictive silencer elements (NRSEs) scattered in the fugu protocadherin cluster and demonstrated that these elements bind specifically to NRSF/REST in vitro and in vivo. By using a transgenic Xenopus approach, we show that these NRSEs regulate neuronal specificity of protocadherin promoters by suppressing their activity in non-neuronal tissues. We provide evidence that protocadherin genes that do not contain an NRSE in their 5' intergenic region are regulated by NRSEs in the regulatory region of their neighboring genes. We also show that protocadherin clusters in other vertebrates such as elephant shark, zebrafish, coelacanth, lizard, mouse and human, contain different sets of multiple NRSEs. Taken together, our data suggest that the neuronal specificity of protocadherin cluster genes in vertebrates is regulated by the NRSE-NRSF/REST system.

SCL-GFP transgenic zebrafish: in vivo imaging of blood and endothelial development and identification of the initial site of definitive hematopoiesis

The bHLH transcription factor SCL plays a central role in the generation of hematopoietic cells in vertebrates. We modified a PAC containing the whole zebrafish scl locus, inserting GFP into the first coding exon of scl. In germline-transgenic zebrafish generated using this construct, GFP expression completely recapitulates the endogenous expression of scl in blood, endothelium and CNS. We performed in vivo timelapse imaging of blood and endothelial precursor migration at the single-cell level and show that these cells migrate from the posterior lateral plate mesoderm to their site of differentiation in the intermediate cell mass. The anterior lateral plate domain of GFP expression gives rise to primitive macrophages and the blood vessels of the head. In later embryos, GFP expression identifies clusters of hematopoietic cells that develop between the dorsal aorta and posterior cardinal veins after primitive erythrocytes have entered circulation. Two treatments that block definitive hematopoiesis (treatment with dioxin (TCDD), and injection of an antisense morpholino oligonucleotide targeted to runx1) ablate these hematopoietic clusters. This indicates that these clusters represent the first site of definitive hematopoiesis in zebrafish. This site is anatomically homologous to the proposed source of hematopoietic stem cells in amniotes, the aorta-gonad-mesonephros (AGM) region. A second transgenic line, containing the promoter of scl driving GFP, lacks expression in the definitive clusters.

Computational analysis of base composition pattern and promoter elements in the putative promoter regions in relation to expression profiles of 682 human genes on chromosome 22

Abstract The base composition pattern (BCP) in the putative promoter region (PPRs) up to 5 Kb lengths of 682 human genes on Chromosome 22 (Chr22) was examined. Two-dimensional (2D) and three-dimensional (3D) functions were designed to delineate the DNA base composition, with four major patterns identified. It is found that 17.6% genes include TATA box, 28.0% GC box, 18.9% CAAT box and 38.4% CpG islands, and approximately 10% genes have one of four putative initiator (Inr) motifs. The occurrence of the promoter elements is tightly associated with the base composition features in the promoter regions, and the associations of the base composition features with occurrence of the promoter elements in the promoter regions mediate tissue-wide expression of the genes in human. The occurrence of two or more promoter elements in the promoter regions is required for the medium- and wide-range expression profiles of the human genes on Chr22. Thus, the reported data shed light on the characteristics of the PPRs of the human genes on Chr22, which may improve our understanding of regulatory roles of the PPRs with occurrence of the promoter elements in gene expression.

The Fugu tyrp1 promoter directs specific GFP expression in zebrafish: tools to study the RPE and the neural crest-derived melanophores

In vertebrates, pigment cells account for a small percentage of the total cell population and they intermingle with other cell types. This makes it difficult to isolate them for analyzes of their functions in the context of development. To alleviate such difficulty, we generated two stable transgenic zebrafish lines (pt101 and pt102) that express green fluorescent protein (GFP) in melanophores under the control of the 1 kb Fugu tyrp1 promoter. In pt101, GFP is expressed in both retinal pigment epithelium (RPE) cells and the neural crest-derived melanophores (NCDM), whereas in pt102, GFP is predominately expressed in the NCDM. Our results indicate that the Fugu tyrp1 promoter can direct transgene expression in a cell-type-specific manner in zebrafish. In addition, our findings provide evidence supporting differential regulations of melanin-synthesizing genes in RPE cells and the NCDM in zebrafish. Utilizing the varying GFP expression levels in these fish, we have isolated melanophores via flow cytometry and revealed the capability of sorting the NCDM from RPE cells as well. Thus, these transgenic lines are useful tools to study melanophores in zebrafish.

Comparative genomics using fugu: a tool for the identification of conserved vertebrate cis-regulatory elements

With the imminent completion of the whole genome sequence of humans, increasing attention is being focused on the annotation of cis-regulatory elements in the human genome. Comparative genomics approaches based on evolutionary conservation have proved useful in the detection of conserved cis-regulatory elements. The pufferfish, Fugu rubripes, is an attractive vertebrate model for comparative genomics, by virtue of its compact genome and maximal phylogenetic distance from mammals. Fugu has lost a large proportion of nonessential DNA, and retained single orthologs for many duplicate genes that arose in the fish lineage. Non-coding sequences conserved between fugu and mammals have been shown to be functional cis-regulatory elements. Thus, fugu is a model fish genome of choice for discovering evolutionarily conserved regulatory elements in the human genome. Such evolutionarily conserved elements are likely to be shared by all vertebrates, and related to regulatory interactions fundamental to all vertebrates. The functions of these conserved vertebrate elements can be rapidly assayed in mammalian cell lines or in transgenic systems such as zebrafish/medaka and Xenopus, followed by validation of crucial elements in transgenic rodents.

Xenopus: a prince among models for pronephric kidney development

Recent advances in techniques that are available to study the molecular development of the frog Xenopus make developmental studies using this amphibian amenable to experimentation. This review outlines some of the attractive features of this model organism and describes how these techniques can be and are being used in studies on the organogenesis of the larval amphibian kidney, the pronephros. The roles of micromanipulation, grafting, and in vitro culturing of animal caps are discussed as tools in the analysis of kidney development and as a source of tissue for subtractive hybridization strategies. The importance of expression cloning and functional analysis of newly identified pronephros-specific genes are also described. Finally, transgenesis and electroporation are discussed as potentially new methods of gene delivery to the pronephros. These techniques can be used to help identify the gene networks that control organogenesis of this larval kidney form, which will undoubtedly have applicability to higher vertebrate kidney development.