Genomic Signature Tags (GSTs): A System for Profiling Genomic DNA

Dunn, John J.; McCorkle, S.; Praissman, Laura A.; Hínd, Geoffrey; Lelie, Daniël van der; Bahou, Wadie F.; Gnatenko, Dmitri V.; Krause, Maureen K.

doi:10.1101/gr.306102

Cited by 33 publications

(25 citation statements)

References 31 publications

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“…A genomic signature tag (GST) approach for determining differences between CO-92 and EV76 (biovar Orientalis) was reported recently, and suggested the potential absence of six regions in the EV76 genome (Dunn et al 2002). Our data reveals that only two of the regions appear to be absent from the EV76 genome, both of which were predicted, but not fully defined, by the GST method.…”

Section: Microarray Validationmentioning

confidence: 64%

Application of DNA Microarrays to Study the Evolutionary Genomics of Yersinia pestis and Yersinia pseudotuberculosis

Hinchliffe¹,

Isherwood²,

Stabler³

et al. 2003

Genome Res.

158

151

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Yersinia pestis, the causative agent of plague, diverged from Yersinia pseudotuberculosis, an enteric pathogen, an estimated 1500–20,000 years ago. Genetic characterization of these closely related organisms represents a useful model to study the rapid emergence of bacterial pathogens that threaten mankind. To this end, we undertook genome-wide DNA microarray analysis of 22 strains of Y. pestis and 10 strains of Y. pseudotuberculosis of diverse origin. Eleven Y. pestis DNA loci were deemed absent or highly divergent in all strains of Y. pseudotuberculosis. Four were regions of phage origin, whereas the other seven included genes encoding a vitamin B12 receptor and the insect toxin sepC. Sixteen differences were identified between Y. pestis strains, with biovar Antiqua and Mediaevalis strains showing most divergence from the arrayed CO92 Orientalis strain. Fifty-eight Y. pestis regions were specific to a limited number of Y. pseudotuberculosis strains, including the high pathogenicity island, three putative autotransporters, and several possible insecticidal toxins and hemolysins. The O-antigen gene cluster and one of two possible flagellar operons had high levels of divergence between Y. pseudotuberculosis strains. This study reports chromosomal differences between species, biovars, serotypes, and strains of Y. pestis and Y. pseudotuberculosis that may relate to the evolution of these species in their respective niches.

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Section: Microarray Validationmentioning

confidence: 64%

Application of DNA Microarrays to Study the Evolutionary Genomics of Yersinia pestis and Yersinia pseudotuberculosis

Hinchliffe¹,

Isherwood²,

Stabler³

et al. 2003

Genome Res.

158

151

View full text Add to dashboard Cite

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“…These methods involve profiling clones with microarrays that identify previously unknown genes in environmental samples (107), subtractive hybridization to eliminate all sequences that hybridize with another environment, or subtractive hybridization to identify differentially expressed genes (35), and genomic sequence tags (28). These methods will enhance the efficiency of screening and aid in identifying minor components in communities and genes that define community uniqueness.…”

Section: Identifying Sequences Of Interest In Large Metagenomic Libramentioning

confidence: 99%

Metagenomics: Genomic Analysis of Microbial Communities

2004

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▪ Abstract Uncultured microorganisms comprise the majority of the planet's biological diversity. Microorganisms represent two of the three domains of life and contain vast diversity that is the product of an estimated 3.8 billion years of evolution. In many environments, as many as 99% of the microorganisms cannot be cultured by standard techniques, and the uncultured fraction includes diverse organisms that are only distantly related to the cultured ones. Therefore, culture-independent methods are essential to understand the genetic diversity, population structure, and ecological roles of the majority of microorganisms. Metagenomics, or the culture-independent genomic analysis of an assemblage of microorganisms, has potential to answer fundamental questions in microbial ecology. This review describes progress toward understanding the biology of uncultured Bacteria, Archaea, and viruses through metagenomic analyses.

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“…However, our understanding of large structural rearrangements in the human genomes is just beginning. SAGE-based digital karyotyping (Dunn et al 2002;Wang et al 2002), array comparative genomic hybridization (aCGH) (Pinkel et al 1998), and whole-genome tiling arrays (Kim et al 2005) have contributed to this field by identifying large chunks of deletions and assessing copy number variations of amplified regions in disease genomes compared to normal and reference genomes. However, neither the single-tag sequencing approach nor the hybridization methods can identify balanced structural variations such as insertions, inversions, and translocations in genome rearrangements.…”

Section: Dna-pet For Genome Structure Analysismentioning

confidence: 99%

Next-generation DNA sequencing of paired-end tags (PET) for transcriptome and genome analyses

Fullwood¹,

Wei²,

Liu³

et al. 2009

Genome Res.

308

229

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Comprehensive understanding of functional elements in the human genome will require thorough interrogation and comparison of individual human genomes and genomic structures. Such an endeavor will require improvements in the throughputs and costs of DNA sequencing. Next-generation sequencing platforms have impressively low costs and high throughputs but are limited by short read lengths. An immediate and widely recognized solution to this critical limitation is the paired-end tag (PET) sequencing for various applications, collectively called the PET sequencing strategy, in which short and paired tags are extracted from the ends of long DNA fragments for ultra-high-throughput sequencing. The PET sequences can be accurately mapped to the reference genome, thus demarcating the genomic boundaries of PETrepresented DNA fragments and revealing the identities of the target DNA elements. PET protocols have been developed for the analyses of transcriptomes, transcription factor binding sites, epigenetic sites such as histone modification sites, and genome structures. The exclusive advantage of the PET technology is its ability to uncover linkages between the two ends of DNA fragments. Using this unique feature, unconventional fusion transcripts, genome structural variations, and even molecular interactions between distant genomic elements can be unraveled by PET analysis. Extensive use of PET data could lead to efficient assembly of individual human genomes, transcriptomes, and interactomes, enabling new biological and clinical insights. With its versatile and powerful nature for DNA analysis, the PET sequencing strategy has a bright future ahead.Genomics holds much promise for huge improvements in human healthcare. However, genomics faces several practical challenges. Human genomes are read out as linear sequences, but in the cell, there are many complex interactions and mechanisms that operate around human DNA to transduce DNA information into biological function (The ENCODE Project Consortium 2007). Conventional DNA sequencing has been used to extensively explore genetic elements and structures; however, high sequencing costs and low throughputs have historically limited in-depth analysis of a broad range of genomic elements, making the development of new sequencing strategies necessary.Next-generation sequencing technologies are transforming the field of genomic science (Schuster 2008). The currently available next-generation sequencing methods (Margulies et al. 2005;Shendure et al. 2005;Barski et al. 2007;Johnson et al. 2007) read DNA templates in a highly parallel manner to generate massive amounts of sequencing data, but the read length for each DNA template is short compared with that of traditionally used Sanger capillary sequencing instruments. This massively parallel and short read strategy of DNA sequencing opens many new ways for interrogating human genomes (Wold and Myers 2008). However, the short read lengths lead to serious limitations in applying this enormous sequencing power to many biological applicati...

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Genomic Signature Tags (GSTs): A System for Profiling Genomic DNA

Cited by 33 publications

References 31 publications

Application of DNA Microarrays to Study the Evolutionary Genomics of Yersinia pestis and Yersinia pseudotuberculosis

Application of DNA Microarrays to Study the Evolutionary Genomics of Yersinia pestis and Yersinia pseudotuberculosis

Metagenomics: Genomic Analysis of Microbial Communities

Next-generation DNA sequencing of paired-end tags (PET) for transcriptome and genome analyses

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