Homologous Recombination-dependent Gene Targeting and an Active DNA Transposon nDart-promoted Gene Tagging for Rice Functional Genomics

Johzuka-Hisatomi, Yasuyo; Maekawa, Masahiko; Takagi, Kyoko; Eun, Chang Ho; Yamauchi, Takaki; Shimatani, Zenpei; Ahmed, Nisar; Urawa, Hiroko; Tsugane, Kazuo; Terada, Rie; Iida, Shigeru

doi:10.1007/978-3-540-74250-0_7

Cited by 11 publications

(15 citation statements)

References 49 publications

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“…1; Takagi et al 2007), we employed PCR analysis to examine whether Dart1-51 could be excised in the pyl-v plants. No such excisions were detectable (data not shown), confirming the previous assumption that only the elements belonging to the nDart1-3 subgroup could transpose actively (Tsugane et al 2006;Johzuka-Hisatomi et al 2008). We also tried to visualize Dart2 (including Dart1-52/53), Dart3, and Dart4 elements with the appropriate primers ( Fig.…”

Section: Resultssupporting

confidence: 78%

“…Because their transposition can be induced under natural growth conditions by crossing with a line containing an active autonomous aDart1 element and stabilized by segregating aDart1 and because revertants due to the excision of the inserted nDart1 are easily obtainable (Tsugane et al 2006), our nDart1-promoted tagging system has desirable features of gene tagging in rice. We are currently generating a large number of mutant lines tagged by the nDart1-3 subgroup elements, and about one-third of these mutant lines were found to confer various phenotypes (Johzuka-Hisatomi et al 2008;Maekawa et al 2010).…”

Section: Discussionmentioning

confidence: 99%

“…In these tagging systems, however, the concomitant occurrence of somaclonal variation associated with tissue cultures (Kaeppler et al 2000) is inevitable because tissue cultures are necessary to either introduce the maize elements or T-DNAs into rice calli or activate dormant Tos17 in the genome. Among active endogenous DNA transposons, mPing and nDart1-3 subgroup elements have been reported to transpose actively in particular rice varieties under normal growth conditions (Nakazaki et al 2003;Naito et al 2006;Tsugane et al 2006;Johzuka-Hisatomi et al 2008;Nishimura et al 2008), and their insertional mutants should be free from somaclonal variation. Available data indicate that mPing seems to be integrated more preferentially into noncoding or promoter distal regions (Naito et al 2006(Naito et al , 2009 than the nDart1-3 subgroup elements (this study).…”

Section: Discussionmentioning

confidence: 99%

“…According to the 4.0 pseudomolecules of the Nipponbare genome (International Rice Genome Sequencing Project 2005), the small nDart1 and longer Dart1/dDart1 elements have 18 and 53 copies, respectively, and 38 Dart1 elements are likely to be epigenetically silenced autonomous elements because their putative transposase genes carry no apparent nonsense or frameshift mutations (Takagi et al 2007;Johzuka-Hisatomi et al 2008;Shimatani et al 2009). Based on the results of Dart-TD, only the nDart1-3 subgroup elements, including nDart1-0, out of seven subgroup elements were shown to transpose actively in the pyl-v plant (Figs.…”

Section: Discussionmentioning

confidence: 99%

“…1; Nishimura et al 2008;Shimatani et al 2009) and basing on the structure of its presumed exon. Nipponbare is likely to carry 35 iDart1, 15 dDart1 including three internal deletion elements, one iDart1-51, two iDart1-52/ 53, one iDart2, six dDart2, one dDart3, and two iDart4 (Takagi et al 2007;Johzuka-Hisatomi et al 2008). Moreover, we have demonstrated that the active autonomous aDart1 element in the pyl-v line corresponds to iDart1-27 on chromosome 6 in Nipponbare and that aDart1 and iDart1-27 are identical in their sequences and chromosomal locations (Shimatani et al 2009).…”

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confidence: 81%

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Transposition and target preferences of an active nonautonomous DNA transposon nDart1 and its relatives belonging to the hAT superfamily in rice

et al. 2010

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The nonautonomous nDart1 element in the hAT superfamily is one of a few active DNA transposons in rice. Its transposition can be induced by crossing with a line containing an active autonomous element, aDart1, and stabilized by segregating aDart1. No somaclonal variation should occur in nDart1-promoted gene tagging because no tissue culture is involved in nDart1 activation. By transposon display analysis, we examined the activities of nDart1-related elements in the selfed progeny of a mutable virescent pyl-v plant containing aDart1. Although various nDart1-related elements are present in the rice genome, only nDart1-3 subgroup elements, nDart1-0 and nDart1-3 in particular, were found to be transposed frequently and integrated into various sites almost all over the genome, and a fraction of the transposed elements were found to be transmitted to the next generation. More than half of the newly integrated elements were identified as nDart1-0. Analysis of the newly inserted sites revealed that the nDart1-3 subgroup elements were predominantly integrated into single-copy regions. More than 60% of the transposed elements were inserted into the genic regions that comprise putative coding regions and their 0.5-kb flanking segments, and approximately two-thirds of them were within the 0.5-kb area in front of the putative initiation codons, i.e., promoter-proximal genic regions. These characteristic features of nDart1-3 subgroup elements seem to be suitable for developing an efficient and somaclonal variation-free gene tagging system for rice functional genomics.

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Section: Resultssupporting

confidence: 78%

Section: Discussionmentioning

confidence: 99%

Section: Discussionmentioning

confidence: 99%

Section: Discussionmentioning

confidence: 99%

mentioning

confidence: 81%

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Transposition and target preferences of an active nonautonomous DNA transposon nDart1 and its relatives belonging to the hAT superfamily in rice

et al. 2010

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Transgenerational activation of an autonomous DNA transposon, Dart1-24, by 5-azaC treatment in rice

et al. 2019

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Characterization of autonomous Dart1 transposons belonging to the hAT superfamily in rice

et al. 2009

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An endogenous 0.6-kb rice DNA transposon, nDart1-0, was found as an active nonautonomous element in a mutable virescent line, pyl-v, displaying leaf variegations. Here, we demonstrated that the active autonomous element aDart in pyl-v corresponds to Dart1-27 on chromosome 6 in Nipponbare, which carries no active aDart elements, and that aDart and Dart1-27 are identical in their sequences and chromosomal locations, indicating that Dart1-27 is epigenetically silenced in Nipponbare. The identiWcation of aDart in pyl-v was Wrst performed by map-based cloning and by detection of the accumulated transposase transcripts. Subsequently, various transposition activities of the cloned Dart1-27 element from Nipponbare were demonstrated in Arabidopsis. Dart1-27 in Arabidopsis was able to excise nDart1-0 and Dart1-27 from cloned sites, generating footprints, and to integrate into new sites, generating 8-bp target site duplications. In addition to Dart1-27, Nipponbare contains 37 putative autonomous Dart1 elements because their putative transposase genes carry no apparent nonsense or frameshift mutations. Of these, at least four elements were shown to become active aDart elements in transgenic Arabidopsis plants, even though considerable sequence divergence arose among their transposases. Thus, these four Dart1 elements and Dart1-27 in Nipponbare must be potential autonomous elements silenced epigenetically. The regulatory and evolutionary implications of the autonomous Dart1 elements and the development of an eYcient transposon-tagging system in rice are discussed.

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Homologous Recombination-dependent Gene Targeting and an Active DNA Transposon nDart-promoted Gene Tagging for Rice Functional Genomics

Cited by 11 publications

References 49 publications

Transposition and target preferences of an active nonautonomous DNA transposon nDart1 and its relatives belonging to the hAT superfamily in rice

Transposition and target preferences of an active nonautonomous DNA transposon nDart1 and its relatives belonging to the hAT superfamily in rice

Transgenerational activation of an autonomous DNA transposon, Dart1-24, by 5-azaC treatment in rice

Characterization of autonomous Dart1 transposons belonging to the hAT superfamily in rice

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