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  • 1
    Online Resource
    Online Resource
    Cold Spring Harbor Laboratory ; 2006
    In:  Genome Research Vol. 16, No. 4 ( 2006-04), p. 550-556
    In: Genome Research, Cold Spring Harbor Laboratory, Vol. 16, No. 4 ( 2006-04), p. 550-556
    Abstract: Modern molecular biology has brought many new tools to the geneticist as well as an exponentially expanding database of genomes and new genes for study. Of particular use in the analysis of these genes is the synthetic gene, a nucleotide sequence designed to the specifications of the investigator. Typically, synthetic genes encode the same product as the gene of interest, but the synthetic nucleotide sequence for that protein may contain modifications affecting expression or base composition. Other desirable changes typically involve the revision of restriction sites. Designing synthetic genes by hand is a time-consuming and error-prone process that may involve several computer programs. We have developed a tools environment that combines many modules to provide a platform for rapid synthetic gene design for multikilobase sequences. We have used GeneDesign to successfully design a synthetic Ty1 element and a large variety of other synthetic sequences. GeneDesign has been implemented as a publicly accessible Web-based resource and can be found at http://slam.bs.jhmi.edu/gd.
    Type of Medium: Online Resource
    ISSN: 1088-9051
    RVK:
    Language: English
    Publisher: Cold Spring Harbor Laboratory
    Publication Date: 2006
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    SSG: 12
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  • 2
    Online Resource
    Online Resource
    Cold Spring Harbor Laboratory ; 2012
    In:  Genome Research Vol. 22, No. 4 ( 2012-04), p. 693-703
    In: Genome Research, Cold Spring Harbor Laboratory, Vol. 22, No. 4 ( 2012-04), p. 693-703
    Abstract: The Saccharomyces cerevisiae genome contains about 35 copies of dispersed retrotransposons called Ty1 elements. Ty1 elements target regions upstream of tRNA genes and other Pol III-transcribed genes when retrotransposing to new sites. We used deep sequencing of Ty1-flanking sequence amplicons to characterize Ty1 integration. Surprisingly, some insertions were found in mitochondrial DNA sequences, presumably reflecting insertion into mitochondrial DNA segments that had migrated to the nucleus. The overwhelming majority of insertions were associated with the 5′ regions of Pol III transcribed genes; alignment of Ty1 insertion sites revealed a strong sequence motif centered on but extending beyond the target site duplication. A strong sequence-independent preference for nucleosomal integration sites was observed, in distinction to the preferences of the Hermes DNA transposon engineered to jump in yeast and the Tf1 retrotransposon of Schizosaccharomyces pombe , both of which prefer nucleosome free regions. Remarkably, an exquisitely specific relationship between Ty1 integration and nucleosomal position was revealed by alignment of hotspot Ty1 insertion position regions to peak nucleosome positions, geographically implicating nucleosomal DNA segments at specific positions on the nucleosome lateral surface as targets, near the “bottom” of the nucleosome. The specificity is observed in the three tRNA 5′-proximal nucleosomes, with insertion frequency dropping off sharply 5′ of the tRNA gene. The sites are disposed asymmetrically on the nucleosome relative to its dyad axis, ruling out several simple molecular models for Ty1 targeting, and instead suggesting association with a dynamic or directional process such as nucleosome remodeling associated with these regions.
    Type of Medium: Online Resource
    ISSN: 1088-9051
    RVK:
    Language: English
    Publisher: Cold Spring Harbor Laboratory
    Publication Date: 2012
    detail.hit.zdb_id: 1483456-X
    SSG: 12
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  • 3
    Online Resource
    Online Resource
    Proceedings of the National Academy of Sciences ; 2013
    In:  Proceedings of the National Academy of Sciences Vol. 110, No. 29 ( 2013-07-16)
    In: Proceedings of the National Academy of Sciences, Proceedings of the National Academy of Sciences, Vol. 110, No. 29 ( 2013-07-16)
    Abstract: A codon-optimized mouse LINE-1 element, ORFeus , exhibits dramatically higher retrotransposition frequencies compared with its native long interspersed element 1 counterpart. To establish a retrotransposon-mediated mouse model with regulatable and potent mutagenic capabilities, we generated a tetracycline (tet)-regulated ORFeus element harboring a gene-trap cassette. Here, we show that mice expressing tet- ORFeus broadly exhibit robust retrotransposition in somatic tissues when treated with doxycycline. Consistent with a significant mutagenic burden, we observed a reduced number of double transgenic animals when treated with high-level doxycycline during embryogenesis. Transgene induction in skin resulted in a white spotting phenotype due to somatic ORFeus -mediated mutations that likely disrupt melanocyte development. The data suggest a high level of transposition in melanocyte precursors and consequent mutation of genes important for melanoblast proliferation, differentiation, or migration. These findings reveal the utility of a retrotransposon-based mutagenesis system as an alternative to existing DNA transposon systems. Moreover, breeding these mice to different tet-transactivator/reversible tet-transactivator lines supports broad functionality of tet- ORFeus because of the potential for dose-dependent, tissue-specific, and temporal-specific mutagenesis.
    Type of Medium: Online Resource
    ISSN: 0027-8424 , 1091-6490
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    Language: English
    Publisher: Proceedings of the National Academy of Sciences
    Publication Date: 2013
    detail.hit.zdb_id: 209104-5
    detail.hit.zdb_id: 1461794-8
    SSG: 11
    SSG: 12
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  • 4
    Online Resource
    Online Resource
    Cold Spring Harbor Laboratory ; 2005
    In:  Genome Research Vol. 15, No. 8 ( 2005-08), p. 1073-1078
    In: Genome Research, Cold Spring Harbor Laboratory, Vol. 15, No. 8 ( 2005-08), p. 1073-1078
    Abstract: The L1 retrotransposon is the most highly successful autonomous retrotransposon in mammals. This prolific genome parasite may on occasion benefit its host through genome rearrangements or adjustments of host gene expression. In examining possible effects of L1 elements on host gene expression, we investigated whether a full-length L1 element inserted in the antisense orientation into an intron of a cellular gene may actually split the gene's transcript into two smaller transcripts: (1) a transcript containing the upstream exons and terminating in the major antisense polyadenylation site (MAPS) of the L1, and (2) a transcript derived from the L1 antisense promoter (ASP) that includes the downstream exons of the gene. Bioinformatic analysis and experimental follow-up provide evidence for this L1 “gene-breaking” hypothesis. We identified three human genes apparently “broken” by L1 elements, as well as 12 more candidate genes. Most of the inserted L1 elements in our 15 candidate genes predate the human/chimp divergence. If indeed split, the transcripts of these genes may in at least one case encode potentially interacting proteins, and in another case may encode novel proteins. Gene-breaking represents a new mechanism through which L1 elements remodel mammalian genomes.
    Type of Medium: Online Resource
    ISSN: 1088-9051
    RVK:
    Language: English
    Publisher: Cold Spring Harbor Laboratory
    Publication Date: 2005
    detail.hit.zdb_id: 1483456-X
    SSG: 12
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  • 5
    In: Cell, Elsevier BV, Vol. 141, No. 7 ( 2010-06), p. 1171-1182
    Type of Medium: Online Resource
    ISSN: 0092-8674
    RVK:
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    Language: English
    Publisher: Elsevier BV
    Publication Date: 2010
    detail.hit.zdb_id: 187009-9
    detail.hit.zdb_id: 2001951-8
    SSG: 12
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  • 6
    Online Resource
    Online Resource
    Royal Society of Chemistry (RSC) ; 2008
    In:  Molecular BioSystems Vol. 4, No. 7 ( 2008), p. 726-
    In: Molecular BioSystems, Royal Society of Chemistry (RSC), Vol. 4, No. 7 ( 2008), p. 726-
    Type of Medium: Online Resource
    ISSN: 1742-206X , 1742-2051
    Language: English
    Publisher: Royal Society of Chemistry (RSC)
    Publication Date: 2008
    detail.hit.zdb_id: 2188635-0
    SSG: 12
    SSG: 15,3
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  • 7
    Online Resource
    Online Resource
    Proceedings of the National Academy of Sciences ; 2006
    In:  Proceedings of the National Academy of Sciences Vol. 103, No. 47 ( 2006-11-21), p. 17632-17637
    In: Proceedings of the National Academy of Sciences, Proceedings of the National Academy of Sciences, Vol. 103, No. 47 ( 2006-11-21), p. 17632-17637
    Abstract: Mobile elements are important components of our genomes, with diverse and significant effects on phenotype. Not only can transposons inactivate genes by direct disruption and shuffle the genome through recombination, they can also alter gene expression subtly or powerfully. Currently active transposons are highly polymorphic in host populations, including, among hundreds of others, L1 and Alu elements in humans and Ty1 elements in yeast. For this reason, we wished to develop a simple genome-wide method for identifying all transposons in any given sample. We have designed a transposon insertion site profiling chip (TIP-chip), a microarray intended for use as a high-throughput technique for mapping transposon insertions. By selectively amplifying transposon flanking regions and hybridizing them to the array, we can locate all transposons present in a sample. We have tested the TIP-chip extensively to map Ty1 retrotransposon insertions in yeast and have achieved excellent results in two laboratory strains as well as in evolved Ty1 high-copy strains. We are able to identify all of the theoretically detectable transposons in the FY2 lab strain, with essentially no false positives. In addition, we mapped many new transposon copies in the high-copy Ty1 strain and determined its Ty1 insertion pattern.
    Type of Medium: Online Resource
    ISSN: 0027-8424 , 1091-6490
    RVK:
    RVK:
    Language: English
    Publisher: Proceedings of the National Academy of Sciences
    Publication Date: 2006
    detail.hit.zdb_id: 209104-5
    detail.hit.zdb_id: 1461794-8
    SSG: 11
    SSG: 12
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  • 8
    Online Resource
    Online Resource
    Proceedings of the National Academy of Sciences ; 2006
    In:  Proceedings of the National Academy of Sciences Vol. 103, No. 49 ( 2006-12-05), p. 18662-18667
    In: Proceedings of the National Academy of Sciences, Proceedings of the National Academy of Sciences, Vol. 103, No. 49 ( 2006-12-05), p. 18662-18667
    Abstract: Long interspersed element type 1 (L1) retrotransposons are ubiquitous mammalian mobile elements and potential tools for in vivo mutagenesis; however, native L1 elements are relatively inactive in mice when introduced as transgenes. We have previously described a synthetic L1 element, ORFeus , containing two synonymously recoded ORFs relative to mouse L1. It is significantly more active for retrotransposition in cell culture than all native L1 elements tested. To study its activity in vivo , we developed a transgenic mouse model in which ORFeus expression was controlled by a constitutive heterologous promoter, and we established definitive evidence for ORFeus retrotransposition activity both in germ line and somatic tissues. Germ line retrotransposition frequencies resulting in 0.33 insertions per animal are seen among progeny of ORFeus donor element heterozygotes derived from a single founder, representing a 〉 20-fold increase over native L1 elements. We observe somatic transposition events in 100% of the ORFeus donor-containing animals, and an average of 17 different insertions are easily recovered from each animal; modeling suggests that the number of somatic insertions per animal exceeds this number by perhaps several orders of magnitude. Nearly 200 insertions were precisely mapped, and their distribution in the mouse genome appears random relative to transcription units and guanine-cytosine content. The results suggest that ORFeus may be developed into useful tools for in vivo mutagenesis.
    Type of Medium: Online Resource
    ISSN: 0027-8424 , 1091-6490
    RVK:
    RVK:
    Language: English
    Publisher: Proceedings of the National Academy of Sciences
    Publication Date: 2006
    detail.hit.zdb_id: 209104-5
    detail.hit.zdb_id: 1461794-8
    SSG: 11
    SSG: 12
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  • 9
    In: Proceedings of the National Academy of Sciences, Proceedings of the National Academy of Sciences, Vol. 109, No. 21 ( 2012-05-22)
    Abstract: The role of Ncoa2 in regulating glucose metabolism may play a role in its antitumorigenic activity. Mice lacking Ncoa2 develop glycogen storage disease type 1 (Von Gierke’s disease) and exhibit decreased activity of G6pase. Similarly, a genetic deficiency of G6PC leads to Von Gierke’s disease in humans and in mice. Patients who have Von Gierke’s disease and G6Pase −/− mice develop liver adenomas and are at high risk of progression to HCC. Moreover, inhibition of hexokinase, which has the same functional effect as increasing G6Pase activity, is antitumorigenic. Based on these findings, loss of Ncoa2 may promote liver tumorigenesis at least in part through a subsequent reduction in G6Pase activity, which would be expected to increase glycolytic flux by increasing levels of glucose-6-phosphate. Thus, reduction of Ncoa2 and G6Pase may contribute to the metabolic reprogramming of cancer cells and fuel tumor growth. However, Ncoa2 loss of function also leads to broader dysregulation of gene expression in liver ( 5 ), including the altered expression of genes involved in signal transduction and cell death. Therefore, Ncoa2 likely functions as a tumor suppressor by controlling the activity of multiple pathways and targets relevant to hepatocarcinogenesis. Future studies will focus on the detailed mechanistic dissection of NCOA2-mediated tumor suppression. Among the genes identified in our screen, Ncoa2 was of particular interest. Ncoa2 is a member of the p160 family of transcriptional coactivators that activates expression of Glucose 6 phosphatase ( G6Pase ) and other important genes by acting in concert with nuclear receptors such as RORα. G6Pase is a rate-limiting enzyme that dephosphorylates glucose-6-phosphate, the initial substrate for glycolysis. Analysis of gene-expression data from human HCC revealed that low expression of NCOA2 and its target G6PC are associated with poor patient survival. Furthermore, we documented that genetic ablation of Ncoa2/Src-2 in mice promotes liver tumorigenesis in a carcinogen-induced hepatocarcinogenesis model. These findings establish a tumor-suppressor role for Ncoa2 in HCC and demonstrate that transposon-mediated mutagenesis screens in mice can identify clinically relevant genes that participate in the pathogenesis of human cancer. We next validated that the genes identified in the SB screen contribute to tumor initiation and/or progression using in vitro and in vivo cancer model systems. First, we used liver progenitor cells that form tumors only after sustaining additional genetic alterations. Candidate gene function was inhibited using shRNAs, and cells were transplanted into recipient mice to assess tumor-forming potential. These experiments validated the tumor-suppressor activity of several genes, including Nuclear receptor coactivator 2 ( Ncoa2/Src-2 ), Zinc finger transcription factor ( Zfx ) , and Beta-Dystrobrevin ( Dtnb ). Next, we compared our SB hit list with an expression-profiling dataset from a large cohort of human liver tumors to determine the relevance of the CISs to human liver cancer pathogenesis. We found that several of the genes identified in our screen exhibit dysregulated expression in human hepatocellular carcinoma (HCC). In this study, we sought to identify genes that, when mutated, contribute to accelerated liver tumor development ( Fig. P1 ). Specifically, a screening approach was designed to recover mutations that cooperate with MYC , one of the most commonly dysregulated genes in human malignancy. We bred mice containing an active SB transposon to mice that develop MYC-induced liver cancer. A cohort of mice containing the SB transposon, a transposase, and the MYC oncogene expressed specifically in liver cells was generated. Control mice expressed MYC but lacked an active SB transposon. A significantly higher percentage of animals harboring the active SB element developed liver tumors compared with controls. We used high-throughput sequencing to characterize transposon insertion sites in tumors and to identify regions of the genome that harbored insertions at a statistically significantly greater frequency than expected by chance. These common insertion sites (CISs) mark genes that are likely to accelerate tumorigenesis when their functions are altered. This approach identified at least 16 genes/loci that contribute to liver tumor development. Emerging data from cancer genome-sequencing studies have demonstrated that human tumors exhibit tremendous complexity and heterogeneity in the number and nature of identified mutations ( 1 ). Based on these findings, there is an increasing need for in vivo validation of genes whose altered function contributes to cancer pathogenesis. Transposons are DNA sequences that can insert themselves into new locations within the genome and thereby serve as powerful mutagens. Sleeping Beauty ( SB ), a member of the Tc1/mariner superfamily of DNA transposons, is highly active in mammalian cells ( 2 ). A growing body of evidence has revealed that the SB system is an efficient tool for cancer gene discovery ( 3 , 4 ). We have performed a forward genetic screen using the SB system to identify genes that accelerate liver tumorigenesis in mice. Our findings reveal genes and pathways that participate in tumorigenesis and therefore may provide targets for liver cancer therapy.
    Type of Medium: Online Resource
    ISSN: 0027-8424 , 1091-6490
    RVK:
    RVK:
    Language: English
    Publisher: Proceedings of the National Academy of Sciences
    Publication Date: 2012
    detail.hit.zdb_id: 209104-5
    detail.hit.zdb_id: 1461794-8
    SSG: 11
    SSG: 12
    Location Call Number Limitation Availability
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