Gene duplication and exon shuffling by helitron-like transposons generate intraspecies diversity in maize

Morgante, Michèle; Brunner, Stephan; Pea, G.; Fengler, Kevin; Zuccolo, Andrea; Rafalski, Antoni

doi:10.1038/ng1615

Cited by 469 publications

(462 citation statements)

References 30 publications

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“…TEs also capture and shuffle gene fragments (Jiang et al 2004;Brunner et al 2005;Lai et al 2005). Maize helitrons, for example, capture and move gene fragments to the extent that *20% of genes (or gene fragments) differ in location between two maize lines (Lai et al 2005;Morgante et al 2005). Additionally, in A. thaliana, helitrons proliferated after the acquisition of exon fragments (Hollister and Gaut 2007).…”

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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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: 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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“…This suggests that the host gene was destroyed during the acquisition process. In contrast, Morgante et al (2005) demonstrate that the wild type progenitor of four different gene fragments captured by a Helitron exist in the maize genome. These investiga- tors speculate that Helitron transposition involves replication and strand replacement that preserves the integrity of the donor host sequence.…”

Section: The Mechanism By Which Helitrons Capture and Mobilize Gene Smentioning

confidence: 94%

“…Like other transposable elements, the conserved terminal ends of these non-autonomous Helitrons suggest that their movement may be mediated by the transposition protein provided in trans by a master or autonomous member of the family. Searches for candidate autonomous Helitrons have identified several instances in which sequences bearing similarity to DNA helicases are localized in close proximity to Replication protein A, a characteristic of the proposed autonomous Helitron (Gupta et al 2005;Morgante et al 2005). However, the presence of premature in-frame stop-codons or large insertions shows that the isolated sequences represent inactive elements.…”

Section: Isolated Maize Helitrons Represent a Sub-class Of Helitronsmentioning

confidence: 99%

“…For example, it was proposed that transposition is initiated at the 5' end of the element and the inefficient recognition of the 3' palindrome sequence as a termination signal by the transposition machinery results in the capture of 3' flanking host sequences (Feschotte and Wessler 2001). The strong conservation of the 3' end and not the 5' end of a family of nonautonomous Helitrons led Morgante et al (2005) to propose that transposition is initiated at the 3' end of the Helitrons and the capture of 5' host flanking sequence occurs during transposition via an unknown mechanism. Kapitinov and Jurka (2007) have proposed that gene piece incorporation occurs through double stranded breaks within the transposing Helitron and the random incorporation of "filler" DNA coming from the host genome.…”

Section: The Mechanism By Which Helitrons Capture and Mobilize Gene Smentioning

confidence: 99%

“…This accounted for the haplotype variability at the bz locus between these two inbred lines. In a parallel study, the extent of lack of gene colinearity between inbred lines B73 and Mo17 was investigated by using oligonucleotide probes (Morgante, Brunner, Pea, Fengler, Zuccolo, Rafalski 2005). Here, 20% of the detected 20,656 genes were found in only one of the inbred lines.…”

Section: Introduction and Overview Of Helitronsmentioning

confidence: 99%

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Helitrons: Their Impact on Maize Genome Evolution and Diversity

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Abstract.Gene movement by the newly-described Helitron family of transposable elements apparently has significantly impacted the evolution of this genome and has contributed to the lack of intra-specific gene collinearity between different maize inbred lines. The abundance of these elements and the extent of diversity among them remain largely undetermined. Several hypotheses have been proposed to explain their transposition and mechanism by which these elements prolifically capture and mobilize gene sequences, but each lacks supporting experimental evidence. A more complete understanding of this process requires molecular and genetic evidence of Helitron activity in modern maize genome. Establishment of in vivo and in vitro systems to assay transposition activity would also aid our understanding of this new class of transposable elements.

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Gene Fusion

Williford¹,

Betrán²

2013

Encyclopedia of Life Sciences

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Gene fusion is a process by which the complete or partial sequences of two or more distinct genes are fused into a single chimeric gene or transcript, as a result of deoxyribonucleic acid ‐ or ribonucleic acid ‐derived rearrangements. This phenomenon is widespread and has been observed across all domains of life. Comparative genomics studies reveal high and persistent incidence of gene fusions and identify lineage‐specific factors that promote or hinder the formation of chimeric genes. Studies of recent gene fusions expose the mechanisms of their origin and the diversity of functional changes that accompany their formation. Gene fusions prominently contribute to evolutionary change by providing a continuous source of new genes. Gene duplications often precede gene fusions, permitting the evolution of chimeric genes, but at the same time preserving the original functions. Despite the reputation of gene fusions as drivers of adaptive evolution, gene fusions can have devastating consequences, often leading to genomic disorders or cancer. Key Concepts: Gene fusions form through DNA‐derived rearrangements or through transcription‐mediated mechanisms (novel cis ‐ or trans ‐splicing). Gene or domain duplications often precede gene fusions preserving the original functions of parental genes and therefore facilitating the evolution of new functions by chimeric gene products. Young gene fusions (polymorphic or recently fixed) retain molecular signatures of their formations revealing the mechanisms of origin. The formation of chimeric genes generally involves two steps: juxtaposition of the sequences involved in fusion and subsequent mutations that generate a single chimeric transcriptional unit under the control of a single regulatory system. Various replicative (i.e. replication related) and nonreplicative mechanisms of DNA break repair can result in gene duplication and gene movement. Transposable elements greatly facilitate gene fusions by (1) mediating gene duplication and gene movements, (2) providing the source of reverse transcriptase required for retropositions and (3) directly participating in gene fusions. Gene fusion often generates a novel product with functional capabilities distinct from those of its parental genes, ensuring frequent contribution of chimeric genes to adaptive evolution. Gene fusions in the germline can lead to genomic disorders, whereas gene fusions in somatic cells are associated with many different cancers, frequently as mutations that initiate tumourigenesis.

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Gene duplication and exon shuffling by helitron-like transposons generate intraspecies diversity in maize

Cited by 469 publications

References 30 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

Helitrons: Their Impact on Maize Genome Evolution and Diversity

Gene Fusion

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