Genomic alterations upon integration of zebrafish L1 elements revealed by the TANT method

Ichiyanagi, Kenji; Okada, Norihiro

doi:10.1016/j.gene.2006.07.038

Cited by 8 publications

(7 citation statements)

References 52 publications

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“…Rather, host factors are likely involved in the processes for joining of the target and NLR DNAs at the 5Ј junction. Consistent with this idea, we have recently revealed that zebrafish L1-clade NLRs are approximately three times more frequently associated with extra 5Ј nucleotides than human L1s are (Ichiyanagi and Okada 2006). Interestingly, it has been reported that several host-encoded DNA repair proteins are involved in the mobility of a bacterial group II intron (Smith et al 2005), which retrotransposes and retrohomes via TPRT (Saldanha et al 1999), and that the pathway utilization for its retrotransposition is dictated by the host (Coros et al 2005).…”

Section: Pathways For Joining the 5ј Junction Are Dictated By The Hosmentioning

confidence: 52%

Novel retrotransposon analysis reveals multiple mobility pathways dictated by hosts

Ichiyanagi¹,

Nakajima²,

Kajikawa³

et al. 2006

Genome Res.

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Autonomous non-long-terminal-repeat retrotransposons (NLRs) proliferate by retrotransposition via coordinated reactions of target DNA cleavage and reverse transcription by a mechanism called target-primed reverse transcription (TPRT). Whereas this mechanism guarantees the covalent attachment of the NLR and its target site at the 3Ј junction, mechanisms for the joining at the 5Ј junction have been conjectural. To better understand the retrotransposition pathways, we analyzed target-NLR junctions of zebrafish NLRs with a new method of identifying genomic copies that reside within other transposons, termed "target analysis of nested transposons" (TANT). Application of the TANT method revealed various features of the zebrafish NLR integrants; for example, half of the integrants carry extra nucleotides at the 5Ј junction, which is in stark contrast to the major human NLR, LINE-1. Interestingly, in a cell culture assay, retrotransposition of the zebrafish NLR in heterologous human cells did not bear extra 5Ј nucleotides, indicating that the choice of the 5Ј joining pathway is affected by the host. Our results suggest that several pathways exist for NLR retrotransposition and argue in favor of host protein involvement. With genomic sequence information accumulating exponentially, our data demonstrate the general applicability of the TANT method for the analysis of a wide variety of retrotransposons.

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Section: Pathways For Joining the 5ј Junction Are Dictated By The Hosmentioning

confidence: 52%

Novel retrotransposon analysis reveals multiple mobility pathways dictated by hosts

Ichiyanagi¹,

Nakajima²,

Kajikawa³

et al. 2006

Genome Res.

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“…Human L1 and Alu are usually flanked by ~15-bp TSDs [9,33,34]. TSDs are used to determine the junctions of L1 insertions in genome-wide screening [9].…”

Section: Introductionmentioning

confidence: 99%

“…Target analysis of nested transposons (TANT) is a method to characterize LINE insertions with short TSDs. It is, however, limited by the low copy number of insertions nested in other transposons [34-36]. The advantage of this method is its ability to assume pre-inserted empty sites.…”

Section: Introductionmentioning

confidence: 99%

Different integration site structures between L1 protein-mediated retrotransposition in cis and retrotransposition in trans

Kojima

2010

Mobile DNA

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BackgroundLong interspersed nuclear element-1 (LINE-1 or L1) is a dominant repetitive sequence in the human genome. Besides mediating its own retrotransposition, L1 can mobilize Alu and messenger RNA (mRNA) in trans, and probably also SVA and non-coding RNA. The structures of L1 copies and trans-mobilized retrocopies are variable and can be classified into three categories: full-length; 5'-truncated; and 5'-inverted insertions. These structures may be generated by different 5' integration mechanisms.ResultsIn this study, a method to correctly characterize insertions with short target site duplications (TSDs) is developed and extranucleotides, TSDs and microhomologies (MHs) at junctions were analysed for the three types of insertions. Only 5'-truncated L1 insertions were found to be associated with short TSDs. Both full-length and 5'-truncated retrotransposed sequences in trans, including Alu, SVA and mRNA retrocopies and also full-length and 5'-inverted L1, were not associated with short TSDs, indicating the difference of 5' attachment between retrotransposition in cis and retrotransposition in trans. Target sequence analysis suggested that short TSDs were generated in an L1 endonuclease-dependent manner. The MHs were longer for 5'-inverted L1 than for 5'-truncated L1, indicating less dependence on annealing in 5'-truncated L1 insertions.ConclusionsThe results suggest that insertions flanked by short TSDs occur more often coupled with the insertion of 5'-truncated L1 than with those of other types of insertions in vivo. The method used in this study can be used to characterize elements without any apparent boundary structures.

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“…Churakov et al [ 45 ] recently applied a novel method based on the single-case patterns of nested retroposons to characterize the historical appearance of various armadillo-specific SINE subfamilies. Similarly, Ichiyanagi and Okada used this method to determine the full lengths of SINEs in zebrafish [ 46 ] and Pace and Feschotte to investigate DNA transposon activity in the human genome [ 47 ].…”

Section: Introductionmentioning

confidence: 99%

Waves of genomic hitchhikers shed light on the evolution of gamebirds (Aves: Galliformes)

et al. 2007

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BackgroundThe phylogenetic tree of Galliformes (gamebirds, including megapodes, currassows, guinea fowl, New and Old World quails, chicken, pheasants, grouse, and turkeys) has been considerably remodeled over the last decades as new data and analytical methods became available. Analyzing presence/absence patterns of retroposed elements avoids the problems of homoplastic characters inherent in other methodologies. In gamebirds, chicken repeats 1 (CR1) are the most prevalent retroposed elements, but little is known about the activity of their various subtypes over time. Ascertaining the fixation patterns of CR1 elements would help unravel the phylogeny of gamebirds and other poorly resolved avian clades.ResultsWe analyzed 1,978 nested CR1 elements and developed a multidimensional approach taking advantage of their transposition in transposition character (TinT) to characterize the fixation patterns of all 22 known chicken CR1 subtypes. The presence/absence patterns of those elements that were active at different periods of gamebird evolution provided evidence for a clade (Cracidae + (Numididae + (Odontophoridae + Phasianidae))) not including Megapodiidae; and for Rollulus as the sister taxon of the other analyzed Phasianidae. Genomic trace sequences of the turkey genome further demonstrated that the endangered African Congo Peafowl (Afropavo congensis) is the sister taxon of the Asian Peafowl (Pavo), rejecting other predominantly morphology-based groupings, and that phasianids are monophyletic, including the sister taxa Tetraoninae and Meleagridinae.ConclusionThe TinT information concerning relative fixation times of CR1 subtypes enabled us to efficiently investigate gamebird phylogeny and to reconstruct an unambiguous tree topology. This method should provide a useful tool for investigations in other taxonomic groups as well.

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Genomic alterations upon integration of zebrafish L1 elements revealed by the TANT method

Cited by 8 publications

References 52 publications

Novel retrotransposon analysis reveals multiple mobility pathways dictated by hosts

Novel retrotransposon analysis reveals multiple mobility pathways dictated by hosts

Different integration site structures between L1 protein-mediated retrotransposition in cis and retrotransposition in trans

Waves of genomic hitchhikers shed light on the evolution of gamebirds (Aves: Galliformes)

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