Elsevier

Gene

Volume 436, Issues 1–2, 1 May 2009, Pages 23-29
Gene

Guinea pig ID-like families of SINEs

https://doi.org/10.1016/j.gene.2009.02.004Get rights and content

Abstract

Previous studies have indicated a paucity of SINEs within the genomes of the guinea pig and nutria, representatives of the Hystricognathi suborder of rodents. More recent work has shown that the guinea pig genome contains a large number of B1 elements, expanding to various levels among different rodents. In this work we utilized A–B PCR and screened GenBank with sequences from isolated clones to identify potentially uncharacterized SINEs within the guinea pig genome, and identified numerous sequences with a high degree of similarity (> 92%) specific to the guinea pig. The presence of A-tails and flanking direct repeats associated with these sequences supported the identification of a full-length SINE, with a consensus sequence notably distinct from other rodent SINEs. Although most similar to the ID SINE, it clearly was not derived from the known ID master gene (BC1), hence we refer to this element as guinea pig ID-like (GPIDL). Using the consensus to screen the guinea pig genomic database (Assembly CavPor2) with Ensembl BlastView, we estimated at least 100,000 copies, which contrasts markedly to just over 100 copies of ID elements. Additionally we provided evidence of recent integrations of GPIDL as two of seven analyzed conserved GPIDL-containing loci demonstrated presence/absence variants in Cavia porcellus and C. aperea. Using intra-IDL PCR and sequence analyses we also provide evidence that GPIDL is derived from a hystricognath-specific SINE family. These results demonstrate that this SINE family continues to contribute to the dynamics of genomes of hystricognath rodents.

Introduction

Short interspersed DNA elements (SINEs) are non-autonomous retrotransposons found throughout eukaryotic species. Based on DNA sequence analyses, SINEs are presumptively derived from either the 7SL RNA gene, tRNA genes, or 5S rRNA genes (Deininger, 2003, Kapitov and Jurka, 2003), and believed to rely on the proteins encoded by long interspersed DNA elements (LINEs) for amplification in the genome. This hypothesis has been supported using a cell culture retrotransposition assay (Dewannieux et al., 2003, Dewannieux and Heidmann, 2005a). Genomes from a variety of mammalian species have shown a high abundance of retrotransposons including roughly 42% of genome mass in humans (Lander et al., 2001) and 37% in mouse (Waterston et al., 2002). Of that, there are 1.5 million SINEs in the mouse that comprise 8.2% of its genome, as well as roughly 1.5 million SINEs in the human, predominantly the Alu element, that comprise about 13% of its genome. Therefore, retrotranspositions have made a significant contribution to the organization of mammalian genomes.

Certain families of SINEs are specific to different taxonomic levels. For example, Alu elements are found in primates (Deininger, 1989); whereas the B1, B2, and ID are among elements that have been found in rodents (Deininger, 1989). However, two analyzed rodents in the suborder Hystricognathi, the guinea pig and nutria, were shown to either have very low copies or no copies of ID and B2 elements, respectively (Kass et al., 1996, Kass, 1997). Two potential explanations for this find are (i) this group of rodents has avoided a “take-over” by these genomic parasites due to either containing specific repressors or lacking the necessary retrotransposition machinery (perhaps LINEs), or (ii) these rodents contain a unique group of SINEs not found in the Sciurognathi suborder which includes mice, rats, and squirrels among other rodents. There has been controversy as to whether the guinea pig is a rodent (Graur et al., 1991; Frye and Hedges, 1995; D'Erchia et al., 1996, Philippe, 1997, Konno, 1999), but even if guinea pigs are considered rodents, the time of divergence between suborders may be sufficient for different SINE families to have been derived and amplified. While we were investigating the paucity of SINEs in the guinea pig, Vassetzky et al. (2003) determined that the B1 family does exist in high copy number (150,000) in the guinea pig and therefore demonstrated SINEs can amplify among hystricognaths. This study therefore investigates the potential finding of undefined SINEs that may be in the guinea pig and other hystricognaths to assess their contributions to the dynamics of the genomes of this understudied group of rodents.

Section snippets

Tissue and DNA samples

Tissue samples of various hystricognath rodents were kindly provided by the Museum of Vertebrate Zoology of the University of California at Berkely. These include the paca (Agouti paca; MVZ 153575), rock rat (Aconaemys porteri; MVZ 184959), Mesomys hispidus (MVZ 155158), prehensile-tail porcupine (Coendou bicolor; MVZ 155200), and the pacarana (Dinomys branikii; MVZ 153574). Nutria (Myocaster coypus), grey squirrel (Sciurus carolinensis), European house mouse (Mus musculus), Norway rat (Rattus

Isolation of SINEs based on AB-PCR and data mining

The focus of this study was to identify any undiscovered SINE family in the guinea pig and other hystricognath rodents. We utilized the technique of A–B PCR (Borodulina and Kramerov, 1999) since the A and B box regions of SINEs are most conserved. We identified bands of equivalent size in the guinea pig and the rat (Fig. 1). Using A–B PCR of the rat genome as a control, we identified a B2 clone demonstrating the effectiveness of this technique (data not shown). Using A–B PCR of the guinea pig

Discussion

This study was initiated to investigate the paucity of known rodent SINEs, B2 and ID elements, within the guinea pig and nutria genomes, two members of the Hystricognathi suborder. During this study another group found the rodent B1 SINE to have amplified to various levels in hystricognath rodents, including over 200,000 in the guinea pig (Veniaminova et al., 2007). However, beginning with A–B PCR we unraveled a previously unknown SINE in the guinea pig that is distinct from, but most similar

Acknowledgments

This work was supported by a National Institutes of Health AREA grant GM62828-01A1 to DHK, an EMU Biology Department Helwig Research Apprenticeship to BAS, and an EMU Honor's College Fellowship to NJ. We also thank Sarah Killian for initiating the development of intra-IDL PCR conditions. We greatly appreciate the tissue donations from Drs. Mike Angell and Theresa Lee, as well as the tissue loans from the Museum of Vertebrate Zoology at the University of California at Berkeley, and the

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