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Results for “Functional genes”

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PubMed2006

Systematic gene function prediction from gene expression data by using a fuzzy nearest-cluster method.

BACKGROUND: Quantitative simultaneous monitoring of the expression levels of thousands of genes under various experimental conditions is now possible using microarray experiments. However, there are still gaps toward whole-genome functional annotation of genes using the gene expression data. RESULTS: In this paper, we propose a novel technique called Fuzzy Nearest Clusters for genome-wide functional annotation of unclassified genes. The technique consists of two steps: an initial hierarchical clustering step to detect homogeneous co-expressed gene subgroups or clusters in each possibly heterogeneous functional class; followed by a classification step to predict the functional roles of the unclassified genes based on their corresponding similarities to the detected functional clusters. CONCLUSION: Our experimental results with yeast gene expression data showed that the proposed method can accurately predict the genes' functions, even those with multiple functional roles, and the prediction performance is most independent of the underlying heterogeneity of the complex functional classes, as compared to the other conventional gene function prediction approaches.

Algorithms↗

PubMed1992

Antisense oligodeoxynucleotides as probes of T-lymphocyte gene function.

Conventional and thiophosphonate-derivatized oligonucleotides were employed to specifically regulate functional gene expression in murine T-cell hybridomas. For example, induction of apoptotic cell death following activation of T-cell hybridomas was examined using antisense oligonucleotides corresponding to several protooncogenes. We found that antisense oligodeoxynucleotides corresponding to c-myc inhibited both the characteristic DNA fragmentation and the loss of cell viability following activation without affecting production of lymphokines. Functional antisense oligonucleotides corresponding to c-fos had no effect in this system. These results demonstrate the use of antisense oligonucleotides to regulate function in T-cell hybridomas and provide valuable insights into the molecular bases of this biological phenomenon. Antisense oligonucleotides were also used to study another problem, the relation of T-cell-derived antigen-specific immunoregulatory factors to the T-cell receptor (TCR). Because the translation start of each TCR gene usually varies from one T cell to another, antisense oligonucleotides corresponding to the TCR V alpha or V beta of different cells were shown to act in a cell-specific manner. Furthermore, this method was used to demonstrate that a soluble antigen-specific regulatory activity produced by one of the T-cell lines depends on expression of the specific TCRa, an observation that has since been confirmed by gene transfer experiments. Expression of the CD3-TCR complex on the cell surface was also blocked by antisense oligonucleotides corresponding to CD3 gamma and CD3 zeta; however, neither these nor TCR V beta antisense oligonucleotides had any effect on production of the soluble regulatory activity.

Animals↗

PubMed2006

Experimental reconstruction of functional gene transfer from the tobacco plastid genome to the nucleus.

Eukaryotic cells arose through the uptake of free-living bacteria by endosymbiosis and their gradual conversion into organelles (plastids and mitochondria). Capture of the endosymbionts was followed by massive translocation of their genes to the genome of the host cell. How genes were transferred from the (prokaryotic) organellar genome to the (eukaryotic) nuclear genome and how the genes became functional in their new eukaryotic genetic environment is largely unknown. Here, we report the successful experimental reconstruction of functional gene transfer between an organelle and the nucleus, a process that normally occurs only on large evolutionary timescales. In consecutive genetic screens, we first transferred a chloroplast genome segment to the nucleus and then selected for gene activation in the nuclear genome. We show that DNA-mediated gene transfer can give rise to functional nuclear genes if followed by suitable rearrangements in the nuclear genome. Acquisition of gene function involves (1) transcriptional activation by capture of the promoter of an upstream nuclear gene and (2) utilization of AT-rich noncoding sequences downstream of the plastid gene as RNA cleavage and polyadenylation sites. Our results reveal the molecular mechanisms of how organellar DNA transferred to the nucleus gives rise to functional genes and reproduce in the laboratory a key process in the evolution of eukaryotic cells.

Base Sequence↗

PubMed2005

MEGO: gene functional module expression based on gene ontology.

Existing analysis tools to study the collective properties of gene functional modules cannot return highly homogeneous modules and do not provide quantitative measures of module activity level. By partitioning genes according to multiple gene functional categorization principles and summarizing gene expression values into module expression values, MEGO (module expression based on gene ontology), a standalone microarray data analysis program, is able to extract highly activated gene functional modules that are of much interest to microarray experimenters. With multiple functional categorization principles simultaneously introduced in MEGO, the partition of genes is more delicate, and the collective property of a group of genes is sharpened and easier to capture. The quantitative measures of module activity levels returned by MEGO give users a quick impression of the direction and degree of module regulation. MEGO efficiently determines the answers to frequently asked questions, such as which functional classes have been induced or repressed under a specific experiment and to which levels these functional classes have been affected. MEGO is available free of charge for academic use and may be downloaded from http://www.dxy.cn/mego/MEGOInstall.EXE. Supplementary information can be found on the authors' web page at http://www.dxy.cn/mego/ and at the BioTechniques' web site at http://www. BioTechniques.com/February2005/TuSupplementary.html.

Algorithms↗

PubMed1985

Characterization of the functional gene and several processed pseudogenes in the human triosephosphate isomerase gene family.

The functional gene and three intronless pseudogenes for human triosephosphate isomerase were isolated from a recombinant DNA library and characterized in detail. The functional gene spans 3.5 kilobase pairs and is split into seven exons. Its promoter contains putative TATA and CCAAT boxes and is extremely rich in G and C residues (76%). The pseudogenes share a high degree of homology with the functional gene but contain mutations that preclude the synthesis of an active triosephosphate isomerase enzyme. Sequence divergence calculations indicate that these pseudogenes arose approximately 18 million years ago. We present evidence that there is a single functional gene in the human triosephosphate isomerase gene family.

Amino Acid Sequence↗

PubMed2006

Computational prediction of cancer-gene function.

Most cancer genes remain functionally uncharacterized in the physiological context of disease development. High-throughput molecular profiling and interaction studies are increasingly being used to identify clusters of functionally linked gene products related to neoplastic cell processes. However, in vivo determination of cancer-gene function is laborious and inefficient, so accurately predicting cancer-gene function is a significant challenge for oncologists and computational biologists alike. How can modern computational and statistical methods be used to reliably deduce the function(s) of poorly characterized cancer genes from the newly available genomic and proteomic datasets? We explore plausible solutions to this important challenge.

Computational Biology↗

PubMed1989

Cellular senescence involves stochastic processes causing loss of expression of differentiated function genes: transfection with SV40 as a means for dissociating effects of senescence on growth and on differentiated function gene expression.

In the accompanying work we demonstrated that the decline in expression of steroid 17 alpha-hydroxylase in mass cultures and clones of adrenocortical cells is the result of a stochastic switching process which yields mixtures of expressing and nonexpressing cells. There is an apparent positive correlation between the replicative potential of adrenocortical cell cultures and the number of cells in the culture that can express 17 alpha-hydroxylase. We investigated this by extending the cells' replicative potential by transfecting them with cloned SV40 virus. Cells from a senescent subclone, with very limited remaining replicative potential, were transfected. The cell population showed a progressive increase in growth rate and gave rise to a line of cells that expressed T antigen and which was apparently immortalized. Induction of mRNA for 17 alpha-hydroxylase by cyclic AMP was absent in this line of cells, as it was in the senescent cells prior to transfection. The cells remained responsive to gene induction by cyclic AMP as evidenced by increases in mRNA and activity for cholesterol side-chain cleavage. The absence of 17 alpha-hydroxylase expression in this line was not the result of interference by SV40 T antigen. When early passage cells were transfected with pSV3neo, which contains the early region of SV40 and neo, and were selected with G418, SV40 T antigen-expressing lines were derived which showed high levels of expression of 17 alpha-hydroxylase after induction with cyclic AMP. These cells maintained high levels of expression of 17 alpha-hydroxylase through four successive recloning events, over a period of replication much longer than that achievable by nontransfected cells. Thus, transfection by SV40 can be used to dissociate effects of senescence on growth and differentiated gene expression. T antigen expression selectively affects growth, but preserves the state of expression of a differentiated function gene as it was prior to transfection.

Adrenal Cortex↗

PubMed2005

[The analysis of rbcS gene function by post-transcription gene silencing in Nicotiana benthamiana].

A system of virus-induced post-transcriptional gene silencing for studying rbcS gene function was established and optimized using tobacco rattle virus vector and Nicotiana benthamiana as experimental materiaes. The following analyses were conducted: phenotypic characterization of rbcS gene silenced plants, transcription levels of rbcS gene by RT-PCR; protein levels of rbcS by the antibodies of rbcS and rbcL and photosynthetic pigments wntents in rbcS silenced plants by HPLC method. The results showed that the seedlings at 21-24-day-old and Agrobacterium concentration at OD600 = 1-1.5 gave the best results for gene silencing. The expression level of rbcL was very likely regulated by rbcS, and rbcS gene did not relate to the collection of photosynthetic energy. Probability analysis showed that the tobacco rattle virus vector system is a useful and effective technique to study rbcS gene function via post-transcriptional gene silencing.

Agrobacterium tumefaciens↗

PubMed2003

Serotonin transporter gene functional polymorphism: a plausible candidate gene for increased vascular risk in depression.

The evidence of increased vascular morbidity and mortality associated with depression has generated research interest in studying the mechanisms or causal pathways underlying this association. Recent advances in molecular genetics have demonstrated that serotonin transporter gene functional polymorphism may confer susceptibility for affective disorder as well as for some cardiovascular risk factors. Taking into account these genetic findings, this article proposes a hypothesis that serotonin transporter gene functional polymorphism may be a plausible candidate gene to study the genetic mechanisms of depression-related increased vascular morbidity and mortality. Future research projects to test this hypothesis is warranted.

Aged↗

PubMed2006

Optimal gene partition into operons correlates with gene functional order.

Gene arrangement into operons varies between bacterial species. Genes in a given system can be on one operon in some organisms and on several operons in other organisms. Existing theories explain why genes that work together should be on the same operon, since this allows for advantageous lateral gene transfer and accurate stoichiometry. But what causes the frequent separation into multiple operons of co-regulated genes that act together in a pathway? Here we suggest that separation is due to benefits made possible by differential regulation of each operon. We present a simple mathematical model for the optimal distribution of genes into operons based on a balance of the cost of operons and the benefit of regulation that provides 'just-when-needed' temporal order. The analysis predicts that genes are arranged such that genes on the same operon do not skip functional steps in the pathway. This prediction is supported by genomic data from 137 bacterial genomes. Our work suggests that gene arrangement is not only the result of random historical drift, genome re-arrangement and gene transfer, but has elements that are solutions of an evolutionary optimization problem. Thus gene functional order may be inferred by analyzing the operon structure across different genomes.

Bacteria↗

PubMed2000

Quantitative analysis of gene function in the Drosophila embryo.

The specific functions of gene products frequently depend on the developmental context in which they are expressed. Thus, studies on gene function will benefit from systems that allow for manipulation of gene expression within model systems where the developmental context is well defined. Here we describe a system that allows for genetically controlled overexpression of any gene of interest under normal physiological conditions in the early Drosophila embryo. This regulated expression is achieved through the use of Drosophila lines that express a maternal mRNA for the yeast transcription factor GAL4. Embryos derived from females that express GAL4 maternally activate GAL4-dependent UAS transgenes at uniform levels throughout the embryo during the blastoderm stage of embryogenesis. The expression levels can be quantitatively manipulated through the use of lines that have different levels of maternal GAL4 activity. Specific phenotypes are produced by expression of a number of different developmental regulators with this system, including genes that normally do not function during Drosophila embryogenesis. Analysis of the response to overexpression of runt provides evidence that this pair-rule segmentation gene has a direct role in repressing transcription of the segment-polarity gene engrailed. The maternal GAL4 system will have applications both for the measurement of gene activity in reverse genetic experiments as well as for the identification of genetic factors that have quantitative effects on gene function in vivo.

Animals↗

PubMed2005

Complex genomic rearrangements lead to novel primate gene function.

Orthologous genes that maintain a single-copy status in a broad range of species may indicate a selection against gene duplication. If this is the case, then duplicates of such genes that do survive may have escaped the dosage control by rapid and sizable changes in their function. To test this hypothesis and to develop a strategy for the identification of novel gene functions, we have analyzed 22 primate-specific intrachromosomal duplications of genes with a single-copy ortholog in all other completely sequenced metazoans. When comparing this set to genes not exposed to the single-copy status constraint, we observed a higher tendency of the former to modify their gene structure, often through complex genomic rearrangements. The analysis of the most dramatic of these duplications, affecting approximately 10% of human Chromosome 2, enabled a detailed reconstruction of the events leading to the appearance of a novel gene family. The eight members of this family originated from the highly conserved nucleoporin RanBP2 by several genetic rearrangements such as segmental duplications, inversions, translocations, exon loss, and domain accretion. We have experimentally verified that at least one of the newly formed proteins has a cellular localization different from RanBP2's, and we show that positive selection did act on specific domains during evolution.

Alternative Splicing↗

PubMed2001

The ASK1 gene regulates B function gene expression in cooperation with UFO and LEAFY in Arabidopsis.

The Arabidopsis floral regulatory genes APETALA3 (AP3) and PISTILLATA (PI) are required for the B function according to the ABC model for floral organ identity. AP3 and PI expression are positively regulated by the LEAFY (LFY) and UNUSUAL FLORAL ORGANS (UFO) genes. UFO encodes an F-box protein, and we have shown previously that UFO genetically interacts with the ASK1 gene encoding a SKP1 homologue; both the F-box containing protein and SKP1 are subunits of ubiquitin ligases. We show here that the ask1-1 mutation can enhance the floral phenotypes of weak lfy and ap3 mutants; therefore, like UFO, ASK1 also interacts with LFY and AP3 genetically. Furthermore, our results from RNA in situ hybridizations indicate that ASK1 regulates early AP3 and PI expression. These results support the idea that UFO and ASK1 together positively regulate AP3 and PI expression. We propose that the UFO and ASK1 proteins are components of a ubiquitin ligase that mediates the proteolysis of a repressor of AP3 and PI expression. Our genetic studies also indicate that ASK1 and UFO play a role in regulating the number of floral organ primordia, and we discuss possible mechanisms for such a regulation.

Arabidopsis↗

PubMed1992

Identification of a processed pseudogene related to the functional gene encoding the GM2 activator protein: localization of the pseudogene to human chromosome 3 and the functional gene to human chromosome 5.

The GM2 activator protein is an essential substrate cofactor for the hydrolysis of GM2 ganglioside by lysosomal beta-hexosaminidase A (EC 3.2.1.52). There have been conflicting reports as to the chromosomal localization of the gene encoding the activator. We demonstrate here that these conflicts were caused by the presence of a previously unidentified processed activator-pseudogene on chromosome 3, and we confirm a previous ELISA-based localization of the functional activator gene to chromosome 5. Our data indicate that the functional activator locus can still be considered a candidate site for defects causing some forms of spinal muscular atrophy.

Animals↗

PubMed1998

Functional genomics: probing plant gene function and expression with transposons.

Transposable elements provide a convenient and flexible means to disrupt plant genes, so allowing their function to be assessed. By engineering transposons to carry reporter genes and regulatory signals, the expression of target genes can be monitored and to some extent manipulated. Two strategies for using transposons to assess gene function are outlined here: First, the PCR can be used to identify plants that carry insertions into specific genes from among pools of heavily mutagenized individuals (site-selected transposon mutagenesis). This method requires that high copy transposons be used and that a relatively large number of reactions be performed to identify insertions into genes of interest. Second, a large library of plants, each carrying a unique insertion, can be generated. Each insertion site then can be amplified and sequenced systematically. These two methods have been demonstrated in maize, Arabidopsis, and other plant species, and the relative merits of each are discussed in the context of plant genome research.

Journal Article↗

PubMed1998

The human elk-1 gene family: the functional gene and two processed pseudogenes embedded in the IgH locus.

Elk-1 is a transcription factor whose activation by several mitogen-activated protein kinases (MAPKs) mediates the immediate early responses of the c-fos promoter to growth factors and other stimuli. Here, we report the structure of the human elk-1 gene, which we have localized about 6.5kb upstream of the properdin gene on the X chromosome. The coding sequence is interrupted by four introns; two additional introns lie within the 5' untranslated region. We have also found two elk-1-related processed pseudogenes in the human immunoglobulin heavy chain (IgH) locus, accounting for 'elk-2' previously visualized by in-situ hybridization at 14q32. A processed pseudogene evidently inserted downstream of a primordial immunoglobulin Calpha gene and was duplicated along with part of the IgH locus. Gene/pseudogene sequence comparisons and Southern blots of primate DNAs suggest that both the pseudogene insertion and the locus duplication occurred between about 30 and 60 million years ago.

Amino Acid Sequence↗

PubMed1986

The orangutan adult alpha-globin gene locus: duplicated functional genes and a newly detected member of the primate alpha-globin gene family.

We have cloned and sequenced the complete alpha 1- and alpha 2-globin genes of the orangutan, and here we compare them to the homologous genes of the human. The pattern of similarity apparent among the genes is most consistent with a model of gene correction operating on the primate alpha-globin cluster. This correction breaks down in both human and orangutan in the 3'-untranslated region at 14 base pairs downstream from the termination codon. The unit evolutionary period values calculated for either the replacement substitution or the silent substitutions are only slightly higher than the previously established molecular clock predicts. The 7-base-pair insertion in intron 2 of the human alpha 1-globin gene is not present in either orangutan gene, suggesting that this insertion is not the cause of the sequence divergence in the 3'-untranslated regions of primate alpha 2- and alpha 1-globin genes. Finally, blotting hybridization and partial DNA sequencing reveal a newly detected member of the primate alpha-globin gene family, which is located downstream from the duplicated adult alpha-globin genes.

Animals↗

PubMed2000

Prospects for understanding avirulence gene function.

Avirulence genes are originally defined by their negative impact on the ability of a pathogen to infect their host plant. Many avirulence genes are now known to represent a subset of virulence factors involved in the mediation of the host-pathogen interaction. Characterization of avirulence genes has revealed that they encode an amazing assortment of proteins and belong to several gene families. Although the biochemical functions of the avirulence gene products are unknown, studies are beginning to reveal the features and interesting relationships between the avirulence and virulence activities of the proteins. Identification of critical virulence factors and elucidation of their functions promises to provide insight into plant defense mechanisms, and new and improved strategies for the control of plant disease.

Amino Acid Sequence↗