ArticleNucleic acids research2006
Identification of insertion hot spots for non-LTR retrotransposons: computational and biochemical application to Entamoeba histolytica.
Article in Nucleic acids research, 2006. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 9 papers.
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Who cites it
9 citing papers in PubMed, 26 citations in OpenAlex.
- The non-LTR retrotransposons of Entamoeba histolytica: genomic organization and biology.Molecular genetics and genomics : MGG · 2022Review
- Identification and characterization of MGEs and their insertion sites in theMobile genetic elements · 2013Article
- Distribution of MGEs and their insertion sites in the Macaca mulatta genome.Mobile genetic elements · 2012Article
- Detecting motifs and patterns at mobile genetic element insertion site.Bioinformation · 2012Article
- Genome-wide analysis of mobile genetic element insertion sites.Nucleic acids research · 2011Article
- Differential distribution of a SINE element in the Entamoeba histolytica and Entamoeba dispar genomes: role of the LINE-encoded endonuclease.BMC genomics · 2011Article
- High AU content: a signature of upregulated miRNA in cardiac diseases.Bioinformation · 2010Article
- RetroPred: A tool for prediction, classification and extraction of non-LTR retrotransposons (LINEs & SINEs) from the genome by integrating PALS, PILER, MEME and ANN.Bioinformation · 2008Article
- Predicting preferential DNA vector insertion sites: implications for functional genomics and gene therapy.Genome biology · 2007Review
Corrections and comments
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Authors and funding
5 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
The genome of the human pathogen Entamoeba histolytica contains non-long terminal repeat (LTR) retrotransposons, the EhLINEs and EhSINEs, which lack targeted insertion. We investigated the importance of local DNA structure, and sequence preference of the element-encoded endonuclease (EN) in selecting target sites for retrotransposon insertion. Pre-insertion loci were tested computationally to detect unique features based on DNA structure, thermodynamic considerations and protein interaction measures. Target sites could readily be distinguished from other genomic sites based on these criteria. The contribution of the EhLINE1-encoded EN in target site selection was investigated biochemically. The sequence-specificity of the EN was tested in vitro with a variety of mutated substrates. It was possible to assign a consensus sequence, 5'-GCATT-3', which was efficiently nicked between A-T and T-T. The upstream G residue enhanced EN activity, possibly serving to limit retrotransposition in the A+T-rich E.histolytica genome. Mutated substrates with poor EN activity showed structural differences compared with normal substrates. Analysis of retrotransposon insertion sites from a variety of organisms showed that, in general, regions of favorable DNA structure were recognized for retrotransposition. A combination of favorable DNA structure and preferred EN nicking sequence in the vicinity of this structure may determine the genomic hotspots for retrotransposition.
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