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PubMed2003

Maintaining collections of mutants for plant functional genomics.

As the plant genomics era progresses and post-genomic functional research rapidly expands, varied genetic resources of unprecedented power and scope are being developed. Partially by the mandate of public funding, these resources are being shared via stock centers and private laboratories. The successful initiation of any new research requires that advantage be taken of these stocks. Information on most plant genomic resources can be obtained through simple yet powerful. Web searches, and ordering mechanisms are linked to the information. Hence, locating and obtaining materials is rapid and simple. Currently, available genomic resources are described, and references, links for Web data, and ordering information are also included.

Arabidopsis↗

PubMed1999

Functional genomic mapping of an early-activated centromeric mammalian origin of DNA replication.

Ors12, a mammalian autonomously replicating sequence (812 bp), was previously isolated by extrusion of African green monkey (CV-1 cells) nascent DNA from active replication bubbles. It contains a region of alpha-satellite extending 168-bp from the 5'-end, and a nonrepetitive portion extending from nucleotide position 169 to nucleotide 812 that is present in less than nine copies per haploid genome. Ors12 is capable of transient autonomous DNA replication in vivo and in vitro, associates with the nuclear matrix in a cell cycle-dependent manner, and hybridizes at the centromeric region of six CV-1 cell chromosomes as well as a marker chromosome. To demonstrate that DNA replication initiates at ors12 at a native chromosomal locus, a 14.2 kb African green monkey genomic clone was isolated and sequence information was obtained that allowed us to generate eight sets of PCR primers spanning a region of 8 kb containing ors12. One set of primers occurred inside ors12. These primers were used to amplify nascent DNA strands from asynchronously growing CV-1 and African green monkey kidney (AGMK) cells, using noncompetitive and competitive PCR-based mapping methodologies. Both assays showed that DNA replication in vivo initiates preferentially in a 2.3 kb region containing ors12, as well as at a second site located 1.7 kb upstream of ors12. This study provides the first demonstration of genomic function for a centromeric mammalian origin of DNA replication, originally isolated by nascent strand extrusion.

Animals↗

PubMed2004

Development of a targeted transgenesis strategy in highly differentiated cells: a powerful tool for functional genomic analysis.

Functional genomic analysis is a challenging step in the so-called post-genomic field. Identification of potential targets using large-scale gene expression analysis requires functional validation to identify those that are physiologically relevant. Genetically modified cell models are often used for this purpose allowing up- or down-expression of selected targets in a well-defined and if possible highly differentiated cell type. However, the generation of such models remains time-consuming and expensive. In order to alleviate this step, we developed a strategy aimed at the rapid and efficient generation of genetically modified cell lines with conditional, inducible expression of various target genes. Efficient knock-in of various constructs, called targeted transgenesis, in a locus selected for its permissibility to the tet inducible system, was obtained through the stimulation of site-specific homologous recombination by the meganuclease I-SceI. Our results demonstrate that targeted transgenesis in a reference inducible locus greatly facilitated the functional analysis of the selected recombinant cells. The efficient screening strategy we have designed makes possible automation of the transfection and selection steps. Furthermore, this strategy could be applied to a variety of highly differentiated cells.

Animals↗

PubMed2005

Genome projects and the functional-genomic era.

The problems we face today in public health as a result of the -- fortunately -- increasing age of people and the requirements of developing countries create an urgent need for new and innovative approaches in medicine and in agronomics. Genomic and functional genomic approaches have a great potential to at least partially solve these problems in the future. Important progress has been made by procedures to decode genomic information of humans, but also of other key organisms. The basic comprehension of genomic information (and its transfer) should now give us the possibility to pursue the next important step in life science eventually leading to a basic understanding of biological information flow; the elucidation of the function of all genes and correlative products encoded in the genome, as well as the discovery of their interactions in a molecular context and the response to environmental factors. As a result of the sequencing projects, we are now able to ask important questions about sequence variation and can start to comprehensively study the function of expressed genes on different levels such as RNA, protein or the cell in a systematic context including underlying networks. In this article we review and comment on current trends in large-scale systematic biological research. A particular emphasis is put on technology developments that can provide means to accomplish the tasks of future lines of functional genomics.

Animals↗

PubMed2002

Comparative analysis of chloroplast genomes: functional annotation, genome-based phylogeny, and deduced evolutionary patterns.

All protein sequences from 19 complete chloroplast genomes (cpDNA) have been studied using a new computational method able to analyze functional correlations among series of protein sequences contained in complete proteomes. First, all open reading frames (ORFs) from the cpDNAs, comprising a total of 2266 protein sequences, were compared against the 3168 proteins from Synechocystis PCC6803 complete genome to find functionally related orthologous proteins. Additionally, all cpDNA genomes were pairwise compared to find orthologous groups not present in cyanobacteria. Annotations in the cluster of othologous proteins database and CyanoBase were used as reference for the functional assignments. Following this protocol, new functional assignments were made for ORFs of unknown function and for ycfs (hypothetical chloroplast frames), which still lack a functional assignment. Using this information, a matrix of functional relationships was derived from profiles of the presence and/or absence of orthologous proteins; the matrix included 1837 proteins in 277 orthologous clusters. A factor analysis study of this matrix, followed by cluster analysis, allowed us to obtain accurate phylogenetic reconstructions and the detection of genes probably involved in speciation as phylogenetic correlates. Finally, by grouping common evolutionary patterns, we show that it is possible to determine functionally linked protein networks. This has allowed us to suggest putative associations for some unknown ORFs.

Bacterial Proteins↗

PubMed2005

Functional genomics: tools for improving farm animal health and welfare.

The first genome sequence assemblies of farm animal species are now accessible through public domain databases, and further sequencing projects are in rapid progress. In addition, large collections of expressed sequences have been obtained, which will aid in constructing annotated transcript maps for many economically important species. Thus, the breeding of farm animals is entering the post-genome era. Functional genomics, defined as applying global experimental approaches to assess gene function, by using the information and reagents provided by structural genomics (i.e. mapping and sequencing), has become the focus of interest. Combining a holistic view of phenotypes at the molecular level with genetic marker data seems a particularly promising approach for improving health and welfare traits in farm animals. These traits are often difficult to define. They suffer from low heritabilities and a corresponding lack of genetic gain in conventional selection and breeding programmes. At the same time, genomic information from micro-organisms and parasites offers the potential for new vaccines and therapeutics. This review describes major functional genomics tools, lists genomic resources available for farm animals and discusses the prospects and challenges of functional genomics in improving the health and welfare of farm animals.

Animal Welfare↗

PubMed2004

High-throughput RNAi in Caenorhabditis elegans: genome-wide screens and functional genomics.

The phenomenon of RNA-mediated interference (RNAi) was first discovered in the nematode Caenorhabditis elegans, in which introduction of double-stranded RNA causes specific inactivation of genes with corresponding sequences. Technical advances in RNAi methodology and the availability of the complete genome sequence have enabled the high-throughput, genome-wide RNAi analysis of this organism. Several groups have used large-scale RNAi to systematically examine every C. elegans gene for knock-down phenotypes, providing basal information to be mined in more detailed studies. Now, in addition to functional genomic RNAi analyses, high-throughput RNAi is also routinely used for rapid, genome-wide screens for genes involved in specific biological processes. The integration of high-throughput RNAi experiments with other large-scale data, such as DNA microarrays and protein-protein interaction maps, enhances the speed and reliability of such screens. The accumulation of RNAi phenotype data dramatically accelerates our understanding of this organism at the genetic level.

Animals↗

PubMed2005

Global approach to perinatal medicine: functional genomics and proteomics.

Functional genomics (transcriptomics and proteomics) is a global, systematic and comprehensive approach to the identification and description of the processes and pathways involved in normal and abnormal physiological states. The functional genomics methods most applied today are DNA microarrays and proteomics methods, primarily two-dimensional gel electrophoresis coupled with mass spectrometry. To date, interesting research has been carried out, representing milestones for future implementation of functional genomics/proteomics in perinatal medicine. For instance, possible biomarkers of pre-eclampsia, preterm labor and gestational trophoblastic diseases have been discovered. Further systematic examination of differentially regulated genes and proteins in maternal and fetal tissues and fluids will be required. However, high-throughput technologies reflect biological fluctuations and methodological errors. Large amounts of such different data challenge the performance and capacity of the statistical tools and software available at present. Further major developments in this field are pending and the intellectual investment will certainly result in clinical advances.

Female↗

PubMed2002

Functional genomics of osteoarthritis.

Functional genomics is a challenging new way to address a complex disease like osteoarthritis on a molecular level. Despite osteoarthritis being ultimately a biochemical problem, mainly characterized by an imbalanced cartilage matrix turnover, a deeper understanding of molecular events within the tissue cells (i.e., the chondrocytes) will provide not only a better understanding of pathogenetic mechanisms but also new diagnostic markers and cellular targets for therapeutic intervention. This innovative technology represents a challenging approach complementing (not replacing) classical research in previously described and new disease-relevant genes: large-scale functional genomics will open up new areas of so far unrecognized molecular networks. This will include as yet unidentified players in the anabolic-catabolic balance of matrix turnover of articular cartilage as well as disease-relevant intracellular signaling cascades so far hardly investigated in articular chondrocytes. However, care must be taken not to over or misinterpret results and some major challenges must be overcome in order to properly utilize the potential of this technology in the field of osteoarthritis.

Animals↗

PubMedDate not supplied

[cDNA-microarrays in cartilage research - functional genomics of osteoarthritis].

Functional genomics represents a new challenging approach in order to analyze complex diseases such as osteoarthritis on a molecular level. The characterization of the molecular changes of the cartilage cells, the chondrocytes, enables a better understanding of the pathomechanisms of the disease. In particular, the identification and characterization of new target molecules for therapeutic intervention is of interest. Also, potential molecular markers for diagnosis and monitoring of osteoarthritis contribute to a more appropriate patient management. The DNA-microarray technology complements (but does not replace) biochemical and biological research in new disease-relevant genes. Large-scale functional genomics will identify molecular networks such as yet identified players in the anabolic-catabolic balance of articular cartilage as well as disease-relevant intracellular signaling cascades so far rather unknown in articular chondrocytes. However, at the moment it is also important to recognize the limitations of the microarray technology in order to avoid over-interpretation of the results. This might lead to misleading results and prevent to a significant extent a proper use of the potential of this technology in the field of osteoarthritis.

Cartilage↗

PubMed2006

The Mouse Functional Genome Database (MfunGD): functional annotation of proteins in the light of their cellular context.

MfunGD (http://mips.gsf.de/genre/proj/mfungd/) provides a resource for annotated mouse proteins and their occurrence in protein networks. Manual annotation concentrates on proteins which are found to interact physically with other proteins. Accordingly, manually curated information from a protein-protein interaction database (MPPI) and a database of mammalian protein complexes is interconnected with MfunGD. Protein function annotation is performed using the Functional Catalogue (FunCat) annotation scheme which is widely used for the analysis of protein networks. The dataset is also supplemented with information about the literature that was used in the annotation process as well as links to the SIMAP Fasta database, the Pedant protein analysis system and cross-references to external resources. Proteins that so far were not manually inspected are annotated automatically by a graphical probabilistic model and/or superparamagnetic clustering. The database is continuously expanding to include the rapidly growing amount of functional information about gene products from mouse. MfunGD is implemented in GenRE, a J2EE-based component-oriented multi-tier architecture following the separation of concern principle.

Animals↗

PubMed2000

Progress in Arabidopsis genome sequencing and functional genomics.

Arabidopsis thaliana has a relatively small genome of approximately 130 Mb containing about 10% repetitive DNA. Genome sequencing studies reveal a gene-rich genome, predicted to contain approximately 25000 genes spaced on average every 4.5 kb. Between 10 to 20% of the predicted genes occur as clusters of related genes, indicating that local sequence duplication and subsequent divergence generates a significant proportion of gene families. In addition to gene families, repetitive sequences comprise individual and small clusters of two to three retroelements and other classes of smaller repeats. The clustering of highly repetitive elements is a striking feature of the A. thaliana genome emerging from sequence and other analyses.

Agriculture↗

PubMed2002

Putting the Leishmania genome to work: functional genomics by transposon trapping and expression profiling.

Leishmania are important protozoan pathogens of humans in temperate and tropical regions. The study of gene expression during the infectious cycle, in mutants or after environmental or chemical stimuli, is a powerful approach towards understanding parasite virulence and the development of control measures. Like other trypanosomatids, Leishmania gene expression is mediated by a polycistronic transcriptional process that places increased emphasis on post-transcriptional regulatory mechanisms including RNA processing and protein translation. With the impending completion of the Leishmania genome, global approaches surveying mRNA and protein expression are now feasible. Our laboratory has developed the Drosophila transposon mariner as a tool for trapping Leishmania genes and studying their regulation in the form of protein fusions; a classic approach in other microbes that can be termed 'proteogenomics'. Similarly, we have developed reagents and approaches for the creation of DNA microarrays, which permit the measurement of RNA abundance across the parasite genome. Progress in these areas promises to greatly increase our understanding of global mechanisms of gene regulation at both mRNA and protein levels, and to lead to the identification of many candidate genes involved in virulence.

Animals↗

PubMed2005

Functional genomics databases on the web.

Experiments involving high-throughput methods for measuring transcripts, proteins and metabolites constitute the area of functional genomics. These experiments are highly context dependent and require much more detail about the experimental design, sample and protocols used than in genomics. Functional genomics databases are needed that follow established and emerging standards. Functional genomic databases are not yet very common; however, there are a few focused on microbial genomes and a couple integrative systems are available for setting up functional genomics databases.

Computational Biology↗

PubMed2004

An object model and database for functional genomics.

MOTIVATION: Large-scale functional genomics analysis is now feasible and presents significant challenges in data analysis, storage and querying. Data standards are required to enable the development of public data repositories and to improve data sharing. There is an established data format for microarrays (microarray gene expression markup language, MAGE-ML) and a draft standard for proteomics (PEDRo). We believe that all types of functional genomics experiments should be annotated in a consistent manner, and we hope to open up new ways of comparing multiple datasets used in functional genomics. RESULTS: We have created a functional genomics experiment object model (FGE-OM), developed from the microarray model, MAGE-OM and two models for proteomics, PEDRo and our own model (Gla-PSI-Glasgow Proposal for the Proteomics Standards Initiative). FGE-OM comprises three namespaces representing (i) the parts of the model common to all functional genomics experiments; (ii) microarray-specific components; and (iii) proteomics-specific components. We believe that FGE-OM should initiate discussion about the contents and structure of the next version of MAGE and the future of proteomics standards. A prototype database called RNA And Protein Abundance Database (RAPAD), based on FGE-OM, has been implemented and populated with data from microbial pathogenesis. AVAILABILITY: FGE-OM and the RAPAD schema are available from http://www.gusdb.org/fge.html, along with a set of more detailed diagrams. RAPAD can be accessed by registration at the site.

Abstracting and Indexing↗

PubMed2003

Integrating functional genomics data.

Functional annotation of fully sequenced genomes is still a major issue. High-throughput data sets could be used to provide more and better functional annotations. However differences in data quality need to be taken into account. For this purpose these high-throughput data sets need to be integrated so that the data quality can be assessed, hypotheses can be prioritized and existing annotations can be improved and extended.

Computational Biology↗

PubMed2006

High-content screening of functional genomic libraries.

Recent advances in functional genomics have enabled genome-wide genetic studies in mammalian cells. These include the establishment of high-throughput transfection and viral propagation methodologies, the production of large-scale cDNA and siRNA libraries, and the development of sensitive assay detection processes and instrumentation. The latter has been significantly facilitated by the implementation of automated microscopy and quantitative image analysis, collectively referred to as high-content screening (HCS), toward cell-based functional genomics application. This technology can be applied to whole genome analysis of discrete molecular and phenotypic events at the level of individual cells and promises to significantly expand the scope of functional genomic analyses in mammalian cells. This chapter provides a comprehensive guide for curating and preparing function genomics libraries and performing HCS at the level of the genome.

Animals↗

PubMed2001

Functional food ingredients against colorectal cancer. An example project integrating functional genomics, nutrition and health.

Functional Food Ingredients Against Colorectal Cancer is one of the first European Union funded Research Projects at the cross-road of functional genomics [comprising transcriptomics, the measurement of the expression of all messengers RNA (mRNAs) and proteomics, the measurement of expression/state of all proteins], nutrition and human health. The goal of Functional Food Ingredients Against Colorectal Cancer is to develop a colon epithelial cell line-based screening assay for nutrients with presumed anti-colorectal carcinogenic properties. Genes involved in colon carcinogenesis are identified at the RNA and protein level, using a variety of methods (subtractive hybridisation, DNA microarray, proteomics) in combination with models for colorectal cancer development (human biopsies, rat model for colorectal carcinogenesis, colorectal cancer epithelial cell lines). Secondly, colorectal cancer epithelial cell lines are selected, in terms of their capacity to undergo gene/protein expression changes representing different phases in the colorectal carcinogenesis. Thirdly, these cell lines are used to determine the effects of nutrients with presumed anti-carcinogenic properties (e.g. resveratrol, flavonoids) on functional genomics-derived endpoints. Once validated against the effects of these nutrients in in vivo animal models and classical biomarkers for colorectal carcinogenesis, these cell line models combined with functional genomics represent useful tools to study colorectal carcinogenesis and screen for nutrients with anti-carcinogenic properties.

Animals↗