ArticleRNA (New York, N.Y.)2009
EcI5, a group IIB intron with high retrohoming frequency: DNA target site recognition and use in gene targeting.
Article in RNA (New York, N.Y.), 2009. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 26 papers.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
26 citing papers in PubMed, 41 citations in OpenAlex.
- Article
- Computational De Novo Design of Group II Introns Yields Highly Active Ribozymes.Chembiochem : a European journal of chemical biology · 2025Article
- Past, Present, and Future of Genome Modification inMicroorganisms · 2022Review
- Group II Introns: Flexibility and Repurposing.Frontiers in molecular biosciences · 2022Article
- A new RNA-DNA interaction required for integration of group II intron retrotransposons into DNA targets.Nucleic acids research · 2021Article
- Prokaryotic reverse transcriptases: from retroelements to specialized defense systems.FEMS microbiology reviews · 2021Review
- Group II intron as cold sensor for self-preservation and bacterial conjugation.Nucleic acids research · 2020Article
- Group II Intron RNPs and Reverse Transcriptases: From Retroelements to Research Tools.Cold Spring Harbor perspectives in biology · 2019Review
- A Highly Proliferative Group IIC Intron from Geobacillus stearothermophilus Reveals New Features of Group II Intron Mobility and Splicing.Journal of molecular biology · 2018Article
- The XylS/Pm regulator/promoter system and its use in fundamental studies of bacterial gene expression, recombinant protein production and metabolic engineering.Microbial biotechnology · 2017Review
- Localization of a bacterial group II intron-encoded protein in human cells.Scientific reports · 2015Article
- Mobile Bacterial Group II Introns at the Crux of Eukaryotic Evolution.Microbiology spectrum · 2015Review
- Bias in ligation-based small RNA sequencing library construction is determined by adaptor and RNA structure.PloS one · 2015Article
- The role of Mg(II) in DNA cleavage site recognition in group II intron ribozymes: solution structure and metal ion binding sites of the RNA-DNA complex.The Journal of biological chemistry · 2014Article
- Biotechnological applications of mobile group II introns and their reverse transcriptases: gene targeting, RNA-seq, and non-coding RNA analysis.Mobile DNA · 2014Article
- Role of helical constraints of the EBS1-IBS1 duplex of a group II intron on demarcation of the 5' splice site.RNA (New York, N.Y.) · 2014Article
- Insights into the strategies used by related group II introns to adapt successfully for the colonisation of a bacterial genome.RNA biology · 2014Review
- Use of the computer-retargeted group II intron RmInt1 of Sinorhizobium meliloti for gene targeting.RNA biology · 2014Article
- A targetron system for gene targeting in thermophiles and its application in Clostridium thermocellum.PloS one · 2013Article
- Generalized bacterial genome editing using mobile group II introns and Cre-lox.Molecular systems biology · 2013Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
4 authors at 1 institution in 1 country.
Funding
Abstract
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-DeltaORF 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.
Indexed as
Identifiers
What OpenQuestion holds
Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.