RESUMEN
Gene expression patterns assayed across development can offer key clues about a gene's function and regulatory role. Drosophila melanogaster is ideal for such investigations as multiple individual and high-throughput efforts have captured the spatiotemporal patterns of thousands of embryonic expressed genes in the form of in situ images. FlyExpress (www.flyexpress.net), a knowledgebase based on a massive and unique digital library of standardized images and a simple search engine to find coexpressed genes, was created to facilitate the analytical and visual mining of these patterns. Here, we introduce the next generation of FlyExpress resources to facilitate the integrative analysis of sequence data and spatiotemporal patterns of expression from images. FlyExpress 7 now includes over 100,000 standardized in situ images and implements a more efficient, user-defined search algorithm to identify coexpressed genes via Genomewide Expression Maps (GEMs). Shared motifs found in the upstream 5' regions of any pair of coexpressed genes can be visualized in an interactive dotplot. Additional webtools and link-outs to assist in the downstream validation of candidate motifs are also provided. Together, FlyExpress 7 represents our largest effort yet to accelerate discovery via the development and dispersal of new webtools that allow researchers to perform data-driven analyses of coexpression (image) and genomic (sequence) data.
Asunto(s)
Drosophila melanogaster/genética , Regulación de la Expresión Génica , Imagenología Tridimensional , Hibridación in Situ , Programas Informáticos , Animales , Sitios de Unión/genética , Secuencia Conservada/genética , Genoma de los Insectos , Factores de Transcripción/metabolismoRESUMEN
Phylum Hemichordata, composed of worm-like Enteropneusta and colonial Pterobranchia, has been reported to only contain about 100 species. However, recent studies of hemichordate phylogeny and taxonomy suggest the species number has been largely underestimated. One issue is that species must be described by experts, and historically few taxonomists have studied this group of marine invertebrates. Despite this previous lack of coverage, interest in hemichordates has piqued in the past couple of decades, as they are critical to understanding the evolution of chordates-as acorn worms likely resemble the deuterostome ancestor more closely than any other extant animal. This review provides an overview of our current knowledge of hemichordates, focusing specifically on their global biodiversity, geographic distribution, and taxonomy. Using information available in the World Register of Marine Species and published literature, we assembled a list of 130 described, extant species. The majority (83%) of these species are enteropneusts, and more taxonomic descriptions are forthcoming. Ptychoderidae contained the greatest number of species (41 species), closely followed by Harrimaniidae (40 species), of the recognized hemichordate families. Hemichordates are found throughout the world's oceans, with the highest reported numbers by regions with marine labs and diligent taxonomic efforts (e.g. North Pacific and North Atlantic). Pterobranchs are abundant in Antarctica, but have also been found at lower latitudes. We consider this a baseline report and expect new species of Hemichordata will continue to be discovered and described as new marine habitats are characterized and explored.
Asunto(s)
Biodiversidad , Cordados no Vertebrados , Animales , Organismos Acuáticos , Cordados no Vertebrados/anatomía & histología , Cordados no Vertebrados/clasificación , Cordados no Vertebrados/genética , Geografía , FilogeniaRESUMEN
Spatial patterns of gene expression are of key importance in understanding developmental networks. Using in situ hybridization, many laboratories are generating images to describe these spatial patterns and to test biological hypotheses. To facilitate such analyses, we have developed biologist-centric software (myFX) that contains computational methods to automatically process and analyze images depicting embryonic gene expression in the fruit fly Drosophila melanogaster. It facilitates creating digital descriptions of spatial patterns in images and enables measurements of pattern similarity and visualization of expression across genes and developmental stages. myFX interacts directly with the online FlyExpress database, which allows users to search thousands of existing patterns to find co-expressed genes by image comparison.
Asunto(s)
Drosophila melanogaster/genética , Perfilación de la Expresión Génica/métodos , Regulación del Desarrollo de la Expresión Génica , Animales , Drosophila melanogaster/embriología , Expresión Génica , Programas InformáticosRESUMEN
BACKGROUND: Multicellular organisms consist of cells of many different types that are established during development. Each type of cell is characterized by the unique combination of expressed gene products as a result of spatiotemporal gene regulation. Currently, a fundamental challenge in regulatory biology is to elucidate the gene expression controls that generate the complex body plans during development. Recent advances in high-throughput biotechnologies have generated spatiotemporal expression patterns for thousands of genes in the model organism fruit fly Drosophila melanogaster. Existing qualitative methods enhanced by a quantitative analysis based on computational tools we present in this paper would provide promising ways for addressing key scientific questions. RESULTS: We develop a set of computational methods and open source tools for identifying co-expressed embryonic domains and the associated genes simultaneously. To map the expression patterns of many genes into the same coordinate space and account for the embryonic shape variations, we develop a mesh generation method to deform a meshed generic ellipse to each individual embryo. We then develop a co-clustering formulation to cluster the genes and the mesh elements, thereby identifying co-expressed embryonic domains and the associated genes simultaneously. Experimental results indicate that the gene and mesh co-clusters can be correlated to key developmental events during the stages of embryogenesis we study. The open source software tool has been made available at http://compbio.cs.odu.edu/fly/. CONCLUSIONS: Our mesh generation and machine learning methods and tools improve upon the flexibility, ease-of-use and accuracy of existing methods.
Asunto(s)
Inteligencia Artificial , Biología Computacional/métodos , Regulación del Desarrollo de la Expresión Génica , Procesamiento de Imagen Asistido por Computador/métodos , Procesamiento de Imagen Asistido por Computador/normas , Máquina de Vectores de Soporte , Animales , Inteligencia Artificial/normas , Análisis por Conglomerados , Biología Computacional/normas , Drosophila/embriología , Drosophila/genética , Perfilación de la Expresión Génica/métodos , Procesamiento de Imagen Asistido por Computador/estadística & datos numéricos , Programas InformáticosRESUMEN
Recently we employed phylogenetics to predict that the cellular interpretation of TGF-ß signals is modulated by monoubiquitylation cycles affecting the Smad4 signal transducer/tumor suppressor. This prediction was subsequently validated by experiments in flies, frogs and mammalian cells. Here we apply a phylogenetic approach to the Hippo pathway and predict that two of its signal transducers, Salvador and Merlin/Nf2 (also a tumor suppressor) are regulated by monoubiquitylation. This regulatory mechanism does not lead to protein degradation but instead serves as a highly efficient "off/on" switch when the protein is subsequently deubiquitylated. Overall, our study shows that the creative application of phylogenetics can predict new roles for pathway components and new mechanisms for regulating intercellular signaling pathways.
Asunto(s)
Proteínas de Ciclo Celular/metabolismo , Neurofibromina 2/metabolismo , Ubiquitina/metabolismo , Animales , Teorema de Bayes , Proteínas de Drosophila/metabolismo , Drosophila melanogaster , Humanos , Péptidos y Proteínas de Señalización Intracelular/metabolismo , Funciones de Verosimilitud , Lisina/química , Fosforilación , Filogenia , Proteínas Serina-Treonina Quinasas/metabolismo , Transducción de Señal , Proteína Smad4/metabolismo , Factor de Crecimiento Transformador beta/metabolismo , Ubiquitina/químicaRESUMEN
Enteropneust hemichordates share several characteristics with chordates, such as a Hox-specified anterior-posterior axis, pharyngeal gill slits, a dorsal central nervous system (CNS), and a juvenile postanal tail. Ptychoderid hemichordates, such as the indirect-developer Ptychodera flava, have feeding larvae and a remarkable capacity to regenerate their CNS. We compared neurulation of ptychoderid hemichordates and chordates using histological analyses, and found many similarities in CNS development. In ptychoderid hemichordates, which lack a notochord, the proboscis skeleton develops from endoderm after neurulation. The position of the proboscis skeleton directly under the nerve cord suggests that it serves a structural role similar to the notochord of chordates. These results suggest that either the CNS preceded evolution of the notochord or that the notochord has been lost in hemichordates. The evolution of the notochord remains ambiguous, but it may have evolved from endoderm, not mesoderm.
Asunto(s)
Invertebrados/embriología , Neurulación , Animales , Evolución Biológica , Sistema Nervioso Central/embriología , Cordados/embriología , Cordados/crecimiento & desarrollo , Invertebrados/crecimiento & desarrollo , Larva/anatomía & histología , Larva/crecimiento & desarrollo , Metamorfosis BiológicaRESUMEN
BACKGROUND: Overlaps in spatial patterns of gene expression are frequently an initial clue to genetic interactions during embryonic development. However, manual inspection of images requires considerable time and resources impeding the discovery of important interactions because tens of thousands of images exist. The FlyExpress discovery platform was developed to facilitate data-driven comparative analysis of expression pattern images from Drosophila embryos. RESULTS: An image-based search of the BDGP and Fly-FISH datasets conducted in FlyExpress yields fewer but more precise results than text-based searching when the specific goal is to find genes with overlapping expression patterns. We also provide an example of a FlyExpress contribution to scientific discovery: an analysis of gene expression patterns for multigene family members revealed that spatial divergence is far more frequent than temporal divergence, especially after the maternal to zygotic transition. This discovery provides a new clue to molecular mechanisms whereby duplicated genes acquire novel functions. CONCLUSIONS: The application of FlyExpress to understanding the process by which new genes acquire novel functions is just one of a myriad of ways in which it can contribute to our understanding of developmental and evolutionary biology. This resource has many other potential applications, limited only by the investigator's imagination.
Asunto(s)
Biología Computacional/métodos , Drosophila/embriología , Drosophila/genética , Regulación del Desarrollo de la Expresión Génica , Familia de Multigenes , Animales , Biología Computacional/instrumentación , Bases de Datos Factuales , Proteínas de Drosophila/genética , Proteínas de Drosophila/metabolismoRESUMEN
SUMMARY: Images containing spatial expression patterns illuminate the roles of different genes during embryogenesis. In order to generate initial clues to regulatory interactions, biologists frequently need to know the set of genes expressed at the same time at specific locations in a developing embryo, as well as related research publications. However, text-based mining of image annotations and research articles cannot produce all relevant results, because the primary data are images that exist as graphical objects. We have developed a unique knowledge base (FlyExpress) to facilitate visual mining of images from Drosophila melanogaster embryogenesis. By clicking on specific locations in pictures of fly embryos from different stages of development and different visual projections, users can produce a list of genes and publications instantly. In FlyExpress, each queryable embryo picture is a heat-map that captures the expression patterns of more than 4500 genes and more than 2600 published articles. In addition, one can view spatial patterns for particular genes over time as well as find other genes with similar expression patterns at a given developmental stage. Therefore, FlyExpress is a unique tool for mining spatiotemporal expression patterns in a format readily accessible to the scientific community. AVAILABILITY: http://www.flyexpress.net CONTACT: s.kumar@asu.edu.
Asunto(s)
Proteínas de Drosophila/genética , Drosophila melanogaster/embriología , Drosophila melanogaster/genética , Regulación del Desarrollo de la Expresión Génica , Animales , Recursos Audiovisuales , Minería de Datos , Proteínas de Drosophila/metabolismo , Drosophila melanogaster/metabolismo , Desarrollo Embrionario , Perfilación de la Expresión GénicaRESUMEN
The canonical Wnt pathway is one of the oldest and most functionally diverse of animal intercellular signaling pathways. Though much is known about loss-of-function phenotypes for Wnt pathway components in several model organisms, the question of how this pathway achieved its current repertoire of functions has not been addressed. Our phylogenetic analyses of 11 multigene families from five species belonging to distinct phyla, as well as additional analyses employing the 12 Drosophila genomes, suggest frequent gene duplications affecting ligands and receptors as well as co-evolution of new ligand-receptor pairs likely facilitated the expansion of this pathway's capabilities. Further, several examples of recent gene loss are visible in Drosophila when compared to family members in other phyla. By comparison the TGFbeta signaling pathway is characterized by ancient gene duplications of ligands, receptors, and signal transducers with recent duplication events restricted to the vertebrate lineage. Overall, the data suggest that two distinct molecular evolutionary mechanisms can create a functionally diverse developmental signaling pathway. These are the recent dynamic generation of new genes and ligand-receptor interactions as seen in the Wnt pathway and the conservative adaptation of ancient pre-existing genes to new roles as seen in the TGFbeta pathway. From a practical perspective, the former mechanism limits the investigator's ability to transfer knowledge of specific pathway functions across species while the latter facilitates knowledge transfer.
Asunto(s)
Evolución Molecular , Filogenia , Factor de Crecimiento Transformador beta/genética , Factor de Crecimiento Transformador beta/metabolismo , Proteínas Wnt/genética , Proteínas Wnt/metabolismo , Proteínas Adaptadoras Transductoras de Señales/genética , Animales , Análisis por Conglomerados , Proteínas Dishevelled , Drosophila/genética , Receptores Frizzled/genética , Ratones , Fosfoproteínas/genética , Receptores Acoplados a Proteínas G/genética , Anémonas de Mar/genética , Transducción de Señal , Strongylocentrotus purpuratus/genética , Factores de Transcripción/genéticaRESUMEN
MOTIVATION: In functional genomics, it is frequently useful to correlate expression levels of genes to identify transcription factor binding sites (TFBS) via the presence of common sequence motifs. The underlying assumption is that co-expressed genes are more likely to contain shared TFBS and, thus, TFBS can be identified computationally. Indeed, gene pairs with a very high expression correlation show a significant excess of shared binding sites in yeast. We have tested this assumption in a more complex organism, Drosophila melanogaster, by using experimentally determined TFBS and microarray expression data. We have also examined the reverse relationship between the expression correlation and the extent of TFBS sharing. RESULTS: Pairs of genes with shared TFBS show, on average, a higher degree of co-expression than those with no common TFBS in Drosophila. However, the reverse does not hold true: gene pairs with high expression correlations do not share significantly larger numbers of TFBS. Exception to this observation exists when comparing expression of genes from the earliest stages of embryonic development. Interestingly, semantic similarity between gene annotations (Biological Process) is much better associated with TFBS sharing, as compared to the expression correlation. We discuss these results in light of reverse engineering approaches to computationally predict regulatory sequences by using comparative genomics.
Asunto(s)
Biología Computacional/métodos , Drosophila melanogaster/genética , Expresión Génica , Genómica/métodos , Factores de Transcripción/genética , Animales , Sitios de Unión , Drosophila melanogaster/metabolismo , Análisis de Secuencia por Matrices de Oligonucleótidos , Factores de Transcripción/metabolismoRESUMEN
TGFbeta and Wnt pathways play important roles in the development of animals from sponges to humans. In both pathways posttranslational modification as a means of regulating their function, such as lysine modification by ubiquitination and sumoylation, has been observed. However, a gap exists between the immunological observation of posttranslational modification and the identification of the target lysine. To fill this gap, we conducted a phylogenetic analysis of lysine conservation and context in TGFbeta and Wnt pathway receptors and signal transducers and suggest numerous high-probability candidates for posttranslational modification. Further comparison of results from both pathways suggests two general features for biochemical regulation of intercellular signaling: receptors are less frequent targets for modification than signal transduction agonists, and a lysine adjacent to an upstream hydrophobic residue may be a preferred context for modification. Overall the results suggest numerous applications for an evolutionary approach to the biochemical regulation of developmental pathways, including (1) streamlining of the identification of the target lysine, (2) determination of when members of a multigene family acquire distinct activities, (3) application to any conserved protein family, and (4) application to any modification of a specific amino acid.