Methylation of the SIRE1 Retroelement in Glycine max

SIRE1 is a recently active, relatively high copy-number retroelement that is among the most prevalent transposon families in the soybean genome with over 1,000 full-length copies.  It is a member of the Ty1/Copia long terminal repeat (LTR) retrotransposon superfamily and is characterized by an extra, intact ORF (eORF) immediately downstream of pol.  Related elements with and without intact 3’ eORFs are widely dispersed among higher plant genomes.  In soybean, most SIRE1 copies are found in pericentromeric regions, having inserted into the morass of other transposons.  Despite the observations that the ORFs of dozens of SIRE1 copies contain no stop codons or frameshifts and that many insertions have occurred in the last 30,000 years, full-length transcripts have not been detected.  Transcripts of unknown biological function have been detected by RT-PCR of leaf and root tissue.  Cytosine methylation is known to epigenetically silence plant transposons.  But detecting both the specific and the collective methylation of a large, single family of retroelements like SIRE1 is not commonly performed.  The SIRE1 LTRs contain a highly conserved CCGG and the methylation status of this sequence was determined by the amplification of this region after MspI or HpaII cleavage.  PCR amplification of LTRs from individually selected elements that inserted in the last 30,000 years indicated that CCGG was methylated in the youngest, potentially functional elements.  Quantitative PCR of the global SIRE1 family suggested that most if not all of the elements are similarly methylated.  Unsurprisingly, even the newest insertions are apparently silenced by DNA methylation.