Sleeping Beauty awakens

Weiser, Keith C.; Justice, Monica J.

doi:10.1038/436184a

Cited by 11 publications

(8 citation statements)

References 9 publications

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“…Active TEs found in several fish have been reactivated successfully after molecular genetic manipulation from inactive genomic copies [65]. A larger number of TEs or mobile sequences could be useful for identifying genes important in fish aquaculture using inverted terminal repeats [65–67]. Furthermore, understanding the dynamics, control and evolution of fish TEs could allow insertion of selected sequences into fish germ cells to develop transgenics or for identifying genes important for growth and/or in somatic cells to improve DNA vaccination [65].…”

Section: Resultsmentioning

confidence: 99%

Analysis of Genome Survey Sequences and SSR Marker Development for Siamese Mud Carp, Henicorhynchus siamensis, Using 454 Pyrosequencing

Iranawati

Jung

Chand

et al. 2012

IJMS

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Siamese mud carp (Henichorynchus siamensis) is a freshwater teleost of high economic importance in the Mekong River Basin. However, genetic data relevant for delineating wild stocks for management purposes currently are limited for this species. Here, we used 454 pyrosequencing to generate a partial genome survey sequence (GSS) dataset to develop simple sequence repeat (SSR) markers from H. siamensis genomic DNA. Data generated included a total of 65,954 sequence reads with average length of 264 nucleotides, of which 2.79% contain SSR motifs. Based on GSS-BLASTx results, 10.5% of contigs and 8.1% singletons possessed significant similarity (E value < 10−5) with the majority matching well to reported fish sequences. KEGG analysis identified several metabolic pathways that provide insights into specific potential roles and functions of sequences involved in molecular processes in H. siamensis. Top protein domains detected included reverse transcriptase and the top putative functional transcript identified was an ORF2-encoded protein. One thousand eight hundred and thirty seven sequences containing SSR motifs were identified, of which 422 qualified for primer design and eight polymorphic loci have been tested with average observed and expected heterozygosity estimated at 0.75 and 0.83, respectively. Regardless of their relative levels of polymorphism and heterozygosity, microsatellite loci developed here are suitable for further population genetic studies in H. siamensis and may also be applicable to other related taxa.

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Section: Resultsmentioning

confidence: 99%

Analysis of Genome Survey Sequences and SSR Marker Development for Siamese Mud Carp, Henicorhynchus siamensis, Using 454 Pyrosequencing

Iranawati

Jung

Chand

et al. 2012

IJMS

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“…Integrases and recombinases are widely‐used deoxyribonucleic acid (DNA)‐modifying enzymes that enable site‐specific genome modifications in many hosts including mammalian cells. These enzymes, including FLP recombinase [7], ΦC31 integrase [8–12], λ‐integrase [13], and Cre recombinase [14] facilitate genome editing functions such as deletions, insertions, inversions, and exchanges based on recognition of short, palindromic sequences that are typically integrated into the host's genome. Cre recombinase was prolifically utilized in early mouse recombineering efforts [15] and has several distinct advantages: it does not require protein factors [13], has high expression in mammalian systems [16], is more efficient than FLP recombinase [17] and ΦC31 integrase [18], and pseudo Cre recognition sites ( loxP ) do not interfere with recombinase activity in the mammalian genome [19].…”

Section: Introductionmentioning

confidence: 99%

Using the Cre/loxsystem for targeted integration into the human genome:loxFAS‐loxP pairing and delayed introduction of Cre DNA improve gene swapping efficiency

Lanza

Dyess

Alper

2012

Biotechnology Journal

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Cre recombinase is a commonly-used genome editing tool suitable for site-specific integrations in mammalian genomes; however, the efficiency of transgenic swapping events compared to excision remains limited. Here we sought to identify important parameters and limiting factors that influence swapping propensity in this system, especially when using one wild-type loxP site. To modulate and increase the occurrence of swapping events, we identified two novel parameters. First, we identified the loxFAS-loxP pairing, a sequence never before used in mammalian systems, as the best choice for increasing swapping events in human cell lines. Second, for the first time we implicate the importance of delayed introduction of Cre DNA for optimal swapping efficiency. This same modification could potentially be of use to other systems catalyzing trimolecular reactions such as ΦC31 integrase and FLP recombinase where we hypothesize that transport of the exchange cassette is likewise initially rate limiting. The total number of recombination events, but not the ratio of swapping to excision, was found to be influenced by the quantity of Cre DNA transfected. Through this study, we were able to obtain Cre-mediated swapping frequencies of 8-12% without antibiotic enrichment, which represents nearly an order of magnitude increase over prior reports in the literature.

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“…The Sleeping Beauty transposon system has been used for mutagenesis in somatic tissue and holds strong potential utility for the analysis of cancer and other phenotypes both in vitro and in vivo 111,112 . The Sleeping Beauty system consists of the eponymous transposase and transposon, initially found in the genome of salmonid fish in the late 1990s 113 .…”

Section: Transposon-based Phenotypic Screeningmentioning

confidence: 99%

Jump around: transposons in and out of the laboratory

Kumar

2020

F1000Res

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Since Barbara McClintock’s groundbreaking discovery of mobile DNA sequences some 70 years ago, transposable elements have come to be recognized as important mutagenic agents impacting genome composition, genome evolution, and human health. Transposable elements are a major constituent of prokaryotic and eukaryotic genomes, and the transposition mechanisms enabling transposon proliferation over evolutionary time remain engaging topics for study, suggesting complex interactions with the host, both antagonistic and mutualistic. The impact of transposition is profound, as over 100 human heritable diseases have been attributed to transposon insertions. Transposition can be highly mutagenic, perturbing genome integrity and gene expression in a wide range of organisms. This mutagenic potential has been exploited in the laboratory, where transposons have long been utilized for phenotypic screening and the generation of defined mutant libraries. More recently, barcoding applications and methods for RNA-directed transposition are being used towards new phenotypic screens and studies relevant for gene therapy. Thus, transposable elements are significant in affecting biology both in vivo and in the laboratory, and this review will survey advances in understanding the biological role of transposons and relevant laboratory applications of these powerful molecular tools.

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Sleeping Beauty awakens

Cited by 11 publications

References 9 publications

Analysis of Genome Survey Sequences and SSR Marker Development for Siamese Mud Carp, Henicorhynchus siamensis, Using 454 Pyrosequencing

Analysis of Genome Survey Sequences and SSR Marker Development for Siamese Mud Carp, Henicorhynchus siamensis, Using 454 Pyrosequencing

Using the Cre/loxsystem for targeted integration into the human genome:loxFAS‐loxP pairing and delayed introduction of Cre DNA improve gene swapping efficiency

Jump around: transposons in and out of the laboratory

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