Occurrence of a LINE sequence in the 3' UTR of the goat alpha s1-casein E-encoding allele associated with reduced protein synthesis level.

The E allele of the alpha s1-casein (alpha s1-Cas)-encoding gene is associated with a reduced casein content in milk. Structural analysis of mRNA and sequencing of amplified genomic DNA fragments, have revealed that this allele contains a 457-bp insertion within exon 19 (last untranslated exon). This insert is a truncated long interspersed repeated element (LINE) containing part of the ORF-2, the 3' UTR and the poly(A) tail of the original retroposon. This LINE sequence was found to be highly repeated in the goat genome. The threefold reduction in the amount of alpha s1-CasE mRNA in the total, as well as in the polysomal fractions, as compared with its A counterpart, leads one to suppose either a reduced transcriptional rate of allele E or/and a decreased stability of the relevant mRNA. Northern blot and PCR experiments suggested the setting up of highly stable secondary structures involving the 3' UTR of the alpha s1-CasE transcript. The mRNA folding calculations support such an hypothesis, by base-pairing interactions between the E allele messenger poly(A) tail and a long poly(U)-stretch occurring at the 5' end of the insertion. In addition, since A+U-rich motifs are also present in the truncated LINE insertion, we propose that this extra sequence might be responsible for the lower milk alpha s1-Cas content by reducing the allele E mRNA stability.