Mechanisms of Igf2/H19 imprinting: DNA methylation, chromatin and long-distance gene regulation

The mouse Igf2 and H19 genes lie 70-kb apart on chromosome 7 and are reciprocally imprinted. Two regulatory regions are important for their parental allele-specific expression: a differentially methylated region (DMR) upstream of H19 and a set of tissue-specific enhancers downstream of H19. The enhancers specifically activate Igf2 on the paternal chromosome and H19 on the maternal chromosome. The interactions between the enhancers and the genes are regulated by the DMR, which works as a selector by exerting dual functions: a methylated DMR on the paternal chromosome inactivates adjacent H19 and an unmethylated DMR on the maternal chromosome insulates Igf2 from the enhancers. These processes appear to involve methyl-CpG-binding proteins, histone deacetylases and the formation of chromatin insulator complexes. The Igf2/H19 region provides a unique model in which to study the roles of DNA methylation and chromatin structure in the regulation of chromosome domains.     

The DVR gene family in embryonic development.

The DVR gene family consists of at least 15 members, including decapentaplegic from Drosophila, Xenopus Vg1 and the mammalian bone morphogenetic protein genes, encoding secreted proteins closely related to transforming growth factor beta Genetic and biochemical evidence supports the idea that DVR proteins form part of a cascade of extracellular signalling molecules mediating inductive tissue interactions during development.     

Defining a genomic radius for long-range enhancer action: duplicated conserved non-coding elements hold the key

Many conserved non-coding elements (CNEs) in vertebrate genomes have been shown to function as tissue-specific enhancers. However, the target genes of most CNEs are unknown. Here we show that the target genes of duplicated CNEs can be predicted by considering their neighbouring paralogous genes. This enables us to provide the first systematic estimate of the genomic range for distal cis-regulatory interactions in the human genome: half of CNEs are >250 kb away from their associated gene.     

Cell lineages in the embryonic kidney: their inductive interactions and signalling molecules.

The first signalling genes acting in the inductive interactions in the kidney have now been identified. Differentiation of the permanent kidney or the metanephros is critically dependent on inductive signalling between the nephrogenic mesenchyme and ureteric bud epithelium. Further inductive interactions occur between developing nephrons, interstitial stroma, endothelial cells and neurones. Glial-cell-line-derived neurotrophic factor is a signal for the ureteric bud initiation and branching, and Wnt4 is an autocrine epithelializing signal at the pretubular stage of nephron formation. The signals for renal angiogenesis and innervation are less well defined, but seem to include vascular endothelial growth factor and neurotrophins, at least. The ureteric-bud-derived signal for induction of the nephrogenic mesenchyme (to bring the cells to the condensate stage) is not yet known, but fibroblast growth factor 2 is a good candidate. None of the signalling genes identified from the embryonic kidney is specific to the organ, which raises some general questions. How do the organs develop from similar rudiments to various patterns with different cell types and functions? Does the information for organ-specific differentiation pathways retain in the epithelial or mesenchymal compartment? The present, rather fragmentary molecular data would favour the view that similar molecules acting in different combinations and developmental sequences, rather than few organ-specific master genes, could be responsible for the divergence of patterning.     

Genetic basis of skin appendage development

Morphogenesis of hair follicles, teeth, and mammary glands depends on inductive epithelial-mesenchymal interactions mediated by a conserved set of signalling molecules. The early development of different skin appendages is remarkably similar. Initiation of organogenesis is marked by the appearance of a local epithelial thickening, a placode, which subsequently invaginates to produce a bud. These early developmental stages require many of the same genes and signalling circuits and consequently alterations in them often cause similar phenotypes in several skin appendages. After the bud stage, these organs adopt diverse patterns of epithelial growth, reflected in the usage of more divergent genes in each.     

Sequence Requirements for Myosin Gene Expression and Regulation in Caenorhabditis Elegans

Four Caenorhabditis elegans genes encode muscle-type specific myosin heavy chain isoforms: myo-1 and myo-2 are expressed in the pharyngeal muscles; unc-54 and myo-3 are expressed in body wall muscles. We have used transformation-rescue and lacZ fusion assays to determine sequence requirements for regulated myosin gene expression during development. Multiple tissue-specific activation elements are present for all four genes. For each of the four genes, sequences upstream of the coding region are tissue-specific promoters, as shown by their ability to drive expression of a reporter gene (lacZ) in the appropriate muscle type. Each gene contains at least one additional tissue-specific regulatory element, as defined by the ability to enhance expression of a heterologous promoter in the appropriate muscle type. In rescue experiments with unc-54, two further requirements apparently independent of tissue specificity were found: sequences within the 3' non-coding region are essential for activity while an intron near the 5' end augments expression levels. The general intron stimulation is apparently independent of intron sequence, indicating a mechanistic effect of splicing. To further characterize the myosin gene promoters and to examine the types of enhancer sequences in the genome, we have initiated a screen of C. elegans genomic DNA for fragments capable of enhancing the myo-2 promoter. The properties of enhancers recovered from this screen suggest that the promoter is limited to muscle cells in its ability to respond to enhancers.     

When needles look like hay: how to find tissue-specific enhancers in model organism genomes

A major prerequisite for the investigation of tissue-specific processes is the identification of cis-regulatory elements. No generally applicable technique is available to distinguish them from any other type of genomic non-coding sequence. Therefore, researchers often have to identify these elements by elaborate in vivo screens, testing individual regions until the right one is found.Here, based on many examples from the literature, we summarize how functional enhancers have been isolated from other elements in the genome and how they have been characterized in transgenic animals. Covering computational and experimental studies, we provide an overview of the global properties of cis-regulatory elements, like their specific interactions with promoters and target gene distances. We describe conserved non-coding elements (CNEs) and their internal structure, nucleotide composition, binding site clustering and overlap, with a special focus on developmental enhancers. Conflicting data and unresolved questions on the nature of these elements are highlighted. Our comprehensive overview of the experimental shortcuts that have been found in the different model organism communities and the new field of high-throughput assays should help during the preparation phase of a screen for enhancers. The review is accompanied by a list of general guidelines for such a project.     

The Undermethylated State of a CpG Island Region in Igf2 Transgenes Is Dependent on the H19 Enhancers

CpG islands are GC-rich regions located in the promoter regions of housekeeping genes and many tissue-specific genes. While most CpG islands are normally unmethylated, island methylation can occur and is associated with silencing of the corresponding gene. Experiments with transgenic mice and DNA transfection in pluripotential embryonic cells have led to the conclusion that the information required for protecting the islands from methylation is contained within the CpG islands themselves and have identified Sp1 binding sites as an important element in establishing and/or maintaining the methylation-free state of CpG islands. To examine the generality of these observations, we analyzed the methylation of one of the mouse Igf2 CpG islands and its flanks in transgenic mice. We observed that the undermethylated state of this region is dependent on the presence of a separate cis-regulatory element, the H19 enhancers. These tissue-specific enhancers had a ubiquitous, non-tissue-specific effect on island region methylation. Structural alterations outside of the island and these enhancers also affected this region's methylation. These findings indicate that the methylation of some CpG island-containing regions is more sensitive than previously believed to the activity of distant cis-regulatory elements and to structural alterations in nonisland sequences in cis.     

Orchestrating ontogenesis: variations on a theme by sonic hedgehog

Embryonic development is an emergent process in which increasing complexity is generated by sequential cellular interactions. Recently, it has become clear that such interactions are mediated by just a few families of signalling molecules; but how does this limited repertoire elicit the diversity of form that is characteristic of multicellular organisms? Here we review the various ways in which a member of one such family, the sonic hedgehog (SHH) protein, is deployed during embryonic development. These examples of SHH function provide paradigms for inductive interactions that should help to inform attempts to recapitulate cellular programming and organogenesis in vitro.     

A model for the genetic control of differential adhesion in insect epidermis

Adhesive relations among cells are believed to play a major role in determining patterns of serial homology, of intercalary regeneration, and of neuronal connectivity. Models for the genetic control of adhesion during development can provide a framework for further analysis of these phenomena. Investigators studying development of Drosophila have proposed that differentiation of segments and of imaginal discs is controlled by a set of bistable “selector genes”. In each region the settings of the selector genes form a binary “word” which determines the properties of cells in the region, including their adhesiveness. I have made an explicit proposal for the relation between binary words and adhesiveness, by assuming that active selector genes repress synthesis of “adhesor” macromolecules, which promote adhesion. This hypothesis correctly predicts the relative cohesiveness of cells in four pupal tissues of the moth Manduca. Works of cohesion and adhesion among the four cell types are deduced from published results of grafting experiments by modelling insect epidermis as a viscoelastic fluid.Further comparisons between deductions from the genetic and fluid models suggest that selector genes, or the adhesor molecules they regulate, interact within single cells in determining adhesiveness between cells. From a specific version of the genetic model I deduce that pairwise interactions between selector genes or adhesor molecules can determine many, though not all, of the relative works of adhesion between unlike cells in Manduca. The genetic and fluid models thus provide a set of working hypotheses for predicting patterns of intercellular adhesion in insect epidermis and for analyzing results of experiments designed to test such predictions.