An Arabidopsis hAT-like transposase is essential for plant development

Bundock, Paul; Hooykaas, Paul J. J.

doi:10.1038/nature03667

Cited by 151 publications

(144 citation statements)

References 16 publications

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“…Our results reside between two extremes, represented by human studies, which claim that more than 1000 proteins contain TE sequence (Nekrutenko and Li 2001;Britten 2006), and Drosophila melanogaster, which seems to possess very few expressed TE-gene chimeras (Lipatov et al 2005). With very few exceptions (e.g., Gotea and Makalowski, 2006;Bundock and Hooykaas 2005), the directionality of these relationships (contribution or co-option of genic regions by TEs) has not been determined. We have found only a handful of cases for which the evidence of TE contribution to a coding region is strong but expect that larger plant genomes, with correspondingly larger TE complements, contain more evidence for TE contributions to coding regions.…”

Section: Implications Of the Methods And Resultsmentioning

confidence: 99%

“…While it is clear that TEs can capture gene fragments, there are few direct examples that TE sequences have contributed to functional plant genes. One exception is the domestication of a hAT-like transposase by the DAYSLEEPER gene in Arabidopsis (Bundock and Hooykaas 2005), but the genome-wide extent of TE incorporation into functional genes remains unknown.…”

Section: Introductionmentioning

confidence: 99%

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The Contribution of Transposable Elements to Expressed Coding Sequence in Arabidopsis thaliana

Lockton

Gaut

2009

J Mol Evol

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The goal of this study was to assess the extent to which transposable elements (TEs) have contributed to protein-coding regions in Arabidopsis thaliana. To do this, we first characterized the extent of chimeric TE-gene constructs. We compared a genome-wide TE database to genomic sequences, annotated coding regions, and EST data. The comparison revealed that 7.8% of expressed genes contained a region with close similarity to a known TE sequence. Some groups of TEs, such as helitrons, were underrepresented in exons relative to their genome-wide distribution; in contrast, Copia-like and En/Spm-like sequences were overrepresented in exons. These 7.8% percent of genes were enriched for some GO-based functions, particularly kinase activity, and lacking in other functions, notably structural molecule activity. We also examined gene family evolution for these genes. Gene family information helped clarify whether the sequence similarity between TE and gene was due to a TE contributing to the gene or, instead, the TE co-opting a portion of the gene. Most (66%) of these genes were not easily assigned to a gene family, and for these we could not infer the direction of the relationship between TE and gene. For the remainder, where appropriate, we built phylogenetic trees to infer the direction of the TE-gene relationship by parsimony. By this method, we verified examples where TEs contributed to expressed proteins. Our results are undoubtedly conservative but suggest that TEs may have contributed small protein segments to as many as 1.2% of all expressed, annotated A. thaliana genes.

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Section: Implications Of the Methods And Resultsmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

The Contribution of Transposable Elements to Expressed Coding Sequence in Arabidopsis thaliana

Lockton

Gaut

2009

J Mol Evol

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“…Hence, any TEs observed in a grass genome must have been active in the last 5-10 million years, or much more recently, or they would no longer be detectable. It seems likely that regions composed mostly of degenerated fragments of LTR retrotransposons and other TEs, are responsible for most of the 'unannotated' DNA in a genome, although many TE fragments have evolved host-beneficial roles (Hudson et al, 2003;Bundock and Hooykaas, 2005), especially in gene regulation (White et al, 1994;Michaels et al, 2003;Lisch and Bennetzen, 2011).…”

Section: Introductionmentioning

confidence: 99%

The dynamics of LTR retrotransposon accumulation across 25 million years of panicoid grass evolution

2013

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Sample sequence analysis was employed to investigate the repetitive DNAs that were most responsible for the evolved variation in genome content across seven panicoid grasses with 45-fold variation in genome size and different histories of polyploidy. In all cases, the most abundant repeats were LTR retrotransposons, but the particular families that had become dominant were found to be different in the Pennisetum, Saccharum, Sorghum and Zea lineages. One element family, Huck, has been very active in all of the studied species over the last few million years. This suggests the transmittal of an active or quiescent autonomous set of Huck elements to this lineage at the founding of the panicoids. Similarly, independent recent activity of Ji and Opie elements in Zea and of Leviathan elements in Sorghum and Saccharum species suggests that members of these families with exceptional activation potential were present in the genome(s) of the founders of these lineages. In a detailed analysis of the Zea lineage, the combined action of several families of LTR retrotransposons were observed to have approximately doubled the genome size of Zea luxurians relative to Zea mays and Zea diploperennis in just the last few million years. One of the LTR retrotransposon amplification bursts in Zea may have been initiated by polyploidy, but the great majority of transposable element activations are not. Instead, the results suggest random activation of a few or many LTR retrotransposons families in particular lineages over evolutionary time, with some families especially prone to future activation and hyper-amplification.

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“…A much less understood, yet ostensibly recurrent, source of genetic innovation is the recycling of coding material from selfish mobile genetic elements (4)(5)(6)(7)(8)(9). Mobile or transposable elements are ''jumping genes,'' pieces of DNA that can move and replicate within the genomes of virtually all living organisms (10).…”

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confidence: 99%

Birth of a chimeric primate gene by capture of the transposase gene from a mobile element

Cordaux

Udit

Batzer

et al. 2006

Proc. Natl. Acad. Sci. U.S.A.

226

264

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The emergence of new genes and functions is of central importance to the evolution of species. The contribution of various types of duplications to genetic innovation has been extensively investigated. Less understood is the creation of new genes by recycling of coding material from selfish mobile genetic elements. To investigate this process, we reconstructed the evolutionary history of SETMAR, a new primate chimeric gene resulting from fusion of a SET histone methyltransferase gene to the transposase gene of a mobile element. We show that the transposase gene was recruited as part of SETMAR 40 -58 million years ago, after the insertion of an Hsmar1 transposon downstream of a preexisting SET gene, followed by the de novo exonization of previously noncoding sequence and the creation of a new intron. The original structure of the fusion gene is conserved in all anthropoid lineages, but only the N-terminal half of the transposase is evolving under strong purifying selection. In vitro assays show that this region contains a DNA-binding domain that has preserved its ancestral binding specificity for a 19-bp motif located within the terminal-inverted repeats of Hsmar1 transposons and their derivatives. The presence of these transposons in the human genome constitutes a potential reservoir of Ϸ1,500 perfect or nearly perfect SETMAR-binding sites. Our results not only provide insight into the conditions required for a successful gene fusion, but they also suggest a mechanism by which the circuitry underlying complex regulatory networks may be rapidly established.transposable elements ͉ gene fusion ͉ molecular domestication ͉ DNA binding ͉ regulatory network

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An Arabidopsis hAT-like transposase is essential for plant development

Cited by 151 publications

References 16 publications

The Contribution of Transposable Elements to Expressed Coding Sequence in Arabidopsis thaliana

The Contribution of Transposable Elements to Expressed Coding Sequence in Arabidopsis thaliana

The dynamics of LTR retrotransposon accumulation across 25 million years of panicoid grass evolution

Birth of a chimeric primate gene by capture of the transposase gene from a mobile element

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