STRING: a web-server to retrieve and display the repeatedly occurring neighbourhood of a gene

The repeated occurrence of genes in each other’s neighbourhood on genomes has been shown to indicate a functional association between the proteins they encode. Here we introduce STRING (search tool for recurring instances of neighbouring genes), a tool to retrieve and display the genes a query gene repeatedly occurs with in clusters on the genome. The tool performs iterative searches and visualises the results in their genomic context. By finding the genomically associated genes for a query, it delineates a set of potentially functionally associated genes. The usefulness of STRING is illustrated with an example that suggests a functional context for an RNA methylase with unknown specificity. STRING is available at http://www.bork.embl-heidelberg.de/STRING     

Computation method to identify differential allelic gene expression and novel imprinted genes

MOTIVATION: Genomic imprinting plays an important role in both normal development and diseases. Abnormal imprinting is strongly associated with several human diseases including cancers. Most of the imprinted genes were discovered in the neighborhood of the known imprinted genes. This approach is difficult to extend to analyze the whole genome. We have decided to take a computational approach to systematically search the whole genome for the presence of mono-allelic expressed genes and imprinted genes in human genome. RESULTS: A computational method was developed to identify novel imprinted or mono-allelic genes. Individuals represented in human cDNA libraries were genotyped using Bayesian statistics, and differential expression of polymorphic alleles was identified. A significant reduction in the number of libraries that expressed both alleles, measured by Z-statistics, is a strong indicator for an imprinted or a mono-allelic gene. AVAILABILITY: The data sets are available at http://leelab.nci.nih.gov/leelab/jsp/IGDM/IGDM.html     

Antagonistic functional duality of cancer genes

Cancer evolution is a stochastic process both at the genome and gene levels. Most of tumors contain multiple genetic subclones, evolving in either succession or in parallel, either in a linear or branching manner, with heterogeneous genome and gene alterations, extensively rewired signaling networks, and addicted to multiple oncogenes easily switching with each other during cancer progression and medical intervention. Hundreds of discovered cancer genes are classified according to whether they function in a dominant (oncogenes) or recessive (tumor suppressor genes) manner in a cancer cell. However, there are many cancer “gene-chameleons”, which behave distinctly in opposite way in the different experimental settings showing antagonistic duality. In contrast to the widely accepted view that mutant NADP⁺-dependent isocitrate dehydrogenases 1/2 (IDH1/2) and associated metabolite 2-hydroxyglutarate (R)-enantiomer are intrinsically “the drivers” of tumourigenesis, mutant IDH1/2 inhibited, promoted or had no effect on cell proliferation, growth and tumorigenicity in diverse experiments. Similar behavior was evidenced for dozens of cancer genes. Gene function is dependent on genetic network, which is defined by the genome context. The overall changes in karyotype can result in alterations of the role and function of the same genes and pathways. The diverse cell lines and tumor samples have been used in experiments for proving gene tumor promoting/suppressive activity. They all display heterogeneous individual karyotypes and disturbed signaling networks. Consequently, the effect and function of gene under investigation can be opposite and versatile in cells with different genomes that may explain antagonistic duality of cancer genes and the cell type- or the cellular genetic/context-dependent response to the same protein. Antagonistic duality of cancer genes might contribute to failure of chemotherapy. Instructive examples of unexpected activity of cancer genes and “paradoxical” effects of different anticancer drugs depending on the cellular genetic context/signaling network are discussed.     

Genome characterization of lipid-containing marine bacteriophage PM2 by transposon insertion mutagenesis

Bacteriophage PM2 presently is the only member of the Corticoviridae family. The virion consists of a protein-rich lipid vesicle, which is surrounded by an icosahedral protein capsid. The lipid vesicle encloses a supercoiled circular double-stranded DNA genome of 10,079 bp. PM2 belongs to the marine phage community and is known to infect two gram-negative Pseudoalteromonas species. In this study, we present a characterization of the PM2 genome made using the in vitro transposon insertion mutagenesis approach. Analysis of 101 insertion mutants yielded information on the essential and dispensable regions of the PM2 genome and led to the identification of several new genes. A number of lysis-deficient mutants as well as mutants displaying delayed- and/or incomplete-lysis phenotypes were identified. This enabled us to identify novel lysis-associated genes with no resemblance to those previously described from other bacteriophage systems. Nonessential genome regions are discussed in the context of PM2 genome evolution.     

Structure and regulation of human troponin genes

The recent completion of a first draft of the human genome has allowed in silico genome browsing to become routine. Such computer-based research is now a useful adjunct to experiments based at the bench, and is accelerating gene discovery and the analysis and understanding of genes in their genomic contexts. This review summarises recent findings on genes encoding proteins of the troponin complex. We describe the organization of the three pairs of genes which encode isoforms of troponins I and T, and discuss how this relates to their evolution and regulation. Detailed analysis of the chromosomal context of the cardiac troponin I and slow skeletal troponin T genes reveals a region of densely packed differentially expressed genes, including new genes identified by automatic genome annotation. This information is discussed within the context of detailed analysis of the best-studied gene in this region, cardiac troponin I. In this way, we illustrate the uses to which a combination of conventional bench experiments and in silico analyses may be put in understanding the relationship between structure and function within the genome. (Mol Cell Biochem 263: 81–90, 2004)     

Duplication-dependent CG suppression of the seed storage protein genes of maize

This study investigates the prevalence of CG and CNG suppression in single- vs. multicopy DNA regions of the maize genome. The analysis includes the single- and multicopy seed storage proteins (zeins), the miniature inverted-repeat transposable elements (MITEs), and long terminal repeat (LTR) retrotransposons. Zein genes are clustered on specific chromosomal regions, whereas MITEs and LTRs are dispersed in the genome. The multicopy zein genes are CG suppressed and exhibit large variations in CG suppression. The variation observed correlates with the extent of duplication each zein gene has undergone, indicating that gene duplication results in an increased turnover of cytosine residues. Alignment of individual zein genes confirms this observation and demonstrates that CG depletion results primarily from polarized C:T and G:A transition mutations from a less to a more extensively duplicated gene. In addition, transition mutations occur primarily in a CG or CNG context suggesting that CG suppression may result from deamination of methylated cytosine residues. Duplication-dependent CG depletion is likely to occur at other loci as duplicated MITEs and LTR elements, or elements inserted into duplicated gene regions, also exhibit CG depletion.     

The non-redundant Bacillus subtilis (NRSub) database: update 1998.

The non-redundant Bacillus subtilis database (NRSub) has been developed in the context of the sequencing project devoted to this bacterium. As this project has reached completion, the whole genome is now available as a single contig. Thanks to the ACNUC database management system and its associated retrieval system Query_win, each functional region of the genome can be accessed individually. Extra annotations have been added such as accession numbers for the genes, locations on the genetic map, codon adaptation index values, as well as cross-references with other collections. NRSub is distributed through anonymous FTP as a text file in EMBL format and as an ACNUC database. It is also possible to access NRSub through two dedicated World Wide Web servers located in France (http://acnuc. univ-lyon1.fr/nrsub/nrsub.html ) and in Japan (http://ddbjs4h.genes. nig.ac.jp/ ).     

PGMapper: a web-based tool linking phenotype to genes

SUMMARY: With the availability of whole genome sequence in many species, linkage analysis, positional cloning and microarray are gradually becoming powerful tools for investigating the links between phenotype and genotype or genes. However, in these methods, causative genes underlying a quantitative trait locus, or a disease, are usually located within a large genomic region or a large set of genes. Examining the function of every gene is very time consuming and needs to retrieve and integrate the information from multiple databases or genome resources. PGMapper is a software tool for automatically matching phenotype to genes from a defined genome region or a group of given genes by combining the mapping information from the Ensembl database and gene function information from the OMIM and PubMed databases. PGMapper is currently available for candidate gene search of human, mouse, rat, zebrafish and 12 other species. AVAILABILITY: Available online at http://www.genediscovery.org/pgmapper/index.jsp.     

An ancient history of gene duplications, fusions and losses in the evolution of APOBEC3 mutators in mammals

ABSTRACT: BACKGROUND: The APOBEC3 (A3) genes play a key role in innate antiviral defense in mammals by introducing directed mutations in the DNA. The human genome encodes for seven A3 genes, with multiple splice alternatives. Different A3 proteins display different substrate specificity, but the very basic question on how discerning self from non-self still remains unresolved. Further, the expression of A3 activity/ies shapes the way both viral and host genomes evolve. RESULTS: We present here a detailed temporal analysis of the origin and expansion of the A3 repertoire in mammals. Our data support an evolutionary scenario where the genome of the mammalian ancestor encoded for at least one ancestral A3 gene, and where the genome of the ancestor of placental mammals (and possibly of the ancestor of all mammals) already encoded for an A3Z1-A3Z2-A3Z3 arrangement. Duplication events of the A3 genes have occurred independently in different lineages: humans, cats and horses. In all of them, gene duplication has resulted in changes in enzyme activity and/or substrate specificity, in a paradigmatic example of convergent adaptive evolution at the genomic level. Finally, our results show that evolutionary rates for the three A3Z1, A3Z2 and A3Z3 motifs have significantly decreased in the last 100 Mya. The analysis constitutes a textbook example of the evolution of a gene locus by duplication and sub/neofunctionalization in the context of virus-host arms race. CONCLUSIONS: Our results provide a time framework for identifying ancestral and derived genomic arrangements in the APOBEC loci, and to date the expansion of this gene family for different lineages through time, as a response to changes in viral/retroviral/retrotransposon pressure.     

Gene Conversion Drives Within Genic Sequences: Concerted Evolution of Ribosomal RNA Genes in Bacteria and Archaea

Multiple copies of a given ribosomal RNA gene family undergo concerted evolution such that sequences of all gene copies are virtually identical within a species although they diverge normally between species. In eukaryotes, gene conversion and unequal crossing over are the proposed mechanisms for concerted evolution of tandemly repeated sequences, whereas dispersed genes are homogenized by gene conversion. However, the homogenization mechanisms for multiple-copy, normally dispersed, prokaryotic rRNA genes are not well understood. Here we compared the sequences of multiple paralogous rRNA genes within a genome in 12 prokaryotic organisms that have multiple copies of the rRNA genes. Within a genome, putative sequence conversion tracts were found throughout the entire length of each individual rRNA genes and their immediate flanks. Individual conversion events convert only a short sequence tract, and the conversion partners can be any paralogous genes within the genome. Interestingly, the genic sequences undergo much slower divergence than their flanking sequences. Moreover, genomic context and operon organization do not affect rRNA gene homogenization. Thus, gene conversion underlies concerted evolution of bacterial rRNA genes, which normally occurs within genic sequences, and homogenization of flanking regions may result from co-conversion with the genic sequence. Received: 31 March 2000 / Accepted: 15 June 2000     

Structure and regulation of human troponin genes

The recent completion of a first draft of the human genome has allowed "in silico" genome browsing to become routine. Such computer-based research is now a useful adjunct to experiments based at the bench, and is accelerating gene discovery and the analysis and understanding of genes in their genomic contexts. This review summarises recent findings on genes encoding proteins of the troponin complex. We describe the organization of the three pairs of genes which encode isoforms of troponins I and T, and discuss how this relates to their evolution and regulation. Detailed analysis of the chromosomal context of the cardiac troponin I and slow skeletal troponin T genes reveals a region of densely packed differentially expressed genes, including new genes identified by automatic genome annotation. This information is discussed within the context of detailed analysis of the best-studied gene in this region, cardiac troponin I. In this way, we illustrate the uses to which a combination of conventional bench experiments and "in silico" analyses may be put in understanding the relationship between structure and function within the genome.     

Using multiple alignments to improve gene prediction.

The multiple species de novo gene prediction problem can be stated as follows: given an alignment of genomic sequences from two or more organisms, predict the location and structure of all protein-coding genes in one or more of the sequences. Here, we present a new system, N-SCAN (a.k.a. TWINSCAN 3.0), for addressing this problem. N-SCAN can model the phylogenetic relationships between the aligned genome sequences, context dependent substitution rates, and insertions and deletions. An implementation of N-SCAN was created and used to generate predictions for the entire human genome and the genome of the fruit fly Drosophila melanogaster. Analyses of the predictions reveal that N-SCAN's accuracy in both human and fly exceeds that of all previously published whole-genome de novo gene predictors.     

PathoGene: a pathogen coding sequence discovery and analysis resource

PathoGene is a web-based resource that streamlines the process of predicting genes in microorganisms and designs PCR primers for amplification to facilitate sequence analysis and experimentation. PathoGene currently supports primer design for every complete microbial, viral, and fungal genome as cataloged in GenBank by the National Center for Biotechnology Information (NCBI; http://www.ncbi.nlm.nih.gov/). The resulting primers can then be subjected to a stand-alone Basic Local Alignment Search Tool (BLAST) system called PathoBLAST in which the predicted PCR product and/or primers can be compared against the genome of interest or a similar genome to find related genes or estimate primer quality.     

Embryonic stem cells induce pluripotency in somatic cell fusion through biphasic reprogramming

It is a long-held paradigm that cell fusion reprograms gene expression but the extent of reprogramming and whether it is affected by the cell types employed remain unknown. We recently showed that the silencing of somatic genes is attributable to either trans-acting cellular environment or cis-acting chromatin context. Here, we examine how trans- versus cis-silenced genes in a somatic cell type behave in fusions to another somatic cell type or to embryonic stem cells (ESCs). We demonstrate that while reprogramming of trans-silenced somatic genes occurs in both cases, reprogramming of cis-silenced somatic genes occurs only in somatic-ESC fusions. Importantly, ESCs reprogram the somatic genome in two distinct phases: trans-reprogramming occurs rapidly, independent of DNA replication, whereas cis-reprogramming occurs with slow kinetics requiring DNA replication. We also show that pluripotency genes Oct4 and Nanog are cis-silenced in somatic cells. We conclude that cis-reprogramming capacity is a fundamental feature distinguishing ESCs from somatic cells.     

A search for candidate genes for lipodystrophy,obesity and diabetes via gene expression analysis of A-ZIP/F-1 mice

Genome scans for diabetes have identified many regions of the human genome that correlate with the disease state. To identify candidate genes for type 2 diabetes, we examined the transgenic A-ZIP/F-1 mouse. This mouse model has no white fat, resulting in abnormal levels of glucose, insulin, and leptin, making the A-ZIP/F-1 mice a good model for lipodystrophy and insulin resistance. We used cDNA-based microarrays to find differentially expressed genes in four tissues of these mice. We examined these results in the context of human linkage scans for lipodystrophy, obesity, and type 2 diabetes. We combined 199 known human orthologs of the misregulated mouse genes with 33 published human genome scans on a genome map. Integrating expression data with human linkage results permitted us to suggest and prioritize candidate genes for lipodystrophy and related disorders. These genes include a cluster of 3 S100A genes on chromosome 1 and SLPI1 on chromosome 20.     

Cultivated hawthorn (Crataegus pinnatifida var. major) genome sheds light on the evolution of Maleae (apple tribe)

Cultivated hawthorn (Crataegus pinnatifida var. major) is an important medicinal and edible plant with a long history of use for health protection in China. Herein, we provide a de novo chromosome-level genome sequence of the hawthorn cultivar “Qiu Jinxing.” We assembled an 823.41 Mb genome encoding 40 571 genes and further anchored the 779.24 Mb sequence into 17 pseudo-chromosomes, which account for 94.64% of the assembled genome. Phylogenomic analyses revealed that cultivated hawthorn diverged from other species within the Maleae (apple tribe) at approximately 35.4 Mya. Notably, genes involved in the flavonoid and triterpenoid biosynthetic pathways have been significantly amplified in the hawthorn genome. In addition, our results indicated that the Maleae share a unique ancient tetraploidization event; however, no recent independent whole-genome duplication event was specifically detected in hawthorn. The amplification of non-specific long terminal repeat retrotransposons contributed the most to the expansion of the hawthorn genome. Furthermore, we identified two paleo-sub-genomes in extant species of Maleae and found that these two sub-genomes showed different rearrangement mechanisms. We also reconstructed the ancestral chromosomes of Rosaceae and discussed two possible paleo-polyploid origin patterns (autopolyploidization or allopolyploidization) of Maleae. Overall, our study provides an improved context for understanding the evolution of Maleae species, and this new high-quality reference genome provides a useful resource for the horticultural improvement of hawthorn.