The RmInt1 group II intron has two different retrohoming pathways for mobility using predominantly the nascent lagging strand at DNA replication forks for priming

Martı́nez-Abarca, Francisco; Barrientos‐Durán, Antonio; Fernández‐López, Manuel; Toro, Nicolás

doi:10.1093/nar/gkh616

Cited by 58 publications

(86 citation statements)

References 42 publications

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“…These events could even take advantage of lagging strand nicks created during S phase, as observed for the RmInt1 group II intron. 69 The reason for the excess of DSBs in the L1 retrotransposition process is not understood at this time. The DSB intermediates in the retrotransposition process may be repaired efficiently most of the time and therefore do not result in an insertion event (see Figure 1).…”

Section: Mechanistic Implications Of L1 Dsbsmentioning

confidence: 99%

The Human LINE-1 Retrotransposon Creates DNA Double-strand Breaks

Gasior

Wakeman

et al. 2006

Journal of Molecular Biology

445

507

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Long interspersed element-1 (L1) is an autonomous retroelement that is active in the human genome. The proposed mechanism of insertion for L1 suggests that cleavage of both strands of genomic DNA is required. We demonstrate that L1 expression leads to a high level of doublestrand break (DSB) formation in DNA using immunolocalization of γ-H2AX foci and the COMET assay. Similar to its role in mediating DSB repair in response to radiation, ATM is required for L1-induced γ-H2AX foci and for L1 retrotransposition. This is the first characterization of a DNA repair response from expression of a non-long terminal repeat (non-LTR) retrotransposon in mammalian cells as well as the first demonstration that a host DNA repair gene is required for successful integration. Notably, the number of L1-induced DSBs is greater than the predicted numbers of successful insertions, suggesting a significant degree of inefficiency during the integration process. This result suggests that the endonuclease activity of endogenously expressed L1 elements could contribute to DSB formation in germ-line and somatic tissues.

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Section: Mechanistic Implications Of L1 Dsbsmentioning

confidence: 99%

The Human LINE-1 Retrotransposon Creates DNA Double-strand Breaks

Gasior

Wakeman

et al. 2006

Journal of Molecular Biology

445

507

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“…Most CL and B introns encode RTs with an En domain, while lineages A, C, D, E, and F introns encode proteins lacking this domain (denoted En À group II introns) Toro et al 2007;Simon et al 2008). One En À group IIB intron, the Sinorhizobium melilotti RmInt1 intron, has been shown to retrohome efficiently by using a nascent strand at a DNA replication fork to prime reverse transcription (Martínez-Abarca et al 2004). Group IIC introns have the smallest intron RNAs, encode proteins lacking an En domain, and rely on En-independent mechanisms for mobility (Robart et al 2007).…”

Section: Introductionmentioning

confidence: 99%

EcI5, a group IIB intron with high retrohoming frequency: DNA target site recognition and use in gene targeting

Zhuang

Karberg

Perůtka

et al. 2009

RNA

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We find that group II intron EcI5, a subclass CL/IIB1 intron from an Escherichia coli virulence plasmid, is highly active in retrohoming in E. coli. Both full-length EcI5 and an EcI5-DORF intron with the intron-encoded protein expressed separately from the same donor plasmid retrohome into a recipient plasmid target site at substantially higher frequencies than do similarly configured Lactococcus lactis Ll.LtrB introns. A comprehensive view of DNA target site recognition by EcI5 was obtained from selection experiments with donor and recipient plasmid libraries in which different recognition elements were randomized. These experiments suggest that EcI5, like other mobile group II introns, recognizes DNA target sequences by using both the intron-encoded protein and base-pairing of the intron RNA, with the latter involving EBS1, EBS2, and EBS3 sequences characteristic of class IIB introns. The intron-encoded protein appears to recognize a small number of bases flanking those recognized by the intron RNA, but their identity is different than in previously characterized group II introns. A computer algorithm based on the empirically determined DNA recognition rules enabled retargeting of EcI5 to integrate specifically at 10 different sites in the chromosomal lacZ gene at frequencies up to 98% without selection. Our findings provide insight into modes of DNA target site recognition used by mobile group II introns. More generally, they show how the diversity of mobile group II introns can be exploited to provide a large variety of different target specificities and potentially other useful properties for gene targeting.

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“…Unlike intron Ll.LtrA of Lactococcus lactis, which currently serves as paradigm for group II intron mobility (for review, see Lambowitz and Zimmerly 2004), the RmInt1 intron-encoded protein lacks C-terminal DNA endonuclease and DNA-binding domains (Martínez-Abarca et al 2000;Zimmerly et al 2001;Dai and Zimmerly 2002a;San Filippo and Lambowitz 2002;Toro 2003). RmInt1 is nevertheless an efficient mobile element that has two retrohoming pathways for mobility, with predominant use of the nascent lagging strand at DNA replication forks for priming (Martínez-Abarca et al 2004).…”

Section: Introductionmentioning

confidence: 99%

Potential for alternative intron–exon pairings in group II intron RmInt1 from Sinorhizobium meliloti and its relatives

Costa¹,

Michel²,

Toro³

2006

RNA

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Ribozyme constructs derived from group II intron RmInt1 of Sinorhizobium meliloti self-splice in vitro when incubated under permissive conditions, but exon ligation is unusually inefficient when the 5¢ exon is truncated close to the IBS2 intron-binding site. One plausible explanation for this observation is the presence of an alternative intron-exon pairing between an intron segment that overlaps with the EBS2 exon-binding site and a 5¢ exon site located just distal of IBS2 relative to the splice junction. Strikingly, the existence of this pairing is supported by comparative sequence analysis of introns related to RmInt1.

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The RmInt1 group II intron has two different retrohoming pathways for mobility using predominantly the nascent lagging strand at DNA replication forks for priming

Cited by 58 publications

References 42 publications

The Human LINE-1 Retrotransposon Creates DNA Double-strand Breaks

The Human LINE-1 Retrotransposon Creates DNA Double-strand Breaks

EcI5, a group IIB intron with high retrohoming frequency: DNA target site recognition and use in gene targeting

Potential for alternative intron–exon pairings in group II intron RmInt1 from Sinorhizobium meliloti and its relatives

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