Molecular Biology of Maize Ac/Ds Elements: An Overview

Lazarow, Katina; Doll, My-Linh; Kunze, Reinhard

doi:10.1007/978-1-62703-568-2_5

Cited by 39 publications

(29 citation statements)

References 180 publications

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“…The Ds transposon can in principle accommodate extra sequences with no known length limitation (Lazarow et al, 2013). An interesting future development will be to incorporate functional units in the transposon DNA, for instance strong promoters, repressors or terminators, IRESs, recognition sites for DNA-binding proteins (LacI or TetR), recombination sites (LoxP, FRP), or coding sequences for in-frame fusion, such as GFP, protein- or membrane-binding domains, signal sequences, etc.…”

Section: Discussionmentioning

confidence: 99%

Functional mapping of yeast genomes by saturated transposition

Michel

Hatakeyama

Kimmig

et al. 2017

eLife

144

249

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Yeast is a powerful model for systems genetics. We present a versatile, time- and labor-efficient method to functionally explore the Saccharomyces cerevisiae genome using saturated transposon mutagenesis coupled to high-throughput sequencing. SAturated Transposon Analysis in Yeast (SATAY) allows one-step mapping of all genetic loci in which transposons can insert without disrupting essential functions. SATAY is particularly suited to discover loci important for growth under various conditions. SATAY (1) reveals positive and negative genetic interactions in single and multiple mutant strains, (2) can identify drug targets, (3) detects not only essential genes, but also essential protein domains, (4) generates both null and other informative alleles. In a SATAY screen for rapamycin-resistant mutants, we identify Pib2 (PhosphoInositide-Binding 2) as a master regulator of TORC1. We describe two antagonistic TORC1-activating and -inhibiting activities located on opposite ends of Pib2. Thus, SATAY allows to easily explore the yeast genome at unprecedented resolution and throughput.DOI: http://dx.doi.org/10.7554/eLife.23570.001

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Section: Discussionmentioning

confidence: 99%

Functional mapping of yeast genomes by saturated transposition

Michel

Hatakeyama

Kimmig

et al. 2017

eLife

144

249

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“…: insertion sequences (IS elements) in bacteria (reviewed in (25)), P-elements in Drosophila (reviewed in (26)), Ac/Ds elements in maize (reviewed in (27)), and PiggyBac elements from the cabbage looper moth (28–30)). Due to their mutagenic potential, DNA transposons recently have been exploited as genetic tools for various molecular biological applications (reviewed in (31–33)).…”

Section: Transposable Elements In Mammalian Genomesmentioning

confidence: 99%

The Influence of LINE-1 and SINE Retrotransposons on Mammalian Genomes

et al. 2015

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Transposable elements have had a profound impact on the structure and function of mammalian genomes. The retrotransposon Long INterspersed Element-1 (LINE-1 or L1), by virtue of its replicative mobilization mechanism, comprises ∼17% of the human genome. Although the vast majority of human LINE-1 sequences are inactive molecular fossils, an estimated 80–100 copies per individual retain the ability to mobilize by a process termed retrotransposition. Indeed, LINE-1 is the only active, autonomous retrotransposon in humans and its retrotransposition continues to generate both intra-individual and inter-individual genetic diversity. Here, we briefly review the types of transposable elements that reside in mammalian genomes. We will focus our discussion on LINE-1 retrotransposons and the non-autonomous Short INterspersed Elements (SINEs) that rely on the proteins encoded by LINE-1 for their mobilization. We review cases where LINE-1-mediated retrotransposition events have resulted in genetic disease and discuss how the characterization of these mutagenic insertions led to the identification of retrotransposition-competent LINE-1s in the human and mouse genomes. We then discuss how the integration of molecular genetic, biochemical, and modern genomic technologies have yielded insight into the mechanism of LINE-1 retrotransposition, the impact of LINE-1-mediated retrotransposition events on mammalian genomes, and the host cellular mechanisms that protect the genome from unabated LINE-1-mediated retrotransposition events. Throughout this review, we highlight unanswered questions in LINE-1 biology that provide exciting opportunities for future research. Clearly, much has been learned about LINE-1 and SINE biology since the publication of Mobile DNA II thirteen years ago. Future studies should continue to yield exciting discoveries about how these retrotransposons contribute to genetic diversity in mammalian genomes.

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“…DNA transposons are active in numerous organisms (e.g. : insertion sequences (IS elements) in bacteria (reviewed in (25)), P-elements in Drosophila (reviewed in (26)), Ac/Ds elements in maize (reviewed in (27)), and PiggyBac elements from the cabbage looper moth (28)(29)(30)). Due to their mutagenic potential, DNA transposons recently have been exploited as genetic tools for various molecular biological applications (reviewed in (31)(32)(33)).…”

Section: Dna Transposons: Abundance and Structure In The Human Genomementioning

confidence: 99%

The Influence of LINE-1 and SINE Retrotransposons on Mammalian Genomes

et al. 2015

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Transposable elements (TEs) or "jumping genes" historically have been disparaged as a class of "junk DNA" in mammalian genomes (1,2). The advent of whole genome DNA sequencing, in conjunction with molecular genetic, biochemical, and modern genomic and functional studies, is revealing that TEs are biologically important components of mammalian genomes. TEs are classified by whether they mobilize via a DNA or an RNA intermediate (detailed in (3)). Classical DNA transposons, such as the maize Activator/ Dissociation (Ac/Ds) elements originally discovered by Barbara McClintock, move via a DNA intermediate (4,5). Their mobility (i.e., transposition) can impact organismal phenotypes such as corn kernel variegation. Retrotransposons, the predominant class of TEs in most mammalian genomes, mobilize via an RNA intermediate by a process termed retrotransposition (6).The completion of the human genome reference sequence (HGR) (7, 8) confirmed the results of DNA hybridization-based re-annealing studies (9, 10) and revealed that retrotransposons have been a major force in shaping the structure and function of mammalian genomes. The mobility of non-long terminal repeat (non-LTR) retrotransposons, namely autonomously active Long INterspersed Element-1 sequences (LINE-1s, also known proteins can work efficiently in trans, it is formally possible that trans-complementation might allow the assembly of functional virus-like particles from partially defective HERVs, allowing the generation of new retrotransposition events. Advances in DNA sequencing technologies may reveal rare, active HERV-K elements or de novo germline or somatic HERV-K retrotransposition events in individual human genomes.LTR-retrotransposons are present at greater than 600,000 copies in mouse DNA and comprise approximately 10% of the genome (21). In contrast to the human genome, the mouse genome contains multiple, active ERV subfamilies (reviewed in (50, 51)). These include autonomously active Mus D and intracisternal A particle (IAP) elements, as well as non-autonomous early transposons (ETns) and mammalian apparent LTR retrotransposons (MALRs). It is estimated that ERV insertions are responsible for approximately ten percent of spontaneously arising mouse mutations (reviewed in (51)) (discussed in greater detail in other Chapters of Mobile DNA III). LINE-1 Retrotransposons: abundance and structureA brief overview of human LINE-1 evolution and nomenclature-LINE-1 retrotransposons have been amplifying in mammalian genomes for greater than 160 million years (52-54). In humans, the vast majority of LINE-1 sequences have amplified since the divergence of the ancestral mouse and human lineages approximately 65-75 million years ago (7). As a consequence, LINE-1-derived sequences now account for approximately 17% of human genomic DNA (7) (Figure 1).Sequence comparisons between individual genomic LINE-1 sequences and a consensus sequence derived from modern, active LINE-1s can be used to estimate the age of genomic LINE-1s. These analyses uncovered sixteen LINE-1 pri...

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Molecular Biology of Maize Ac/Ds Elements: An Overview

Cited by 39 publications

References 180 publications

Functional mapping of yeast genomes by saturated transposition

Functional mapping of yeast genomes by saturated transposition

The Influence of LINE-1 and SINE Retrotransposons on Mammalian Genomes

The Influence of LINE-1 and SINE Retrotransposons on Mammalian Genomes

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