Conserved Regulation of p53 Network Dosage by MicroRNA–125b Occurs through Evolving miRNA–Target Gene Pairs

MicroRNAs regulate networks of genes to orchestrate cellular functions. MiR-125b, the vertebrate homologue of the Caenorhabditis elegans microRNA lin-4, has been implicated in the regulation of neural and hematopoietic stem cell homeostasis, analogous to how lin-4 regulates stem cells in C. elegans. Depending on the cell context, miR-125b has been proposed to regulate both apoptosis and proliferation. Because the p53 network is a central regulator of both apoptosis and proliferation, the dual roles of miR-125b raise the question of what genes in the p53 network might be regulated by miR-125b. By using a gain- and loss-of-function screen for miR-125b targets in humans, mice, and zebrafish and by validating these targets with the luciferase assay and a novel miRNA pull-down assay, we demonstrate that miR-125b directly represses 20 novel targets in the p53 network. These targets include both apoptosis regulators like Bak1, Igfbp3, Itch, Puma, Prkra, Tp53inp1, Tp53, Zac1, and also cell-cycle regulators like cyclin C, Cdc25c, Cdkn2c, Edn1, Ppp1ca, Sel1l, in the p53 network. We found that, although each miRNA–target pair was seldom conserved, miR-125b regulation of the p53 pathway is conserved at the network level. Our results lead us to propose that miR-125b buffers and fine-tunes p53 network activity by regulating the dose of both proliferative and apoptotic regulators, with implications for tissue stem cell homeostasis and oncogenesis

Gradient Models in Developmental Biology: A Historical Perspective

The problem of complexity formation in the development of organisms has fascinated biologists for centuries. The contribution provides a historical perspective on research work in this field of developmental biology, starting at the beginning of the 20th century, when Theodor Boveri suggested that cell fates may depend on a graded distribution of some substance in the egg. In the 1920s, Hans Spemann discovered an organiser region in the newt embryo. In 1952, Alan Turing proposed a mathematical model to explain self-organisation from initially homogeneous states based on chemical interactions. In 1969, Lewis Wolpert coined the term ‘positional information’ and proposed a model of a gradient of a morphogen that elicits different responses depending on its concentration. In 1972, Gierer and Meinhardt formulated their gradient theory of local activation and lateral inhibition based on non-linear kinetics. This view was supported by mutant phenotypes in Drosophila. Systematic mutant screens in Drosophila and subsequent cloning of the genes have led to the identification of a large number of morphogenetic proteins

How fish colour their skin: A paradigm for development and evolution of adult patterns: Multipotency, plasticity, and cell competition regulate proliferation and spreading of pigment cells in Zebrafish coloration.

Pigment cells in zebrafish - melanophores, iridophores, and xanthophores - originate from neural crest-derived stem cells associated with the dorsal root ganglia of the peripheral nervous system. Clonal analysis indicates that these progenitors remain multipotent and plastic beyond embryogenesis well into metamorphosis, when the adult color pattern develops. Pigment cells share a lineage with neuronal cells of the peripheral nervous system; progenitors propagate along the spinal nerves. The proliferation of pigment cells is regulated by competitive interactions among cells of the same type. An even spacing involves collective migration and contact inhibition of locomotion of the three cell types distributed in superimposed monolayers in the skin. This mode of coloring the skin is probably common to fish, whereas different patterns emerge by species specific cell interactions among the different pigment cell types. These interactions are mediated by channels involved in direct cell contact between the pigment cells, as well as unknown cues provided by the tissue environment

A fate map for the larval epidermis ofDrosophila melanogaster: localized cuticle defects following irradiation of the blastoderm with an ultraviolet laser microbeam

Drosophila melanogaster embryos at the cellular blastoderm stage were irradiated with a uv laser microbeam (257 nm, 7 erg) of 20-μm diameter. Depending on the site of irradiation, up to 90% of the resulting first-instar larvae showed defects in the integument. The location of the defects within the cuticular pattern corresponded closely to the site of irradiation. The data indicate that the anlagen for the left and right parts of the larval epidermis are separated ventrally and each occupies an area extending from 20 to 60% of the egg length (EL) in the anteroposterior direction (0% EL = posterior pole). Within this area, the anlagen for the three thoracic and eight abdominal segments are equally spaced, each occupying a transverse stripe of a width of about 3.9 EL, corresponding to three to four cell diameters. The region of the blastoderm from which the epidermis of these segments develops comprises about 2200 cells which is one-third of the cells of the blastoderm. The paper includes a detailed description of the cuticular pattern of aDrosophila melanogaster first-instar larva

Evolution of Colour Patterning in Danio Species

Colour patterns are prominent features of many animals. They show a high variability and, serving in camouflage and communication, they are under natural and sexual selection. The zebrafish, Danio rerio, is an important vertebrate model organism for bio-medical and basic research. The fish display a very characteristic and stereotyped pattern of horizontal light and dark stripes on the flanks and the anal and tailfins. This pigment pattern is generated by three different types of pigment cells, dark melanophores, orange xanthophores and light reflecting iridophores. Other Danio species, closely related to zebrafish, can be bred in captivity; they possess the same three types of pigment cells but most of them show patterns that are very different from zebrafish. For the time being we concentrate on two additional species: Danio aesculapii and Danio albolineatus. Danio aesculapii, the closest sister species of zebrafish, has a pattern of vertical bars anteriorly that changes into an irregular ‘snake skin’ pattern more to the posterior. Danio albolineatus has almost no pattern, just a short posterior remnant of one horizontal stripe. Hybrids with zebrafish are viable but sterile; they produce patterns of horizontal stripes similar to zebrafish. We have begun to analyse the genetic and molecular bases for the pattern differences in these species. Starting from our detailed knowledge of the patterning process in zebrafish we have identified the first genes that are differentially required between zebrafish and Danio aesculapii and might therefore be the basis for the rapid evolution of pigmentation patterns in the Danio clade

Differential and stage-related expression in embryonic tissues of a new human homoeobox gene

The homoeobox is a 183 base-pair (bp) DNA sequence conserved in several Drosophila genes controlling segmentation and segment identity. Homoeobox sequences have been detected in the genome of species ranging from insects and anellids to vertebrates and homoeobox containing genes have been cloned from Xenopus, mouse and man. We recently isolated human homoeobox containing complementary DNA clones, that represent transcripts from four different human genes. One clone (HHO.c10) is selectively expressed in a 2.1 kilobase (kb) polyadenylated transcript in the spinal cord of human embryos and fetuses 5-10 weeks after fertilization. We report the characterization of a second cDNA clone, termed HHO.c13, that represents a new homoeobox gene. This clone encodes a protein of 255 amino-acid residues, which includes a pentapeptide, upstream of the homoeo domain, conserved in other Drosophila, Xenopus, murine and human homoeobox genes. By Northern analysis HHO.c13 detects multiple embryonic transcripts, which are differentially expressed in spinal cord, brain, backbone rudiments, limb buds and heart in 5-9-week-old human embryos and fetuses, in a striking organ- and stage-specific pattern. These observations suggest that in early mammalian development homoeobox genes may exert a wide spectrum of control functions in a variety of organs and body parts, in addition to the spinal cord