Integration of the 5' end of the retrotransposon, R2Bm, can be complemented by homologous recombination

Fujimoto, Haruhiro; Hirukawa, Yukiko; Tani, Hideki; Matsuura, Yoshiharu; Hashido, Kazuo; Tsuchida, Kozo; Takada, Naoko; Kobayashi, Masahiko; Maekawa, Hideaki

doi:10.1093/nar/gkh304

Cited by 21 publications

(23 citation statements)

References 27 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…This may be due to the replacement of upstream 28S sequences and R1-5′UTR to polyhedrin 5′UTR and GST sequence. The inclusion of 28S sequence to its 5′ termini of the construct achieved intact 5′ junction formation in R2 (26,29), so it may be the same for R1. This implicates that the free ends generated during this process are repaired by the cellular proteins.…”

Section: Discussionmentioning

confidence: 96%

“…The newly cloned R1 from the silkworm genome was found to be active for retrotransposition, and it turned out that the baculovirus-based in vivo retrotransposition assay could be applied to the study of various site-specific LINEs (17,26). The most distinctive feature of R1 retrotransposition is its requirement of 3′ downstream sequence derived from 28S gene for the precise, efficient integration into its target DNA.…”

Section: Discussionmentioning

confidence: 99%

See 1 more Smart Citation

Functional roles of 3'-terminal structures of template RNA during in vivo retrotransposition of non-LTR retrotransposon, R1Bm

Anzai

Osanai

Hamada

et al. 2005

Nucleic Acids Research

View full text Add to dashboard Cite

R1Bm is a non-LTR retrotransposon found specifically within 28S rRNA genes of the silkworm. Different from other non-LTR retrotransposons encoding two open reading frames (ORFs), R1Bm structurally lacks a poly (A) tract at its 3′ end. To study how R1Bm initiates reverse transcription from the poly (A)-less template RNA, we established an in vivo retrotransposition system using recombinant baculovirus, and characterized retrotransposition activities of R1Bm. Target-primed reverse transcription (TPRT) of R1Bm occurred from the cleavage site generated by endonuclease (EN). The 147 bp of 3′-untranslated region (3′UTR) was essential for efficient retrotransposition of R1Bm. Even using the complete R1Bm element, however, reverse transcription started from various sites of the template RNA mostly with 5′-UG-3′ or 5′-UGU-3′ at their 3′ ends, which are presumably base-paired with 3′ end of the EN-digested 28S rDNA target sequence, 5′-AGTAGATAGGGACA-3′. When the downstream sequence of 28S rDNA target was added to the 3′ end of R1 unit, reverse transcription started exactly from the 3′ end of 3′UTR and retrotransposition efficiency increased. These results indicate that 3′-terminal structure of template RNA including read-through region interacts with its target rDNA sequences of R1Bm, which plays important roles in initial process of TPRT in vivo.

show abstract

Section: Discussionmentioning

confidence: 96%

Section: Discussionmentioning

confidence: 99%

Functional roles of 3'-terminal structures of template RNA during in vivo retrotransposition of non-LTR retrotransposon, R1Bm

Anzai

Osanai

Hamada

et al. 2005

Nucleic Acids Research

View full text Add to dashboard Cite

show abstract

“…Transposable elements (TEs) were the most represented group of sequences in the SSH with 37 clones displaying significant similarity to Pol-like proteins of non-long terminal repeat (non-LTR) retrotransposons, such as R2Bm from the silk moth, Bombyx mori [57], MsquI-Aa2 from the mosquito, Aedes aegypti [58], and bilbo from the fruit fly, Drosophila subobscura [59] among others (Table 3). TEs are genetic entities capable of insertion at different positions in the genome and of inducing alteration of the function of the genes with which they become associated [60].…”

Section: Transposable Elementsmentioning

confidence: 99%

Differential expression of immune-related genes and transposable elements in black tiger shrimp (Penaeus monodon) exposed to a range of environmental stressors

Vega

Degnan

Hall

et al. 2007

Fish & Shellfish Immunology

View full text Add to dashboard Cite

“…5D, 4 and 5). Homologous recombinational repair is thought to facilitate R2 5Ј-end integration (Fujimoto et al 2004) and was reported for L1s integrating into pre-existing older L1 elements, resulting in hybrid or toggled insertions Symer et al 2002). Unlike this special case of toggled insertions, where host DNA had prior homology to the retrotransposon allowing for detectable sequence changes after recombination, a more general case will involve recombination between identical stretches of DNA, and no sequence changes will be produced.…”

Section: Model Of 5ј-end Attachment and L1 Integrationmentioning

confidence: 99%

L1 integration in a transgenic mouse model

et al. 2005

View full text Add to dashboard Cite

To study integration of the human LINE-1 retrotransposon (L1) in vivo, we developed a transgenic mouse model of L1 retrotransposition that displays de novo somatic L1 insertions at a high frequency, occasionally several insertions per mouse. We mapped 3Ј integration sites of 51 insertions by Thermal Asymmetric Interlaced PCR (TAIL-PCR). Analysis of integration locations revealed a broad genomic distribution with a modest preference for intergenic regions. We characterized the complete structures of 33 de novo retrotransposition events. Our results highlight the large number of highly truncated L1s, as over 52% (27/51) of total integrants were <1/3 the length of a full-length element. New integrants carry all structural characteristics typical of genomic L1s, including a number with inversions, deletions, and 5Ј-end microhomologies to the target DNA sequence. Notably, at least 13% (7/51) of all insertions contain a short stretch of extra nucleotides at their 5Ј end, which we postulate result from template-jumping by the L1-encoded reverse transcriptase. We propose a unified model of L1 integration that explains all of the characteristic features of L1 retrotransposition, such as 5Ј truncations, inversions, extra nucleotide additions, and 5Ј boundary and inversion point microhomologies.[Supplemental material is available online at www.genome.org.]The long interspersed nucleotide element-1 (L1) retrotransposon enjoyed tremendous evolutionary success in colonizing eukaryotic genomes (Kazazian Jr. 2004); its roughly 500,000 copies comprise ∼17% of human DNA (Lander et al. 2001). The full-length 6-kb L1 encodes a 5Ј UTR containing an internal promoter, two proteins-ORF1, a nucleic acid-binding protein with chaperone activity (Hohjoh andSinger 1996, 1997;Martin and Bushman 2001), and ORF2, a protein with endonuclease (EN) and reverse transcriptase (RT) activities (Mathias et al. 1991;Feng et al. 1996), and a 3Ј UTR ending with a poly(A) tail (Fig. 1A). Both ORF1 and ORF2 proteins are required for retrotransposition . Once transcribed and translated, L1 RNA is copied into the genome by target-primed reverse transcription (TPRT) (Luan et al. 1993;Cost et al. 2002). During TPRT, one strand of host DNA is cleaved by the EN to expose a free 3Ј-hydroxyl, which is then used by the RT as a primer in reverse transcription, copying the L1 RNA template directly into the host genome. To complete integration, the second strand of host DNA must be cleaved, RNA removed, the newly synthesized strand copied, and breaks resolved. The mechanism by which these later steps are accomplished is only beginning to be understood, with recent biochemical data from a related non-LTR retrotransposon R2 of the silkmoth, Bombyx mori, suggesting that a second R2 protein is involved in cleavage, RNA displacement, and synthesis of the second strand (Bibillo and Eickbush 2002a; Christensen and Eickbush 2005).Following essentially random integration, endogenous L1s are thought to be lost over time due to strong negative selection leading to their uneven ...

show abstract

Integration of the 5' end of the retrotransposon, R2Bm, can be complemented by homologous recombination

Cited by 21 publications

References 27 publications

Functional roles of 3'-terminal structures of template RNA during in vivo retrotransposition of non-LTR retrotransposon, R1Bm

Functional roles of 3'-terminal structures of template RNA during in vivo retrotransposition of non-LTR retrotransposon, R1Bm

Differential expression of immune-related genes and transposable elements in black tiger shrimp (Penaeus monodon) exposed to a range of environmental stressors

L1 integration in a transgenic mouse model

Contact Info

Product

Resources

About