The reverse transcriptase of the R2 non-LTR retrotransposon: continuous synthesis of cDNA on non-continuous RNA templates

Bibiłło, Arkadiusz; Eickbush, Thomas H.

doi:10.1006/jmbi.2001.5369

Cited by 78 publications

(107 citation statements)

References 40 publications

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“…We have previously described sensitive in vitro TPRT assays for the R2 element found in B. mori (Yang and Eickbush 1998;Bibillo and Eickbush 2002). In these assays, short labeled DNA substrates containing the 28S gene target site are incubated with purified B. mori R2 protein (hereafter referred to as R2Bm) and template RNA.…”

Section: Utr Rnas With No Primary Sequence Similarity Are Recognized mentioning

confidence: 99%

“…Each RNA template contains ∼250 nt from the 3Ј end of the R2 element as well as 20 nt from the flanking downstream 28S gene sequences. Reverse transcription is initiated at the junction between the R2 and 28S gene sequences, not at the 3Ј end of the RNA (Luan and Eickbush 1996;Bibillo and Eickbush 2002).…”

Section: Utr Rnas With No Primary Sequence Similarity Are Recognized mentioning

confidence: 99%

“…of this product was confirmed by PCR reactions, using primers specific to either orientation of the DNA substrate and to the RNA sequence (data not shown). The band at ∼590 nt resulted from the R2 protein synthesizing to the end of a first RNA molecule and then jumping to a second RNA molecule, where it continued reverse transcription (60 nt DNA substrate + 255 nt first RNA template + 275 nt of the second RNA template; see Bibillo and Eickbush 2002 for more detailed studies of these template jumps).…”

Section: Utr Rnas With No Primary Sequence Similarity Are Recognized mentioning

confidence: 99%

“…Synthesis of labeled DNA target sites and purification of the R2Bm protein and the TPRT assays were conducted as described in Bibillo and Eickbush (2002).…”

Section: Tprt Assaysmentioning

confidence: 99%

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Secondary structure models of the 3′ untranslated regions of diverse R2 RNAs

Ruschak

Mathews²,

Bibiłło³

et al. 2004

RNA

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The RNA structure of the 3 untranslated region (UTR) of the R2 retrotransposable element is recognized by the R2-encoded reverse transcriptase in a reaction called target primed reverse transcription (TPRT). To provide insight into structure-function relationships important for TPRT, we have created alignments that reveal the secondary structure for 22 Drosophila and five silkmoth 3 UTR R2 sequences. In addition, free energy minimization has been used to predict the secondary structure for the 3 UTR R2 RNA of Forficula auricularia. The predicted structures for Bombyx mori and F. auricularia are consistent with chemical modification data obtained with ␤-ethoxy-␣-ketobutyraldehyde (kethoxal), dimethyl sulfate, and 1-cyclohexyl-3-(2-morpholinoethyl)carbodiimide metho-p-toluene sulfonate. The structures appear to have common helices that are likely important for function.

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Section: Utr Rnas With No Primary Sequence Similarity Are Recognized mentioning

confidence: 99%

Section: Utr Rnas With No Primary Sequence Similarity Are Recognized mentioning

confidence: 99%

Section: Utr Rnas With No Primary Sequence Similarity Are Recognized mentioning

confidence: 99%

“…Synthesis of labeled DNA target sites and purification of the R2Bm protein and the TPRT assays were conducted as described in Bibillo and Eickbush (2002).…”

Section: Tprt Assaysmentioning

confidence: 99%

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Secondary structure models of the 3′ untranslated regions of diverse R2 RNAs

Ruschak

Mathews²,

Bibiłło³

et al. 2004

RNA

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“…However, recombination between multiple copies of the same SINE family during retrotransposition is a novel observation. The demonstrated properties of RT to displace the RNA template during complementary DNA (cDNA) synthesis, and to perform multiple template jumping 27,28 could lead to these recombinants. The template jumping activity reported for non-LTR retrotransposons involves end-to-end jumping between the template RNAs, and this is frequently accompanied by the addition of nontemplated nucleotides at the junction.…”

Section: Discussionmentioning

confidence: 99%

Recombinant SINEs are formed at high frequency during induced retrotransposition in vivo

et al. 2012

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non-long terminal repeat Retrotransposons are referred to as long interspersed nuclear elements (LInEs) and their non-autonomous partners are short interspersed nuclear elements (sInEs). It is believed that an active sInE copy, upon retrotransposition, generates near identical copies of itself, which subsequently accumulate mutations resulting in sequence polymorphism. Here we show that when a retrotransposition-competent cell line of the parasitic protist Entamoeba histolytica, transfected with a marked sInE copy, is induced to retrotranspose, > 20% of the newly retrotransposed copies are neither identical to the marked sInE nor to the mobilized resident sInEs. Rather they are recombinants of resident sInEs and the marked sInE. They are a consequence of retrotransposition and not DnA recombination, as they are absent in cells not expressing the retrotransposition functions. This high-frequency recombination provides a new explanation for the existence of mosaic sInEs, which may impact on genetic analysis of sInE lineages, and measurement of phylogenetic distances.

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Biological Roles of Self‐Cleaving Ribozymes

Weinberg

2021

Ribozymes

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The reverse transcriptase of the R2 non-LTR retrotransposon: continuous synthesis of cDNA on non-continuous RNA templates

Cited by 78 publications

References 40 publications

Secondary structure models of the 3′ untranslated regions of diverse R2 RNAs

Secondary structure models of the 3′ untranslated regions of diverse R2 RNAs

Recombinant SINEs are formed at high frequency during induced retrotransposition in vivo

Biological Roles of Self‐Cleaving Ribozymes

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