Genomes and Genes
sequence tagged sites
Summary: Short tracts of DNA sequence that are used as landmarks in GENOME mapping. In most instances, 200 to 500 base pairs of sequence define a Sequence Tagged Site (STS) that is operationally unique in the human genome (i.e., can be specifically detected by the polymerase chain reaction in the presence of all other genomic sequences). The overwhelming advantage of STSs over mapping landmarks defined in other ways is that the means of testing for the presence of a particular STS can be completely described as information in a database.
- Faulkner G, Forrest A, Chalk A, Schroder K, Hayashizaki Y, Carninci P, et al. A rescue strategy for multimapping short sequence tags refines surveys of transcriptional activity by CAGE. Genomics. 2008;91:281-8 pubmed publisher..These results suggest that the multimap tags produced by high-throughput, short sequence tag-based approaches can be rescued to augment greatly the transcriptome coverage provided by single-map tags alone. ..
- Zambrowicz B, Abuin A, Ramirez Solis R, Richter L, Piggott J, BeltrandelRio H, et al. Wnk1 kinase deficiency lowers blood pressure in mice: a gene-trap screen to identify potential targets for therapeutic intervention. Proc Natl Acad Sci U S A. 2003;100:14109-14 pubmed..These results demonstrate that Wnk1 is a regulator of blood pressure critical for development and illustrate the utility of a functional screen driven by a sequence-based mutagenesis approach. ..
- Boheler K, Stern M. The new role of SAGE in gene discovery. Trends Biotechnol. 2003;21:55-7; discussion 57-8 pubmed..Genome and transcriptome complexity is thus greater than predicted and many of the missing genes are probably expressed in low copy numbers or only in early embryonic tissues. ..
- Larmande P, Gay C, Lorieux M, Perin C, Bouniol M, Droc G, et al. Oryza Tag Line, a phenotypic mutant database for the Genoplante rice insertion line library. Nucleic Acids Res. 2008;36:D1022-7 pubmed..8004 and 6101 of the 13,928 lines are characterized by at least one T-DNA and one Tos17 FST, respectively that OTL links to the rice genome browser OryGenesDB. ..
- Choi I, Hyten D, Matukumalli L, Song Q, Chaky J, Quigley C, et al. A soybean transcript map: gene distribution, haplotype and single-nucleotide polymorphism analysis. Genetics. 2007;176:685-96 pubmed
- Droc G, Ruiz M, Larmande P, Pereira A, Piffanelli P, Morel J, et al. OryGenesDB: a database for rice reverse genetics. Nucleic Acids Res. 2006;34:D736-40 pubmed..As a first step toward plant comparative genomics, we have linked the rice and Arabidopsis whole genome using all the predicted pairs of orthologs by best BLAST mutual hit (BBMH) connectors. ..
- Shultz J, Kurunam D, Shopinski K, Iqbal M, Kazi S, Zobrist K, et al. The Soybean Genome Database (SoyGD): a browser for display of duplicated, polyploid, regions and sequence tagged sites on the integrated physical and genetic maps of Glycine max. Nucleic Acids Res. 2006;34:D758-65 pubmed..The genome browser portal showed each data type as a separate track. Tetraploid, octoploid, diploid and homologous regions are shown clearly in relation to an integrated genetic and physical map. ..
- Ng P, Tan J, Ooi H, Lee Y, Chiu K, Fullwood M, et al. Multiplex sequencing of paired-end ditags (MS-PET): a strategy for the ultra-high-throughput analysis of transcriptomes and genomes. Nucleic Acids Res. 2006;34:e84 pubmed
- Fullwood M, Wei C, Liu E, Ruan Y. Next-generation DNA sequencing of paired-end tags (PET) for transcriptome and genome analyses. Genome Res. 2009;19:521-32 pubmed publisher..With its versatile and powerful nature for DNA analysis, the PET sequencing strategy has a bright future ahead. ..
- Hwang T, Sayama T, Takahashi M, Takada Y, Nakamoto Y, Funatsuki H, et al. High-density integrated linkage map based on SSR markers in soybean. DNA Res. 2009;16:213-25 pubmed publisher..8. Our high-density linkage map should facilitate ongoing and future genomic research such as analysis of quantitative trait loci and positional cloning in addition to marker-assisted selection in soybean breeding. ..
- Silva A, De Souza J, Galante P, Riggins G, de Souza S, Camargo A. The impact of SNPs on the interpretation of SAGE and MPSS experimental data. Nucleic Acids Res. 2004;32:6104-10 pubmed..The availability of our SNP-associated alternative tag database will certainly improve the interpretation of SAGE and MPSS experiments. ..
- Meyer M, Stenzel U, Myles S, Prüfer K, Hofreiter M. Targeted high-throughput sequencing of tagged nucleic acid samples. Nucleic Acids Res. 2007;35:e97 pubmed..PTS dramatically increases the sequencing throughput of samples in parallel and thus fully mobilizes the resources of the 454 technology for targeted sequencing. ..
- McKay S, Schnabel R, Murdoch B, Aerts J, Gill C, Gao C, et al. Construction of bovine whole-genome radiation hybrid and linkage maps using high-throughput genotyping. Anim Genet. 2007;38:120-5 pubmed..0) in a fraction of the time it would have taken with conventional typing and genotyping methods. ..
- Rotmistrovsky K, Jang W, Schuler G. A web server for performing electronic PCR. Nucleic Acids Res. 2004;32:W108-12 pubmedElectronic PCR' (e-PCR) refers to a computational procedure that is used to search DNA sequences for sequence tagged sites (STSs), each of which is defined by a pair of primer sequences and an expected PCR product size...
- Cronn R, Liston A, Parks M, Gernandt D, Shen R, Mockler T. Multiplex sequencing of plant chloroplast genomes using Solexa sequencing-by-synthesis technology. Nucleic Acids Res. 2008;36:e122 pubmed publisher..056%, and conspicuous errors are evident from the assembly process. This efficient sequencing approach yields high-quality draft genomes and should have immediate applicability to genomes with comparable complexity. ..
- Zhang Z, Dietrich F. Mapping of transcription start sites in Saccharomyces cerevisiae using 5' SAGE. Nucleic Acids Res. 2005;33:2838-51 pubmed..The TSS data allowed the identification of a previously unrecognized gene, uncovered errors in previous annotation, and identified potential regulatory RNAs and upstream open reading frames in 5'-untranslated region. ..
- Chen J, Sun M, Lee S, Zhou G, Rowley J, Wang S. Identifying novel transcripts and novel genes in the human genome by using novel SAGE tags. Proc Natl Acad Sci U S A. 2002;99:12257-62 pubmed..Our study indicates that by using novel SAGE tags as probes, we should be able to identify efficiently many novel transcripts/novel genes in the human genome that are difficult to identify by conventional methods. ..
- Nielsen K, Høgh A, Emmersen J. DeepSAGE--digital transcriptomics with high sensitivity, simple experimental protocol and multiplexing of samples. Nucleic Acids Res. 2006;34:e133 pubmed..Importantly, many transcripts were detected that cannot be matched to known genes, but is likely to be part of the abiotic stress-response in potato. ..
- Bianchetti L, Wu Y, Guerin E, Plewniak F, Poch O. SAGETTARIUS: a program to reduce the number of tags mapped to multiple transcripts and to plan SAGE sequencing stages. Nucleic Acids Res. 2007;35:e122 pubmed..SAGETTARIUS is web interfaced and freely accessible to academic users. ..
- Hansen J, Floss T, Van Sloun P, Füchtbauer E, Vauti F, Arnold H, et al. A large-scale, gene-driven mutagenesis approach for the functional analysis of the mouse genome. Proc Natl Acad Sci U S A. 2003;100:9918-22 pubmed..Thus, gene trapping allows a large-scale and cost-effective production of ES cell clones with mutations distributed throughout the genome, a resource likely to accelerate genome annotation and the in vivo modeling of human disease. ..
- Huang L, Brooks S, Li W, Fellers J, Trick H, Gill B. Map-based cloning of leaf rust resistance gene Lr21 from the large and polyploid genome of bread wheat. Genetics. 2003;164:655-64 pubmed..The successful map-based cloning approach as demonstrated here now opens the door for cloning of many crop-specific agronomic traits located in the gene-rich regions of bread wheat. ..
- Li Y, Rosso M, Viehoever P, Weisshaar B. GABI-Kat SimpleSearch: an Arabidopsis thaliana T-DNA mutant database with detailed information for confirmed insertions. Nucleic Acids Res. 2007;35:D874-8 pubmed..This information not only helps users to evaluate the usefulness of the mutant lines, but also covers a big part of the molecular characterization of the insertion alleles. ..
- Hsing Y, Chern C, Fan M, Lu P, Chen K, Lo S, et al. A rice gene activation/knockout mutant resource for high throughput functional genomics. Plant Mol Biol. 2007;63:351-64 pubmed..Our mutant population offers a highly valuable resource for high throughput rice functional analyses using both forward and reverse genetic approaches. ..
- Rong J, Abbey C, Bowers J, Brubaker C, Chang C, Chee P, et al. A 3347-locus genetic recombination map of sequence-tagged sites reveals features of genome organization, transmission and evolution of cotton (Gossypium). Genetics. 2004;166:389-417 pubmed..These data provide new insights into polyploid evolution and represent a foundation for assembly of a finished sequence of the cotton genome. ..
- LeDuc R, Taylor G, Kim Y, Januszyk T, Bynum L, Sola J, et al. ProSight PTM: an integrated environment for protein identification and characterization by top-down mass spectrometry. Nucleic Acids Res. 2004;32:W340-5 pubmed..The user can optionally control how much of this biological variability should be searched. ..
- Oh J, Fung E, Price M, Dehal P, Davis R, Giaever G, et al. A universal TagModule collection for parallel genetic analysis of microorganisms. Nucleic Acids Res. 2010;38:e146 pubmed publisher..The publicly available TagModule collection is a platform-independent resource for the functional genomics of a wide range of microbial systems in the post-genome era. ..
- Malig R, Varela C, Agosin E, Melo F. Accurate and unambiguous tag-to-gene mapping in serial analysis of gene expression. BMC Bioinformatics. 2006;7:487 pubmed..This is supported by the results obtained here and also by the large impact that the erroneous interpretation of these data could have on downstream applications. ..
- Crowe M, Serizet C, Thareau V, Aubourg S, Rouze P, Hilson P, et al. CATMA: a complete Arabidopsis GST database. Nucleic Acids Res. 2003;31:156-8 pubmed..The database is searchable by sequence name, sequence homology or direct SQL query, and is available through the CATMA website at http://www.catma.org/. ..
- Winter P, Pfaff T, Udupa S, Hüttel B, Sharma P, Sahi S, et al. Characterization and mapping of sequence-tagged microsatellite sites in the chickpea (Cicer arietinum L.) genome. Mol Gen Genet. 1999;262:90-101 pubmed..05) from the expected 1:1 ratio. The majority of these loci (73%) were located in three distinct regions of the genome. The present STMS marker map represents the most advanced co-dominant DNA marker map of the chickpea genome. ..
- Shubitowski D, Venta P, Douglass C, Zhou R, Ewart S. Polymorphism identification within 50 equine gene-specific sequence tagged sites. Anim Genet. 2001;32:78-88 pubmed..The pool-and-sequence method allows identification of polymorphisms in horse populations and will be a valuable tool for future disease gene and comparative mapping in horses...
- Suzuki Y, Taira H, Tsunoda T, Mizushima Sugano J, Sese J, Hata H, et al. Diverse transcriptional initiation revealed by fine, large-scale mapping of mRNA start sites. EMBO Rep. 2001;2:388-93 pubmed..They were distributed over 61.7 bp with a standard deviation of 19.5. Our finding may reflect the dynamic nature of transcriptional initiation events of human genes in vivo. ..
- Stollberg J, Urschitz J, Urban Z, Boyd C. A quantitative evaluation of SAGE. Genome Res. 2000;10:1241-8 pubmed..It also is shown that while in many cases it is probable that a given tag sequence is unique within the genome, in larger genomes this cannot be safely assumed. ..
- Lash A, Tolstoshev C, Wagner L, Schuler G, Strausberg R, Riggins G, et al. SAGEmap: a public gene expression resource. Genome Res. 2000;10:1051-60 pubmed
- Tilford C, Kuroda Kawaguchi T, Skaletsky H, Rozen S, Brown L, Rosenberg M, et al. A physical map of the human Y chromosome. Nature. 2001;409:943-5 pubmed..The markers anchor 1,038 bacterial artificial chromosome clones, 199 of which form a tiling path for sequencing. ..
- Osoegawa K, Mammoser A, Wu C, Frengen E, Zeng C, Catanese J, et al. A bacterial artificial chromosome library for sequencing the complete human genome. Genome Res. 2001;11:483-96 pubmed
- Liu S, Anderson J. Targeted molecular mapping of a major wheat QTL for Fusarium head blight resistance using wheat ESTs and synteny with rice. Genome. 2003;46:817-23 pubmed..ndsu-3BS, and this strategy may have broad applications for targeted mapping of other traits in cereal crops. ..
- Bang K, Lee J, Kim Y, Kim D, Lee E, Jeung J. Construction of genomic DNA library of Korean ginseng (Panax ginseng C. A. MEYER) and development of sequence-tagged sites. Biol Pharm Bull. 2010;33:1579-88 pubmedThis study describes an efficient approach for developing sequence tagged sites (STS) for Panax ginseng C.A. MEYER, and their applications for line discrimination...
- Suter B, Graham C, Stagljar I. Exploring protein phosphorylation in response to DNA damage using differentially tagged yeast arrays. Biotechniques. 2008;45:581-4 pubmed publisher..Hence, we demonstrated that the Cross-and-Capture system could be efficiently used to detect posttranslational modifications that modulate and control protein function in eukaryotic cells. ..
- Gale L, Bryant J, Calvo S, Giese H, Katan T, O DONNELL K, et al. Chromosome complement of the fungal plant pathogen Fusarium graminearum based on genetic and physical mapping and cytological observations. Genetics. 2005;171:985-1001 pubmed..A chromosome number of four was confirmed by cytological karyotyping. Further analysis of the genetic map data identified variation in recombination rate in different genomic regions that often spanned several hundred kilobases. ..
- Tian H, Liu D, Xu B, Zheng W, Zhou S. [Analysis of sequence-tagged site in bcr and abl genes by DNA pooling and dHPLC]. Zhongguo Shi Yan Xue Ye Xue Za Zhi. 2005;13:468-71 pubmed..In conclusion, the novel SNP in U07000 fragment shows significantly different frequencies between CML and controled people. ..
- Farkas R, Qian J, Goldberg J, Quigley H, Zack D. Gene expression profiling of purified rat retinal ganglion cells. Invest Ophthalmol Vis Sci. 2004;45:2503-13 pubmed..The profiling, in addition to revealing both known and novel genes underlying the RGC phenotype, also uncovered common patterns of gene expression between RGCs and other sensory ganglia. ..
- Zeggini E, Thomson W, Kwiatkowski D, Richardson A, Ollier W, Donn R. Linkage and association studies of single-nucleotide polymorphism-tagged tumor necrosis factor haplotypes in juvenile oligoarthritis. Arthritis Rheum. 2002;46:3304-11 pubmed..The TNF locus is linked and associated with juvenile oligoarthritis. Information on the htSNPs can be useful in genetic studies of diseases in which TNF may be of relevance. ..
- Ohtsubo K, Nakamura S. Cultivar identification of rice (Oryza sativa L.) by polymerase chain reaction method and its application to processed rice products. J Agric Food Chem. 2007;55:1501-9 pubmed
- Karcanias A, Ichimura K, Mitchell M, Sargent C, Affara N. Analysis of sex chromosome abnormalities using X and Y chromosome DNA tiling path arrays. J Med Genet. 2007;44:429-36 pubmed..These data indicate that the combined X and Y tiling path arrays provide an effective tool for the investigation and diagnosis of sex chromosome copy number aberrations and rearrangements. ..
- Carrico I, Carlson B, Bertozzi C. Introducing genetically encoded aldehydes into proteins. Nat Chem Biol. 2007;3:321-2 pubmed..This genetically encoded 'aldehyde tag' is no larger than a His(6) tag and can be exploited for numerous protein labeling applications. ..
- Koehler R, Issac H, Cloonan N, Grimmond S. The uniqueome: a mappability resource for short-tag sequencing. Bioinformatics. 2011;27:272-4 pubmed publisher..Files, scripts and supplementary data are available from http://grimmond.imb.uq.edu.au/uniqueome/; the ISAS uniqueome aligner is freely available from http://www.imagenix.com/. ..
- Settles A, Holding D, Tan B, Latshaw S, Liu J, Suzuki M, et al. Sequence-indexed mutations in maize using the UniformMu transposon-tagging population. BMC Genomics. 2007;8:116 pubmed..We conclude from these data that the current collection of 1,882 non-redundant insertion sites from UniformMu provide a genome-wide resource for reverse genetics. ..
- Need A, Goldstein D. Genome-wide tagging for everyone. Nat Genet. 2006;38:1227-8 pubmed
- Wenger S, Senft J, Sargent L, Bamezai R, Bairwa N, Grant S. Comparison of established cell lines at different passages by karyotype and comparative genomic hybridization. Biosci Rep. 2004;24:631-9 pubmed..Our study shows the utilization of CGH in comparing cell lines originating from the same specimen. Our study also demonstrates the necessity for periodically evaluating cell lines to confirm their origin. ..
- Ke X, Miretti M, Broxholme J, Hunt S, Beck S, Bentley D, et al. A comparison of tagging methods and their tagging space. Hum Mol Genet. 2005;14:2757-67 pubmed..These results indicate that the tagging space is highly concordant between different tagging methods, despite the fact that they often involve different sets of tagging SNPs. ..
- Ikeda M, Iwata N, Suzuki T, Kitajima T, Yamanouchi Y, Kinoshita Y, et al. No association of haplotype-tagging SNPs in TRAR4 with schizophrenia in Japanese patients. Schizophr Res. 2005;78:127-30 pubmed..Our results indicate that TRAR4 may not play a major role in Japanese schizophrenia patients, and that it is important to examine the possibility of false positives in genetic association analysis. ..
- Farber C, Raney N, Kuhlers D, Nadarajah K, Ernst C. Mapping of porcine genetic markers generated by representational difference analysis. Anim Biotechnol. 2003;14:87-102 pubmed..Development of RDA markers increases the resolution of the pig genome maps and markers located within putative quantitative trait locus (QTL) regions can be used to refine QTL positions. ..
- Esselink G, Smulders M, Vosman B. Identification of cut rose (Rosa hybrida) and rootstock varieties using robust sequence tagged microsatellite site markers. Theor Appl Genet. 2003;106:277-86 pubmed..The selected STMS markers will be useful as a tool for reference collection management, for assessing essential derivation of varieties and illegal propagation. ..
- Ujino Ihara T, Matsumuto A, Iwata H, Yoshimura K, Tsumura Y. Single-strand conformation polymorphism of sequence-tagged site markers based on partial sequences of cDNA clones in Cryptomeria japonica. Genes Genet Syst. 2002;77:251-7 pubmed
- Devos K, Ma J, Pontaroli A, Pratt L, Bennetzen J. Analysis and mapping of randomly chosen bacterial artificial chromosome clones from hexaploid bread wheat. Proc Natl Acad Sci U S A. 2005;102:19243-8 pubmed
- Peyser B, Irizarry R, Tiffany C, Chen O, Yuan D, Boeke J, et al. Improved statistical analysis of budding yeast TAG microarrays revealed by defined spike-in pools. Nucleic Acids Res. 2005;33:e140 pubmed
- Laayouni H, Hasson E, Santos M, Fontdevila A. The evolutionary history of Drosophila buzzatii. XXXV. Inversion polymorphism and nucleotide variability in different regions of the second chromosome. Mol Biol Evol. 2003;20:931-44 pubmed
- Allard L, Cheynet V, Oriol G, Mandrand B, Delair T, Mallet F. Versatile method for production and controlled polymer-immobilization of biologically active recombinant proteins. Biotechnol Bioeng. 2002;80:341-8 pubmed
- Jenkins C, Kedar V, Fuerst J. Gene discovery within the planctomycete division of the domain Bacteria using sequence tags from genomic DNA libraries. Genome Biol. 2002;3:RESEARCH0031 pubmed