Computational prediction of the Helitron-N2 (HeN2) transposable element in the strim1 locus of the Paracentrotus lividus genome

Abstract

Transposons constitute a significant component of the eukaryotic genome. Among others, Helitrons represent a novel major class of eukaryotic transposons, and are fundamentally different from classical ones in terms of their structure and mechanism of transposition [1]. In particular, Helitrons constitute ~1% of the sea urchin genome [2]. By a in silico approach focused on the genome of the Mediterranean sea urchin Paracentrotus lividus, we have predicted regions of high sequence identity to a Helitron-N2 (HeN2) element in the strim1 locus. Of interest, HeN2 sequences lies within the 5’ non coding region of the strim1a and strim1b genes, spanning from -105 to -2255 (the start codon ATG of strim1 is defined as +1). As reported in other species, HeN2 is a non autonomous transposable element, lacking the sequences coding for the DNA polymerase and Helicase enzymes. A deep computational inspection of the HeN2 element revealed its structure. It consists of two terminal palindromic sequences (U5 and U3), and eleven tandemly arranged 155bp-long direct repeats (DR1-11). It is well known that the TRIMcontaining gene family, to which strim1 belongs, is widely complex and heterogeneous due to the combination of exon shuffling, duplication and/or deletion events that likely occurred during evolution [3]. Interestingly, Helitrons are a formidable evolutionary tool owing to their ability to capture host genes [4] and transposition plays important roles in the evolution of duplicated genes [5]. Therefore our finding could suggest a mechanism for the evolution of the TRIM multigenic family. References 1. Kapitonov VV and Jurka J (2007). Helitrons on a roll: eukaryotic rollingcircle transposons. TRENDS in Genetics 23(10), 521-9. 2. Kapitonov VV, Jurka J (2005). Helitron-N2_SP, a family of nonautonomous Helitrons in the sea urchin genome. Repbase Reports 5(11), 395-395. 3. Sardiello, M, Cairo, S, Fontanella, M, Ballabio, A, and Meroni, G (2008). Genomic analysis of the TRIM family reveals two groups of genes with distinct evolutionary properties. BMC Evolutionary Biology 8:225- 4. Gupta S, Gallavotti A, Stryker GA, Schmidt RJ, Lal SK (2005). A novel class of Helitron-related transposable elements in maize contain portions of multiple pseudogenes. Plant Mol Biol 57, 115-27. 5. Han, MV, Demuth, JP, McGrath, CL, Casola, C and Hahn MW (2009). Adaptive evolution of young gene duplicates in mammals. Genome Res 19(5):859-67.