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Intragenomic distribution of RTE retroelements suggests intrachromosomal movement

Montiel, Eugenia E., Ruiz-Ruano, Francisco J., Cabrero, Josefa, Marchal, Juan Alberto, Sánchez, Antonio, Perfectti, Francisco, López-León, María Dolores, Camacho, Juan Pedro M.
Chromosome research 2015 v.23 no.2 pp. 211-223
DNA, Eyprepocnemis plorans, RNA-directed DNA polymerase, chromosomes, clones, genes, genomics, grasshoppers, metaphase, phylogeny, polymerase chain reaction, retrotransposons, sequence analysis, terminal repeat sequences, transposons, variance
Much is known about the abundance of transposable elements (TEs) in eukaryotic genomes, but much is still unknown on their behaviour within cells. We employ here a combination of cytological, molecular and genomic approaches providing information on the intragenomic distribution and behaviour of non-long terminal repeat (LTR) retrotransposon-like elements (RTE). We microdissected every chromosome in a single first meiotic metaphase cell of the grasshopper Eyprepocnemis plorans and polymerase chain reaction (PCR) amplified a fragment of the RTE reverse transcriptase gene with specific primers. PCR products were cloned and 139 clones were sequenced. Analysis of molecular variance (AMOVA) showed significant intragenomic structure for these elements, with 4.6 % of molecular variance being found between chromosomes. A maximum likelihood tree built with the RTE sequences revealed the frequent presence of two or more elements showing very high similarity and being located on the same chromosome, thus suggesting intrachromosome movement. The 454 pyrosequencing of genomic DNA gave strong support to the microdissection results and provided evidence for the existence of 5′ truncated elements. Our results thus indicate a tendency of RTE elements to reinsert into the same chromosome from where they were transcribed, which could be achieved if retrotranscription and insertion takes place immediately after transcription.