Abstract
BackgroundChicken repeat 1 (CR1) is a taxonomically widespread non-LTR retrotransposon. Insertion site bias, or lack thereof, has not been demonstrated for CR1. Recent CR1 retrotranspositions were used to examine flanking regions for GC content and nucleotide bias at the insertion site.ResultsElucidation of the exact octomer repeat sequence (TTCTGTGA) allowed for the identification of younger insertion events. The number of octomer repeats associated with a CR1 element increases after insertion with CR1s having one octomer being youngest. These young CR1s are flanked by regions of low GC content (38%). Furthermore, a bias for specific bases within the first four positions at the site of insertion was revealed.ConclusionThis study focused on those loci where the insertion event has been most recent, as this would tend to minimize noise introduced by post-integration mutational events. Our data suggest that CR1 is not inserting into regions of higher GC content within the coscoroba genome; but rather, preferentially inserting into regions of lower GC content. Furthermore, there appears to be a base preference (TTCT) for the insertion site. The results of this study increase the current level of understanding regarding the elusive CR1 non-LTR retrotransposon.
Highlights
Chicken repeat 1 (CR1) is a taxonomically widespread non-long terminal repeat (LTR) retrotransposon.Insertion site bias, or lack thereof, has not been demonstrated for CR1
Our study benefits from focusing on those loci where the insertion event has been most recent, as this would tend to minimize noise introduced by post-integration mutational events
In 81 cases, cloned CR1s were truncated at a Csp6I restriction site located within
Summary
Chicken repeat 1 (CR1) is a taxonomically widespread non-LTR retrotransposon. Lack thereof, has not been demonstrated for CR1. Recent CR1 retrotranspositions were used to examine flanking regions for GC content and nucleotide bias at the insertion site. Eukaryotic genomes contain a large percentage of highly and moderately repetitive DNA [1]. Included in the moderately repetitive DNA, are transposable elements (TEs). DNA transposons (class II) are able to self-excise and move to a new location in the genome while retrotransposons (class I). Non-LTR retrotransposons are thought to be the oldest of the retrotransposons, originating at least 500–600 million years ago [2]. It has been suggested that the non-LTR retrotransposons gave rise to eukaryotic LTRs, which in turn gave rise to myriad viruses including the vertebrate retroviruses [3]
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