The<i>hAT</i>and CACTA Superfamilies of Plant Transposons

Kunze, Reinhard; Weil, Clifford F.

doi:10.1128/9781555817954.ch24

Cited by 104 publications

(104 citation statements)

References 369 publications

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“…TEs in the En/Spm superfamily are known to preferentially insert into hypomethylated gene-rich regions of plant genomes (Kunze and Weil 2002), to the extent that they are used as plant mutagens (T-DNA) (Wisman et al 1998;Krysan et al 1999). Another surprising result is the significant overrepresentation of copia-like LTR retrotransposons in the putative chimeric gene dataset compared to our whole TE database.…”

Section: Exon Sequences Containing Te-related Fragmentsmentioning

confidence: 88%

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: Exon Sequences Containing Te-related Fragmentsmentioning

confidence: 88%

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

Lockton

Gaut

2009

J Mol Evol

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“…Yet, only four autonomous (self-transposing) maize transposons have been isolated and sequenced to date: Activator (Ac) (Fedoroff et al, 1983;Muller-Neumann et al, 1984;Pohlman et al, 1984) and the related Bergamo (Hartings et al, 1991), suppressor-Mutator/Enhancer (Pereira et al, 1986;Masson et al, 1987), and Mutator-Don Robertson (MuDR) (Chomet et al, 1991;Qin et al, 1991). Ac, suppressor-Mutator, and MuDR are founding members of the hAT, CACTA, and Mutator transposon superfamilies, respectively (Kunze and Weil, 2002;Walbot and Rudenko, 2002). Not surprisingly, these are the maize transposon sequences used in the homology scans of the rice and Arabidopsis genomes.…”

Section: Introductionmentioning

confidence: 99%

Jittery, a Mutator Distant Relative with a Paradoxical Mobile Behavior: Excision without Reinsertion

Yan

Maurais

et al. 2004

Plant Cell

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The unstable mutation bz-m039 arose in a maize (Zea mays) stock that originated from a plant infected with barley stripe mosaic virus. The instability of the mutation is caused by a 3.9-kb mobile element that has been named Jittery (Jit). Jit has terminal inverted repeats (TIRs) of 181 bp, causes a 9-bp direct duplication of the target site, and appears to excise autonomously. It is predicted to encode a single 709-amino acid protein, JITA, which is distantly related to the MURA transposase protein of the Mutator system but is more closely related to the MURA protein of Mutator-like elements (MULEs) from Arabidopsis thaliana and rice (Oryza sativa). Like MULEs, Jit resembles Mutator in the length of the element's TIRs, the size of the target site duplication, and in the makeup of its transposase but differs from the autonomous element Mutator-Don Robertson in that it encodes a single protein. Jit also differs from Mutator elements in the high frequency with which it excises to produce germinal revertants and in its copy number in the maize genome: Jit-like TIRs are present at low copy number in all maize lines and teosinte accessions examined, and JITA sequences occur in only a few maize inbreds. However, Jit cannot be considered a bona fide transposon in its present host line because it does not leave footprints upon excision and does not reinsert in the genome. These unusual mobile element properties are discussed in light of the structure and gene organization of Jit and related elements.

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“…Although these are speculative views, it is interesting to note that the transposase portion is relatively well conserved among the CACTA TE family, including the TNP of TamRSI (data not shown). In contrast, the TNPA part shows a high degree of sequence divergence as reported for the TNPA of En/Spm and Tam1 (Kunze and Weil 2002). Similarly, in a TamRSI-like structure present in the Antirrhinum genome (Causier et al 2005, Suppl. Fig.…”

Section: Rsi Represents a New Type Of Cacta Transposable Elementmentioning

confidence: 74%

“…Secondly, transposons induce characteristic target site duplications upon insertion (Bonas et al 1984;Schwarz-Sommer et al 1984). In addition, sequence repeats are also found at sub-terminal positions with respect to the TIRs (Kunze and Weil 2002). The integrity of the TIRs and of the sub-terminal repeats is essential for the transposition (Schiefelbein et al 1988).…”

Section: Introductionmentioning

confidence: 99%

“…In b, the deletio-fusion event in TamRSI-3 occurred between the XhoI and BamHI sites. The TamRSI-3 structure is not complete as indicated by the two slash lines Deletion derivatives as source of aberrant RSI transcripts Internal deletions within the TEs are common and are generated by aberrant transposition events (Kunze and Weil 2002). The known portion of the TamRSI-3 copy has a genomic structure that fuses part of the TNP coding region with the 5Ј end of the RSI coding region (Fig.…”

Section: Mapping and Excision Analysis Of Tamrsimentioning

confidence: 99%

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ROSINA (RSI) is part of a CACTA transposable element, TamRSI, and links flower development to transposon activity

Roccaro¹,

Sommer³

et al. 2007

Mol Genet Genomics

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ROSINA (RSI) was isolated as a DNA binding factor able to bind to the CArG-box present in the promoter of the MADS-box gene DEFICIENS of Antirrhinum majus. The mosaic nature of RSI and its multi-copy presence in the A. majus genome indicated that RSI could be a part of a mobile genetic element. Here we show that RSI is a part of a CACTA transposable element system of A. majus, named TamRSI, which has evolved and is still evolving within the terminal inverted repeats (TIRs) of this CACTA transposon. Interestingly, RSI is always found in opposite orientation with respect to the transcription of a second gene present within the CACTA transposon, which encodes a putative TRANSPOSASE (TNP). This structural conWguration has not yet been described for any member of the CACTA transposons superfamily. Internal deletion derivatives of the TamRSI produce aberrant RSI transcripts (RSIATs) that carry parts of the RSI RNA fused to parts of the TNP RNA. In addition, an intriguing seed phenotype shown by RNAi transgenic lines generated to silence RSI, relate TamRSI to epigenetic mechanisms and associate the control of Xower development to transposon activity.

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ThehATand CACTA Superfamilies of Plant Transposons

Cited by 104 publications

References 369 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

Jittery, a Mutator Distant Relative with a Paradoxical Mobile Behavior: Excision without Reinsertion

ROSINA (RSI) is part of a CACTA transposable element, TamRSI, and links flower development to transposon activity

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