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PubMed2005

Cataloging transcription factor and major signaling molecule genes for functional genomic studies in Ciona intestinalis.

The ascidian Ciona intestinalis provides an excellent experimental system for functional genomic studies because (1) its genome has been sequenced, (2) the transcription factor genes and genes for major signal transduction molecules have been extensively screened and annotated on a genome-wide scale using the molecular phylogenetical method, and (3) their embryonic expression profiles have been almost completely determined. However, the entire genetic structure, including the 5' and 3' untranslated regions and the protein-coding regions, of most gene models used in these prior studies is not always supported by cDNA evidence, and thus, these gene models are potentially imprecise. To facilitate functional genomic studies based on precise gene structures, our present study determined 406 cDNA sequences for 357 transcription factor genes and 112 cDNA sequences for 107 signal transduction molecule genes, greatly improving the previous gene models and revealing transcript variants for 44 genes. Considering these data alongside those of previously characterized genes deposited in the DNA Data Bank of Japan/European Molecular Biology Laboratory/GENBANK databases, 95.6% of the catalogued transcription factor genes (373/390) and 98.3% of the catalogued signal transduction molecule genes (117/119) have now been verified by cDNA sequences. Thus, the present study greatly improves the resources available for functional genomic studies in C. intestinalis.

Animals↗
PubMed2003

Short hairpin RNAs induced RNA interference in human cells.

BACKGROUND & OBJECTIVE: RNA interference (RNAi) is an evolutionarily conserved posttranscriptional gene silencing, in which the introduction of double-stranded RNA into a cell leads to specific suppression of gene expression. RNAi has become an important tool for gene function studies. The aim of this study was to induce RNAi in mammalian cells by short hairpin RNAs (shRNAs) generated from a DNA vector, therefore, to provide a new approach for gene function analysis. METHODS: Dual Luciferase System was used to assess the intracellular effect of the shRNAs generated from a DNA vector. The inhibitory effect of this DNA vector-driven shRNAs at different condition was measured. RESULTS: shRNAs generated from the DNA vector induced RNAi in human cells, and suppressed gene expression in a sequence-specific manner. The inhibitory effect was highly related to the target sites. CONCLUSION: shRNAs induced RNAi in human cells and suppressed gene expression in a sequence-specific manner. This approach may be used for gene function study.

Gene Silencing↗
PubMed2003

Structurally conserved alpha-neurotoxin genes encode functionally diverse proteins in the venom of Naja sputatrix.

The structure and organization of the genes encoding the long-chain neurotoxins and four other isoforms of weak neurotoxins in the venom of Naja sputatrix are reported. The genes contained three exons interrupted by two introns, a structure similar to other members of the three-finger toxin family. The proteins encoded by these genes, however, show varied affinity towards nicotinic acetylcholine receptors. Phylogenetic analysis of these genes showed that the weak neurotoxin gene is confined to a distinct group. We also observe that specific mutations of the gene provide the diversity in function in these toxins while maintaining a common structural scaffold. This forms the first report where the molecular basis of evolution of postsynaptic neurotoxins from an ancestral gene can be demonstrated using the same species of snake.

Amino Acid Sequence↗
PubMed2004

Automatic extraction of gene/protein biological functions from biomedical text.

MOTIVATION: With the rapid advancement of biomedical science and the development of high-throughput analysis methods, the extraction of various types of information from biomedical text has become critical. Since automatic functional annotations of genes are quite useful for interpreting large amounts of high-throughput data efficiently, the demand for automatic extraction of information related to gene functions from text has been increasing. RESULTS: We have developed a method for automatically extracting the biological process functions of genes/protein/families based on Gene Ontology (GO) from text using a shallow parser and sentence structure analysis techniques. When the gene/protein/family names and their functions are described in ACTOR (doer of action) and OBJECT (receiver of action) relationships, the corresponding GO-IDs are assigned to the genes/proteins/families. The gene/protein/family names are recognized using the gene/protein/family name dictionaries developed by our group. To achieve wide recognition of the gene/protein/family functions, we semi-automatically gather functional terms based on GO using co-occurrence, collocation similarities and rule-based techniques. A preliminary experiment demonstrated that our method has an estimated recall of 54-64% with a precision of 91-94% for actually described functions in abstracts. When applied to the PUBMED, it extracted over 190 000 gene-GO relationships and 150 000 family-GO relationships for major eukaryotes.

Abstracting and Indexing↗
PubMed2003

Mammalian RNAi for the masses.

Just a couple of years ago, only biologists working with plants or Caenorhabditis elegans could use RNA-mediated interference (RNAi) technology to gain insight into gene function. However, the recent groundbreaking discovery that in vitro synthesized, 21- to 23-nucleotide, double-stranded RNAs can act as small interfering RNAs (siRNAs) to elicit gene-specific inhibition in mammalian cells has made RNAi possible in mammalian systems too. Reported only a year ago, mammalian RNAi is already changing our way of studying gene function in higher eukaryotes. And, a recent exciting advance allows delivery of siRNAs into mammalian cells by a DNA vector. In addition to providing a low-cost alternative to the chemically synthesized siRNAs, this DNA-vector-based strategy is capable of mediating stable target gene inhibition, thus allowing gene function analysis over an extended period of time.

Animals↗
PubMed1993

bcl-x, a bcl-2-related gene that functions as a dominant regulator of apoptotic cell death.

We report the isolation of bcl-x, a bcl-2-related gene that can function as a bcl-2-independent regulator of programmed cell death (apoptosis). Alternative splicing results in two distinct bcl-x mRNAs. The protein product of the larger mRNA, bcl-xL, is similar in size and predicted structure to Bcl-2. When stably transfected into an IL-3-dependent cell line, bcl-xL inhibits cell death upon growth factor withdrawal at least as well as bcl-2. Surprisingly, the second mRNA species, bcl-xS, encodes a protein that inhibits the ability of bcl-2 to enhance the survival of growth factor-deprived cells. In vivo, bcl-xS mRNA is expressed at high levels in cells that undergo a high rate of turnover, such as developing lymphocytes. In contrast, bcl-xL is found in tissues containing long-lived postmitotic cells, such as adult brain. Together these data suggest that bcl-x plays an important role in both positive and negative regulation of programmed cell death.

Alternative Splicing↗
PubMed2004

Trypanosoma brucei plasma membrane-type Ca(2+)-ATPase 1 (TbPMC1) and 2 (TbPMC2) genes encode functional Ca(2+)-ATPases localized to the acidocalcisomes and plasma membrane, and essential for Ca(2+) homeostasis and growth.

Trypanosoma brucei adaptation and survival in its host involve integrated regulation of Ca(2+) pumps (Ca(2+)-ATPases), which are essential in calcium ion homeostasis. Here we report the cloning and sequencing of two genes (TbPMC1 and TbPMC2) encoding plasma membrane-type Ca(2+)-ATPases (PMCAs) of T. brucei, an agent of African trypanosomiasis. Indirect immunofluorescence analysis using antibodies against the proteins and against epitope tags introduced into each protein showed that TbPMC1 co-localized with the vacuolar H(+)-pyrophosphatase to the acidocalcisomes while TbPMC2 localized to the plasma membrane. Northern and Western blot analyses revealed that TbPMC1 and TbPMC2 are up-regulated during blood stages. TbPMC1 and TbPMC2 suppressed the Ca(2+) hypersensitivity of a mutant of S. cerevisiae that has a defect in vacuolar Ca(2+) accumulation. T. brucei Ca(2+)-ATPase genes were functionally characterized by using double-stranded RNA interference (RNAi) methodology to produce inducible Ca(2+)-ATPase-deficient procyclic forms. Similar results were obtained with bloodstream form trypomastigotes, except that the RNAi system was leaky and mRNA and protein levels recovered with time. The induction of dsRNA (RNAi) caused gross morphological alterations, and growth inhibition of procyclic forms. Induction of RNAi against TbPMC1 but not against TbPMC2 caused elevated levels of cytosolic Ca(2+) and decreased mobilization of Ca(2+) from intracellular stores following ionophore addition. These results establish that T. brucei PMCA-Ca(2+)-ATPases are essential for parasite viability and validate them as targets for drug development.

Amino Acid Sequence↗
PubMed2026

Enhanced identification of key bacterial motility genes via a cross-species genomic hybrid feature machine learning approach.

Efficient and accurate identification of functional genes is critical to biological research, yet traditional single-species approaches are often limited by low efficiency. Previously, we established a novel method for identifying key genes using cross-species protein domain features and machine learning. However, the high multiplicity of gene members associated with specific domains creates a substantial workload for subsequent experimental validation. To address this, this study proposes an enhanced approach that integrates EggNOG-based protein sequence annotation with domain analysis. Unannotated sequences are subsequently analyzed for protein domains, generating a comprehensive "direct gene annotation plus domain" hybrid feature matrix. While the hybrid matrix model yielded comparable predictive accuracy, it significantly enhanced feature resolution: the top 50 predicted features were all known motility-related genes or domains. Furthermore, among the top 100 ranked features, 58 are confirmed to be directly related to motility based on experimental evidence. Although strict genus-level control still yielded 51 confirmed features, excessive taxonomic restriction drastically reduces the number of training genomes, which may paradoxically impair identification efficiency. These results demonstrate that the new method effectively reduces the subsequent experimental workload and enables high-throughput identification of functional genes in a single analysis. With accuracy and efficiency far exceeding those of existing single-species identification methods, it provides a highly efficient solution for mining key genes underlying other complex bacterial phenotypes.

Machine Learning↗
PubMed2004

Aged mice require full transcription factor, Runx2/Cbfa1, gene dosage for cancellous bone regeneration after bone marrow ablation.

UNLABELLED: Runx2 is prerequisite for the osteoblastic differentiation in vivo. To elucidate Runx2 gene functions in adult bone metabolism, we conducted bone marrow ablation in Runx2 heterozygous knockout mice and found that aged (but not young) adult Runx2 heterozygous knockout mice have reduced new bone formation capacity after bone marrow ablation. We also found that bone marrow cells from aged Runx2 heterozygous knockout mice have reduced ALP(+) colony-forming potential in vitro. This indicates that full Runx2 dosage is needed for the maintenance of osteoblastic activity in adult mice. INTRODUCTION: Null mutation of the Runx2 gene results in total loss of osteoblast differentiation, and heterozygous Runx2 deficiency causes cleidocranial dysplasia in humans and mice. However, Runx2 gene functions in adult bone metabolism are not known. We therefore examined the effects of Runx2 gene function in adult mice with heterozygous loss of the Runx2 gene. MATERIALS AND METHODS: Bone marrow ablation was conducted in young adult (2.5 +/- 0.5 months old) or aged adult (7.5 +/- 0.5 months old) Runx2 heterozygous knockout mice and wildtype (WT) littermates. Cancellous bone regeneration was evaluated by 2D microCT. RESULTS: Although new bone formation was observed after bone marrow ablation in the operated bone marrow cavity of WT mice, such bone formation was significantly reduced in Runx2 heterozygous knockout mice. Interestingly, this effect was observed specifically in aged but not young adult mice. Runx2 heterozygous deficiency in aged mice significantly reduced the number of alkaline phosphatase (ALP)(+) cell colonies in the bone marrow cell cultures, indicating a reduction in the numbers of osteoprogenitor cells. Such effects of heterozygous Runx2 deficiency on osteoblasts in vitro was specific to the cells from aged adult mice, and it was not observed in the cultures of marrow cells from young adult mice. CONCLUSION: These results indicate that full gene dosage of Runx2 is required for cancellous bone formation after bone marrow ablation in adult mice.

Aging↗
PubMed2000

Lineage-specific loss and divergence of functionally linked genes in eukaryotes.

By comparing 4,344 protein sequences from fission yeast Schizosaccharomyces pombe with all available eukaryotic sequences, we identified those genes that are conserved in S. pombe and nonfungal eukaryotes but are missing or highly diverged in the baker's yeast Saccharomyces cerevisiae. Since the radiation from the common ancestor with S. pombe, S. cerevisiae appears to have lost about 300 genes, and about 300 more genes have diverged by far beyond expectation. The most notable feature of the set of genes lost in S. cerevisiae is the coelimination of functionally connected groups of proteins, such as the signalosome and the spliceosome components. We predict similar coelimination of the components of the posttranscriptional gene-silencing system that includes the recently identified RNA-dependent RNA polymerase. Because one of the functions of posttranscriptional silencing appears to be "taming" of retrotransposons, the loss of this system in yeast could have triggered massive retrotransposition, resulting in elimination of introns and subsequent loss of spliceosome components that become dispensable. As the genome database grows, systematic analysis of coordinated gene loss may become a general approach for predicting new components of functional systems or even defining previously unknown functional complexes.

Biological Evolution↗
PubMed1999

HUA1 and HUA2 are two members of the floral homeotic AGAMOUS pathway.

The identities of the four floral organ types in an Arabidopsis flower are specified by the combinatorial activities of the floral homeotic A, B, and C function genes; AGAMOUS is the only known C function gene. We have identified two genes that interact with AG in the specification of floral structure, HUA1 and HUA2, from a screen for enhancers of a weak ag allele, ag-4. HUA1 and HUA2 are involved in all aspects of AG function. HUA2 encodes a novel protein that contains nuclear localization signals and signature motifs that suggest HUA2, like AG, may be a transcription factor. Molecular analyses suggest that HUA2 (and possibly HUA1) acts to facilitate AG action at the same hierarchical level as AG.

AGAMOUS Protein, Arabidopsis↗
PubMed1999

The Cre/loxP system and gene targeting in the kidney.

The Cre/loxP and Flp/FRT systems mediate site-specific DNA recombination and are being increasingly utilized to study gene function in vivo. These systems allow targeted gene disruption in a single cell type in vivo, thereby permitting study of the physiological and pathophysiological impact of a given gene product derived from a particular cell type. In the kidney, the Cre/loxP system has been employed to achieve gene deletion selectively within principal cells of the collecting duct. Disruption of target genes in the collecting duct, such as endothelin-1 or polycystic kidney disease-1 (PKD1), could lead to important insights into the biological roles of these gene products. With selection of the appropriate renal cell-specific promoters, these recombination systems could be used to target gene disruption to virtually any renal cell type. Although transgenic studies utilizing these recombination systems are promising, they are in their relative infancy and can be time consuming and expensive and yield unanticipated results. It is anticipated that continued experience with these systems will produce an important tool for analyzing gene function in renal health and disease.

Animals↗
PubMed2003

Identification of promoter regions in the human genome by using a retroviral plasmid library-based functional reporter gene assay.

Attempts to identify regulatory sequences in the human genome have involved experimental and computational methods such as cross-species sequence comparisons and the detection of transcription factor binding-site motifs in coexpressed genes. Although these strategies provide information on which genomic regions are likely to be involved in gene regulation, they do not give information on their functions. We have developed a functional selection for promoter regions in the human genome that uses a retroviral plasmid library-based system. This approach enriches for and detects promoter function of isolated DNA fragments in an in vitro cell culture assay. By using this method, we have discovered likely promoters of known and predicted genes, as well as many other putative promoter regions based on the presence of features such as CpG islands. Comparison of sequences of 858 plasmid clones selected by this assay with the human genome draft sequence indicates that a significantly higher percentage of sequences align to the 500-bp segment upstream of the transcription start sites of known genes than would be expected from random genomic sequences. We also observed enrichment for putative promoter regions of genes predicted in at least two annotation databases and for clones overlapping with CpG islands. Functional validation of randomly selected clones enriched by this method showed that a large fraction of these putative promoters can drive the expression of a reporter gene in transient transfection experiments. This method promises to be a useful genome-wide function-based approach that can complement existing methods to look for promoters.

3T3 Cells↗
PubMed2002

Morpholino oligos: making sense of antisense?

Since morpholino oligos were first introduced as a means to inhibit gene function in embryos, in the Spring of 2000, they have been tested in a range of model organisms, including sea urchin, ascidian, zebrafish, frog, chick, and mouse. This review surveys the results of these studies and examines the successes and limitations of the approach for targeting maternal and zygotic gene function. The evidence so far suggests that, with careful controls, morpholinos provide a relatively simple and rapid method to study gene function.

Abnormalities, Drug-Induced↗
PubMed2004

Short interfering RNAs can induce unexpected and divergent changes in the levels of untargeted proteins in mammalian cells.

RNA interference (RNAi) mediated by short interfering RNAs (siRNAs) is a widely used method to analyze gene function. To use RNAi knockdown accurately to infer gene function, it is essential to determine the specificity of siRNA-mediated RNAi. We have assessed the specificity of 10 different siRNAs corresponding to the MEN1 gene by examining the expression of two additional genes, TP53 (p53) and CDKN1A (p21), which are considered functionally unrelated to menin but are sensitive markers of cell state. MEN1 RNA and corresponding protein levels were all reduced after siRNA transfection of HeLa cells, although the degree of inhibition mediated by individual siRNAs varied. Unexpectedly, we observed dramatic and significant changes in protein levels of p53 and p21 that were unrelated to silencing of the target gene. The modulations in p53 and p21 levels were not abolished on titration of the siRNAs, and similar results were obtained in three other cell lines; in none of the cell lines tested did we see an effect on the protein levels of actin. These data suggest that siRNAs can induce nonspecific effects on protein levels that are siRNA sequence dependent but that these effects may be difficult to detect until genes central to a pivotal cellular response, such as p53 and p21, are studied. We find no evidence that activation of the double-stranded RNA-triggered IFN-associated antiviral pathways accounts for these effects, but we speculate that partial complementary sequence matches to off-target genes may result in a micro-RNA-like inhibition of translation.

2',5'-Oligoadenylate Synthetase↗
PubMed2002

Arrayed adenoviral expression libraries for functional screening.

With the publication of the sequence of the human genome, we are challenged to identify the functions of an estimated 70,000 human genes and the much larger number of proteins encoded by these genes. Of particular interest is the identification of gene products that play a role in human disease pathways, as these proteins include potential new targets that may lead to improved therapeutic strategies. This requires the direct measurement of gene function on a genomic scale in cell-based, functional assays. We have constructed and validated an individually arrayed, replication-defective adenoviral library harboring human cDNAs, termed PhenoSelect library. The adenoviral vector guarantees efficient transduction of diverse cell types, including primary cells. The arrayed format allows screening of this library in a variety of cellular assays in search for gene(s) that, by overexpression, induce a particular disease-related phenotype. The great majority of phenotypic assays, including morphological assays, can be screened with arrayed libraries. In contrast, pooled-library approaches often rely on phenotype-based isolation or selection of single cells by employing a flow cytometer or screening for cell survival. An arrayed placental PhenoSelect library was screened in cellular assays aimed at identifying regulators of osteogenesis, metastasis, and angiogenesis. This resulted in the identification of known regulators, as well as novel sequences that encode proteins hitherto not known to play a role in these pathways. These results establish the value of the PhenoSelect platform, in combination with cellular screens, for gene function discovery.

Adenoviridae↗
PubMed2005

Prior exercise training improves the outcome of acute myocardial infarction in the rat. Heart structure, function, and gene expression.

OBJECTIVES: The aim of this research was to investigate the structural, functional, and molecular features of the remodeling heart in prior swim-trained infarcted rats. BACKGROUND: Physical exercise training is a known protective factor against cardiovascular morbidity and mortality. The structural and molecular aspects underlying this protection in the remodeling heart have not been investigated. METHODS: After seven weeks of swimming exercise training, rats underwent surgical ligation of the left coronary artery followed by a four-week sedentary period. Untrained control rats underwent the same surgical protocol. Left ventricular function was assessed by echocardiography four weeks after infarction, and hearts were sampled for histological and molecular analysis. Ribonucleic acid from the surviving left ventricle was analyzed by complementary deoxyribonucleic acid arrays followed by Northern blotting or quantitative reverse transcription polymerase chain reaction of selected messenger ribonucleic acids (mRNAs). RESULTS: Scar area was 1.6-fold smaller (p = 0.0002), arteriolar density was 1.7-fold higher (p = 0.0002), and left ventricular shortening fraction was 1.9-fold higher (p = 0.003) in the exercise-trained compared with sedentary hearts. Eleven genes whose expression level varied by at least +/-1.5-fold distinguished the prior exercised rats from their sedentary counterparts. Compared with sedentary, the exercised hearts displayed 9- and 2.4-times lower levels of atrial natriuretic peptide and aldolase mRNA (p = 0.03 and 0.04, respectively), and a 2.7- and 1.9-fold higher abundance of cytochrome c-oxidase and fatty acid binding protein, respectively (p < 0.03, each). CONCLUSIONS: Swimming exercise training before acute myocardial infarction reduces scar size, increases arteriole density, and manifests adaptation of stress- and energy-metabolism-related genes that may contribute to the improved heart function observed during remodeling.

Adenosine Triphosphatases↗
PubMed1994

A Chlorella virus gene promoter functions as a strong promoter both in plants and bacteria.

An upstream region from an algal virus methyltransferase gene was tested for promoter function in transgenic plants, electroporated monocot protoplasts and bacteria. Fusion of the 851 bp upstream region to a reporter gene significantly enhanced the reporter gene expression in transgenic Arabidopsis and potato plants and in electroporated maize and Sorghum cells relative to the cauliflower mosaic virus 35S promoter. The promoter was also functional in several Escherichia coli strains and in three species of phytopathogenic bacteria, Erwinia, Pseudomonas, and Xanthomonas. These findings indicate that the upstream region is a strong promoter uniquely functional in both eukaryotes and prokaryotes and capable of using both eukaryotic RNA polymerase II and bacterial RNA polymerases.

Arabidopsis↗