Pack-MULE transposable elements mediate gene evolution in plants

@article{Jiang2004PackMULETE,
  title={Pack-MULE transposable elements mediate gene evolution in plants},
  author={Ning Jiang and Zhirong Bao and Xiaoyu Zhang and Sean R. Eddy and Susan R. Wessler},
  journal={Nature},
  year={2004},
  volume={431},
  pages={569-573}
}
Mutator-like transposable elements (MULEs) are found in many eukaryotic genomes and are especially prevalent in higher plants. In maize, rice and Arabidopsis a few MULEs were shown to carry fragments of cellular genes. These chimaeric elements are called Pack-MULEs in this study. The abundance of MULEs in rice and the availability of most of the genome sequence permitted a systematic analysis of the prevalence and nature of Pack-MULEs in an entire genome. Here we report that there are over 3… 
Pack-MULEs
TLDR
This analysis using maize, rice, and Arabidopsis genomic sequences indicates that the acquisition of genic sequences by Pack-MULEs is not random and contributes to the increased number of genes with negative GC gradient in grasses.
The Functional Role of Pack-MULEs in Rice Inferred from Purifying Selection and Expression Profile[W]
TLDR
A comprehensive analysis of expression and purifying selection on 2809 Pack-MULEs in rice (Oryza sativa), which are derived from 1501 parental genes, suggests that at least a subset of these duplicates are likely functional and have great potential in regulating gene expression as well as providing novel coding capacities.
Mutator transposon in maize and MULEs in the plant genome.
Nested Insertions and Accumulation of Indels Are Negatively Correlated with Abundance of Mutator-Like Transposable Elements in Maize and Rice
TLDR
The results suggest that the amplification of retrotransposons may limit the amplified of DNA transposons but not vice versa, and more indels are detected among maize elements than rice elements whereas defects caused by point mutations are comparable between the two species.
Evolution of Mutator transposable elements across eukaryotic diversity
TLDR
This study mines MULEs from online databases, combines search results with available transposase sequences retrieved from previously published studies, and performs comprehensive bioinformatic and phylogenetic analyses to address currently available MULE diversity and reconstruct evolution for the group.
The evolutionary fate of MULE-mediated duplications of host gene fragments in rice.
TLDR
It is concluded that MULE-mediated host gene duplication results in the formation of pseudogenes, not novel functional protein-coding genes; however, the transcribed duplications possess characteristics consistent with a potential role in the regulation of host gene expression.
Transposon-mediated expansion and diversification of a family of ULP-like genes.
TLDR
A genome-wide survey of transduplication in Mutator-like elements (MULEs) in Arabidopsis thaliana shows that the phenomenon is generally similar to rice transduPLication, with one important exception: KAONASHI (KI), suggesting that the function of KI may be selfish rather than cellular.
Plant mutator-like transposable elements (MULEs): Their evolutionary dynamics, interaction with genes, and recapitulation of transposition activity in yeast
TLDR
The establishment of the MULE transposition system in yeast laid the foundation for further studying MULE biology, and revealed a critical region of the transposase, where changes of the amino acid compositions resulted in either enhanced or repressed activity.
Pack-Mutator–like transposable elements (Pack-MULEs) induce directional modification of genes through biased insertion and DNA acquisition
TLDR
It is demonstrated that Pack-Mutator–like transposable elements (Pack-MULEs) that carry gene fragments specifically acquire GC-rich fragments and preferentially insert into the 5′ end of genes, thus altering the GC content in those regions.
The widespread nature of Pack-TYPE transposons reveals their importance for plant genome evolution
TLDR
An automated annotation procedure is produced and used to successfully annotate and analyse more than 4000 new Pack-TYPE TEs in the rice and maize genomes and reports examples of the direct contribution of these TEs to coding genes, suggesting a generalised and extensive role of Pack- TYPETEs in plant genome evolution.
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