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PubMed1997

Archaeal nucleosomes.

Archaea contain histones that have primary sequences in common with eukaryal nucleosome core histones and a three-dimensional structure that is essentially only the histone fold. Here we report the results of experiments that document that archaeal histones compact DNA in vivo into structures similar to the structure formed by the histone (H3+H4)2 tetramer at the center of the eukaryal nucleosome. After formaldehyde cross-linking in vivo, these archaeal nucleosomes have been isolated from Methanobacterium thermoautotrophicum and Methanothermus fervidus, visualized by electron microscopy on plasmid and genomic DNAs, and shown by immunogold labeling, SDS/PAGE, and immunoblotting to contain archaeal histones, cross-linked into tetramers. Archaeal nucleosomes protect approximately 60 bp of DNA and multiples of approximately 60 bp from micrococcal nuclease digestion, and immunoprecipitation has demonstrated that most, but not all, M. fervidus genomic DNA sequences are associated in vivo with archaeal histones.

Archaea↗

PubMed1997

Homozygosity mapping of achromatopsia to chromosome 2 using DNA pooling.

Achromatopsia is an autosomal recessive disease of the retina, characterized clinically by an inability to distinguish colors, impaired visual acuity, nystagmus and photophobia. A genome-wide search for linkage was performed using an inbred Jewish kindred from Iran. To facilitate the genome-wide search, we utilized a DNA pooling strategy which takes advantage of the likelihood that the disease in this inbred kindred is inherited by all affected individuals from a common founder. Equal molar amounts of DNA from all affected individuals were pooled and used as the PCR template for short tandem repeat polymorphic markers (STRPs). Pooled DNA from unaffected members of the kindred was used as a control. A reduction in the number of alleles in the affected versus control pool was observed at several loci. Upon genotyping of individual family members, significant linkage was established between the disease phenotype and markers localized on chromosome 2. The highest LOD score observed was 5.4 (theta = 0). When four additional small unrelated families were genotyped, the combined peak LOD score was 8.2. Analysis of recombinant chromosomes revealed that the disease gene lies within a 30 cM interval which spans the centromere. Additional fine-mapping studies identified a region of homozygosity in all affected individuals, narrowing the region to 14 cM. A candidate gene for achromatopsia was excluded from this disease interval by radiation hybrid mapping. Linkage of achromatopsia to chromosome 2 is an essential first step in the identification of the disease-causing gene.

Chromosome Mapping↗

PubMed2004

CHOP: visualization of 'wobbling' and isolation of highly conserved regions from aligned DNA sequences.

The web software CHOP was developed to visualize the 'wobbling' in the third codon position of aligned DNA sequences. The simple features of this tool allow users to easily find regions suspected of containing coding sequences (CDSs). The program also allows visualization of the nucleotide diversity between two genomic or gene sequences by graphically plotting the percentage identity between the two sequences. CHOP can also isolate highly conserved regions within both CDSs and non-CDSs. Highly conserved regions within CDSs include the regions with lower rates of synonymous substitution in which nucleotide sequences are expected to be under strong selective pressure. CHOP is available at http://bunsei2.med.u-tokai.ac.jp:8080/~ohtsuka/cds_finding.html.

Animals↗

PubMed1980

Comparison of foldback sequences of herpes simplex virus types 1 and 2 DNA.

The DNAs of herpes simplex virus types 1 and 2 (HSV-1 and HSV-2) were separately denatured and allowed to renature briefly. The intrastand foldback structures that resulted from base pairing of inverted repeated sequences on otherwise single-stranded (ss) DNA were visualized in the electron microscope. The two genomes were found to contain similar size classes of small duplex stem DNA sequences. However, HSV-2 DNA appeared to possess an additional, larger size class of foldback structures not found on HSV-1 DNA. Both HSV DNAs were found to contain stem-plus-loop structures; the larger stem-plus-loop structures of the two genomes had similar stem lengths but dissimilar loop lengths. Thus, a comparison of the genomes of HSV-1 and HSV-2 showed that they possessed similar size classes of foldback sequences.

Base Sequence↗

PubMed1991

Molecular defects in haemophilia B: detection by direct restriction enzyme analysis.

The common restriction fragment length polymorphisms (RFLPs) associated with the FIX gene: 5' BamH I, Dde I, BamH I (2), Taq I and 3' Hha I were absent or of low incidence in Southern Chinese and are therefore not useful for linkage analysis. No deletion was detected amongst seven consecutive unrelated haemophilia B patients, but one had an insertion of a 15 kb Pvu II fragment containing exon d. Using an alternate strategy of polymerase chain reaction (PCR) amplification and direct sequencing, the molecular defect in the other six patients was defined. The four novel mutations characterized were: nucleotide (nt) 6410 G----C (Gly12----Ala); nt 31261 delta T (stop codon 31 bp downstream); nt 31260 C----G (Thr380----Ser) and nt 31122 C----A (Ala34----Asp). Two patients had the same mutation at nt 6365, G----A (Arg-4----Gln), identical to one previously described in other ethnic groups, suggesting that this is a hotspot for mutation. Each of the mutations was found to affect an enzyme recognition site and could thus be identified by direct visualization of abnormal restriction fragments in amplified genomic DNA. This allows rapid and accurate DNA diagnosis of haemophilia B in an ethnic group which otherwise shows little or no polymorphism for the common RFLP sites.

Blotting, Southern↗

PubMed1996

Multicolor spectral karyotyping of human chromosomes.

The simultaneous and unequivocal discernment of all human chromosomes in different colors would be of significant clinical and biologic importance. Whole-genome scanning by spectral karyotyping allowed instantaneous visualization of defined emission spectra for each human chromosome after fluorescence in situ hybridization. By means of computer separation (classification) of spectra, spectrally overlapping chromosome-specific DNA probes could be resolved, and all human chromosomes were simultaneously identified.

Animals↗

PubMed2000

Molecular mechanisms for constitutional chromosomal rearrangements in humans.

Cytogenetic imbalance in the newborn is a frequent cause of mental retardation and birth defects. Although aneuploidy accounts for the majority of imbalance, structural aberrations contribute to a significant fraction of recognized chromosomal anomalies. This review describes the major classes of constitutional, structural cytogenetic abnormalities and recent studies that explore the molecular mechanisms that bring about their de novo occurrence. Genomic features flanking the sites of recombination may result in susceptibility to chromosomal rearrangement. One such substrate for recombination is low-copy region-specific repeats. The identification of genome architectural features conferring susceptibility to rearrangements has been accomplished using methods that enable investigation of regions of the genome that are too small to be visualized by traditional cytogenetics and too large to be resolved by conventional gel electrophoresis. These investigations resulted in the identification of previously unrecognized structural cytogenetic anomalies, which are associated with genetic syndromes and allowed for the molecular basis of some chromosomal rearrangements to be delineated.

Chromosome Aberrations↗

PubMed2005

Molecular imaging: its application in cardiovascular diagnosis.

The emerging field of molecular and genomic imaging is providing new opportunities to visualize and quantify the biology of living organisms. To reach such goal all the major imaging modalities concur to this new field, each with its mechanism for generating contrast and with its spatial resolution and specificity. This review deals with a brief introduction to the molecular imaging principles and reports on the state-of-the-art in cardiovascular disease.

Animals↗

PubMed1984

[Detection of active genes in mouse metaphase chromosomes using DNAse I in situ].

The active genes of rRNA were localized near the centromere region of metacentric translocation chromosome Rb(9, 19) 163H in early mouse embryos revealed by differential silver staining of NORs. Using nick-translation reaction in situ it was shown that rRNA genes in metaphase chromosomes were in a deoxyribonuclease I sensitive conformation. This method of nick-translation in situ can be used for visualization of various actively transcribed regions of genome at metaphase.

Animals↗

PubMed1996

[A retrotransposon-like element Tca1 was used for taxonomic determination of Candida albicans].

We had isolated from Candida albicans a moderately repetitive sequence designated alpha and a retrovirus-like transposable element Tcal (Transposon Candida albicans). The Tcal consisted of two 388bp direct repeats of the alpha element, called LTR (Long Termination Repeat), which was separated by approximately 5.5kb of DNA. A large number of strains from America and China have been grouped based on patterns of hybridization bands visualized on Southern blots of EcoRI digested genomic DNA probed with alpha and Tcal element internal sequence. Strains from same area have higher relatedness than those from different area. The hybridization patterns with URA3 and other DNA probes were also conserved within the groups. alpha element are species specific, no hybridization was observed with genomic DNA of other yeast species. The data presented here indicate that the alpha element can be employed to distinguish between species and to assess strain relatedness within C. albicans, we suggest that Tcal may be relevant to the genomic evolutions of C. albicans and the pathogenic potential of the organism.

Candida albicans↗

PubMed2005

T1DBase, a community web-based resource for type 1 diabetes research.

T1DBase (http://T1DBase.org) is a public website and database that supports the type 1 diabetes (T1D) research community. The site is currently focused on the molecular genetics and biology of T1D susceptibility and pathogenesis. It includes the following datasets: annotated genome sequence for human, rat and mouse; information on genetically identified T1D susceptibility regions in human, rat and mouse, and genetic linkage and association studies pertaining to T1D; descriptions of NOD mouse congenic strains; the Beta Cell Gene Expression Bank, which reports expression levels of genes in beta cells under various conditions, and annotations of gene function in beta cells; data on gene expression in a variety of tissues and organs; and biological pathways from KEGG and BioCarta. Tools on the site include the GBrowse genome browser, site-wide context dependent search, Connect-the-Dots for connecting gene and other identifiers from multiple data sources, Cytoscape for visualizing and analyzing biological networks, and the GESTALT workbench for genome annotation. All data are open access and all software is open source.

Animals↗

PubMed2002

Detection and visualization of compositionally similar cis-regulatory element clusters in orthologous and coordinately controlled genes.

Evolutionarily conserved noncoding genomic sequences represent a potentially rich source for the discovery of gene regulatory regions. However, detecting and visualizing compositionally similar cis-element clusters in the context of conserved sequences is challenging. We have explored potential solutions and developed an algorithm and visualization method that combines the results of conserved sequence analyses (BLASTZ) with those of transcription factor binding site analyses (MatInspector) (http://trafac.chmcc.org). We define hits as the density of co-occurring cis-element transcription factor (TF)-binding sites measured within a 200-bp moving average window through phylogenetically conserved regions. The results are depicted as a Regulogram, in which the hit count is plotted as a function of position within each of the two genomic regions of the aligned orthologs. Within a high-scoring region, the relative arrangement of shared cis-elements within compositionally similar TF-binding site clusters is depicted in a Trafacgram. On the basis of analyses of several training data sets, the approach also allows for the detection of similarities in composition and relative arrangement of cis-element clusters within nonorthologous genes, promoters, and enhancers that exhibit coordinate regulatory properties. Known functional regulatory regions of nonorthologous and less-conserved orthologous genes frequently showed cis-element shuffling, demonstrating that compositional similarity can be more sensitive than sequence similarity. These results show that combining sequence similarity with cis-element compositional similarity provides a powerful aid for the identification of potential control regions.

Animals↗

PubMed2002

Large-scale prediction of Saccharomyces cerevisiae gene function using overlapping transcriptional clusters.

Genome sequencing has led to the discovery of tens of thousands of potential new genes. Six years after the sequencing of the well-studied yeast Saccharomyces cerevisiae and the discovery that its genome encodes approximately 6,000 predicted proteins, more than 2,000 have not yet been characterized experimentally, and determining their functions seems far from a trivial task. One crucial constraint is the generation of useful hypotheses about protein function. Using a new approach to interpret microarray data, we assign likely cellular functions with confidence values to these new yeast proteins. We perform extensive genome-wide validations of our predictions and offer visualization methods for exploration of the large numbers of functional predictions. We identify potential new members of many existing functional categories including 285 candidate proteins involved in transcription, processing and transport of non-coding RNA molecules. We present experimental validation confirming the involvement of several of these proteins in ribosomal RNA processing. Our methodology can be applied to a variety of genomics data types and organisms.

Algorithms↗

PubMed2005

Comprehensive post-genomic data analysis approaches integrating biochemical pathway maps.

Post-genomic era research is focusing on studies to attribute functions to genes and their encoded proteins, and to describe the regulatory networks controlling metabolic, protein synthesis and signal transduction pathways. To facilitate the analysis of experiments using post-genomic technologies, new concepts for linking the vast amount of raw data to a biological context have to be developed. Visual representations of pathways help biologists to understand the complex relationships between components of metabolic networks, and provide an invaluable resource for the integration of transcriptomics, proteomics and metabolomics data sets. Besides providing an overview of currently available bioinformatic tools for plant scientists, we introduce BioPathAt, a newly developed visual interface that allows the knowledge-based analysis of genome-scale data by integrating biochemical pathway maps (BioPathAtMAPS module) with a manually scrutinized gene-function database (BioPathAtDB) for the model plant Arabidopsis thaliana. In addition, we discuss approaches for generating a biochemical pathway knowledge database for A. thaliana that includes, in addition to accurate annotation, condensed experimental information regarding in vitro and in vivo gene/protein function.

Computational Biology↗

PubMed1997

Individual variation in size of the human red and green visual pigment gene array.

PURPOSE: To determine the size variation of the X-chromosomal human red and green visual pigment gene array in the general population using pulsed field gel electrophoresis and Southern blotting. METHODS: Peripheral blood lymphocytes were prepared from 67 anonymous males. The cells were embedded in agarose and the genomic DNA digested with restriction enzyme Not I. The resulting DNA fragments were resolved on a contour-clamped homogeneous electric field gel, and the Not I fragment containing the red and green pigment genes was visualized by Southern blot hybridization with a human green pigment cDNA probe. RESULTS: In DNA from each male, a single hybridizing fragment was observed in Not I-digested DNA. The lengths of the fragments from different males were observed to vary in steps of approximately 39 kilobases (kb), consistent with earlier studies showing a visual pigment gene repeat unit of 39 kb and a head-to-tail tandem arrangement of the red and green visual pigment genes. In the population studied, the number of repeat units per X-chromosome had a mean of 2.9 and a standard deviation of 0.94. CONCLUSIONS: The sizes of visual pigment gene arrays observed in this study resemble those determined in earlier studies based on ratios of restriction fragments resolved by conventional gel electrophoresis and visualized by whole genome Southern blotting, but differ significantly from those determined using ratios of fragments obtained by the polymerase chain reaction.

Blotting, Southern↗

PubMed2002

Visualization of transcription-dependent association of imprinted genes with the nuclear matrix.

Genomic imprinting is characterized by allele-specific gene expression as a biological phenomenon. To analyze the participation of the nuclear matrix in the expression of imprinted genes, we first examined the allelic expression state of genes by simultaneously visualizing their primary transcripts and the gene sequences in individual cell nuclei using fluorescence in situ hybridization (FISH). We confirmed that each imprinted gene, SNRPN and UBE3A in human lymphocytes and Igf2 and H19 in mouse embryonic fibroblasts, mainly expressed from one allele, although some nuclei showed biallelic expression. We next visualized the gene sequences on the nuclear matrix by FISH with a tyramide signal amplification technique. Interestingly, we predominantly observed one DNA signal of imprinted genes on the nuclear matrix preparation, closely correlated with their expression patterns. Using patient cells, we confirmed that both the transcription and the binding to the nuclear matrix of the SNRPN gene occurred at the paternal allele. Our results suggest that the nuclear matrix plays an important role in gene expression, including imprinted genes, and that the FISH technique used here allows us to visualize the behaviors of genes at an individual cell level.

Alleles↗

PubMed2005

VariScan: Analysis of evolutionary patterns from large-scale DNA sequence polymorphism data.

SUMMARY: VeriScan is a software package for the analysis of DNA sequence polymorphisms at the whole genome scale. Among other features, the software (1) can conduct many population genetic analyses; (2) incorporates a multiresolution wavelet transform-based method that allows capturing relevant information from DNA polymorphism data; (3) facilitates the visualization of the results in the most commonly used genome browsers.

Algorithms↗

PubMed2004

Insertion of green fluorescent protein into nonstructural protein 5A allows direct visualization of functional hepatitis C virus replication complexes.

Hepatitis C virus (HCV) replicates its genome in a membrane-associated replication complex, composed of viral proteins, replicating RNA and altered cellular membranes. We describe here HCV replicons that allow the direct visualization of functional HCV replication complexes. Viable replicons selected from a library of Tn7-mediated random insertions in the coding sequence of nonstructural protein 5A (NS5A) allowed the identification of two sites near the NS5A C terminus that tolerated insertion of heterologous sequences. Replicons encoding green fluorescent protein (GFP) at these locations were only moderately impaired for HCV RNA replication. Expression of the NS5A-GFP fusion protein could be demonstrated by immunoblot, indicating that the GFP was retained during RNA replication and did not interfere with HCV polyprotein processing. More importantly, expression levels were robust enough to allow direct visualization of the fusion protein by fluorescence microscopy. NS5A-GFP appeared as brightly fluorescing dot-like structures in the cytoplasm. By confocal laser scanning microscopy, NS5A-GFP colocalized with other HCV nonstructural proteins and nascent viral RNA, indicating that the dot-like structures, identified as membranous webs by electron microscopy, represent functional HCV replication complexes. These findings reveal an unexpected flexibility of the C-terminal domain of NS5A and provide tools for studying the formation and turnover of HCV replication complexes in living cells.

Amino Acid Sequence↗