Impact of ploidy level on the distribution of Pokey element insertions in the Daphnia pulex complex

Vergilino, Roland; Eagle, Shannon H. C.; Crease, Teresa J.

doi:10.1186/1759-8753-5-1

Cited by 13 publications

(34 citation statements)

References 95 publications

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“…buzzatii ( Fig 6A ). Thus, the maternal cytoplasm could indeed be less efficient in silencing Helena expression and might cause the extensive presence of Helena transcripts noted in F1 and BC1 ovaries of young females ( Fig 5 ) [ 51 ]. Interestingly, there was an atypical Helena expression pattern including ovary follicular cells in F1 hybrids.…”

Section: Discussionmentioning

confidence: 99%

Expression of the Retrotransposon Helena Reveals a Complex Pattern of TE Deregulation in Drosophila Hybrids

Romero‐Soriano

Guerreiro

2016

PLoS ONE

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Transposable elements (TEs), repeated mobile sequences, are ubiquitous in the eukaryotic kingdom. Their mobilizing capacity confers on them a high mutagenic potential, which must be strongly regulated to guarantee genome stability. In the Drosophila germline, a small RNA-mediated silencing system, the piRNA (Piwi-interacting RNA) pathway, is the main responsible TE regulating mechanism, but some stressful conditions can destabilize it. For instance, during interspecific hybridization, genomic stress caused by the shock of two different genomes can lead, in both animals and plants, to higher transposition rates. A recent study in D. buzatii—D. koepferae hybrids detected mobilization of 28 TEs, yet little is known about the molecular mechanisms explaining this transposition release. We have characterized one of the mobilized TEs, the retrotransposon Helena, and used quantitative expression to assess whether its high transposition rates in hybrids are preceded by increased expression. We have also localized Helena expression in the gonads to see if cellular expression patterns have changed in the hybrids. To give more insight into changes in TE regulation in hybrids, we analysed Helena-specific piRNA populations of hybrids and parental species. Helena expression is not globally altered in somatic tissues, but male and female gonads have different patterns of deregulation. In testes, Helena is repressed in F1, increasing then its expression up to parental values. This is linked with a mislocation of Helena transcripts along with an increase of their specific piRNA levels. Ovaries have additive levels of Helena expression, but the ping-pong cycle efficiency seems to be reduced in F1 hybrids. This could be at the origin of new Helena insertions in hybrids, which would be transmitted to F1 hybrid female progeny.

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Section: Discussionmentioning

confidence: 99%

Expression of the Retrotransposon Helena Reveals a Complex Pattern of TE Deregulation in Drosophila Hybrids

Romero‐Soriano

Guerreiro

2016

PLoS ONE

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“…Meganucleases, and their associated introns and inteins, are encoded within phage, prokaryotes and single-cell eukaryotes. They recognize long DNA target sites ( 7 ): meganucleases from the LAGLIDADG protein family (reviewed in ( 8 )) typically recognize and cleave DNA targets spanning 20–22 base pairs in length. The length of their targets provides sufficient specificity to avoid toxicity to their host organism, while their ability to tolerate polymorphisms within those targets allows them to remain active when encountering genetic drift within their host genes ( 9 ).…”

mentioning

confidence: 99%

“…A recent analysis has demonstrated that even when maintaining up to 50% amino acid sequence identity and very close structural similarity, homologous wild-type meganucleases can recognize and cleave highly diverged DNA targets ( 10 ). The ability of these endonucleases to readily adopt new DNA target specificities, with minimal resculpting of their overall folded topology and structure, may reflect their biological function as the enzymatic drivers of intron mobility, transfer and persistence (reviewed in ( 7 )).…”

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confidence: 99%

Crystallographic analyses illustrate significant plasticity and efficient recoding of meganuclease target specificity

Werther¹,

Hallinan²,

Lambert³

et al. 2017

Nucleic Acids Research

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The retargeting of protein–DNA specificity, outside of extremely modular DNA binding proteins such as TAL effectors, has generally proved to be quite challenging. Here, we describe structural analyses of five different extensively retargeted variants of a single homing endonuclease, that have been shown to function efficiently in ex vivo and in vivo applications. The redesigned proteins harbor mutations at up to 53 residues (18%) of their amino acid sequence, primarily distributed across the DNA binding surface, making them among the most significantly reengineered ligand-binding proteins to date. Specificity is derived from the combined contributions of DNA-contacting residues and of neighboring residues that influence local structural organization. Changes in specificity are facilitated by the ability of all those residues to readily exchange both form and function. The fidelity of recognition is not precisely correlated with the fraction or total number of residues in the protein–DNA interface that are actually involved in DNA contacts, including directional hydrogen bonds. The plasticity of the DNA-recognition surface of this protein, which allows substantial retargeting of recognition specificity without requiring significant alteration of the surrounding protein architecture, reflects the ability of the corresponding genetic elements to maintain mobility and persistence in the face of genetic drift within potential host target sites.

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“…Homing endonucleases, also termed ‘meganucleases’, are highly specific DNA cleaving enzymes, encoded by mobile open reading frames, that are present within all microbial life as well as in mitochondria and chloroplasts (Stoddard, 2014). Meganuclease genes are mobilized as a result of the DNA cleavage activity of their gene products.…”

Section: Introductionmentioning

confidence: 99%

Indirect DNA Sequence Recognition and Its Impact on Nuclease Cleavage Activity

et al. 2016

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Summary LAGLIDADG meganucleases are DNA cleaving enzymes used for genome engineering. While their cleavage specificity can be altered using several protein engineering and selection strategies, their overall ‘targetability’ is limited by highly specific indirect recognition of the central four basepairs within their recognition sites. In order to examine the physical basis of indirect sequence recognition and to expand the number of such nucleases available for genome engineering, we have determined the target sites, DNA-bound structures and ‘central four’ cleavage fidelities of 9 related enzymes. Subsequent crystallographic analyses of a meganuclease bound to two noncleavable target sites, each containing a single inactivating basepair substitution at its center, indicates that a localized slip of the mutated basepair causes a small change in the DNA backbone conformation that results in a loss of metal occupancy at one binding site, eliminating cleavage activity.

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Impact of ploidy level on the distribution of Pokey element insertions in the Daphnia pulex complex

Cited by 13 publications

References 95 publications

Expression of the Retrotransposon Helena Reveals a Complex Pattern of TE Deregulation in Drosophila Hybrids

Expression of the Retrotransposon Helena Reveals a Complex Pattern of TE Deregulation in Drosophila Hybrids

Crystallographic analyses illustrate significant plasticity and efficient recoding of meganuclease target specificity

Indirect DNA Sequence Recognition and Its Impact on Nuclease Cleavage Activity

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