Identification and characterization of the Xlsirt cis-acting RNA localization element

There are many RNAs that are localized to the vegetal cortex of Xenopus laevis oocytes. One family of localized transcripts, Xlsirts (Xenopus laevis short interspersed repeat transcripts), are defined by the presence of non-coding repeat units 79-81 nucleotides long. Endogenous Xlsirt RNAs are localized through the METRO (message transport organizer) pathway that localizes RNAs during stages I and II of oogenesis. Interestingly, exogenous Xlsirt RNAs that are injected into oocytes can utilize both the METRO pathway as well as the Late pathway, which localizes RNAs during the late stages of oogenesis (stages III-VI). In all cases thus far analyzed, the localization process relies on the presence of cis-acting elements on the transcripts that are responsible for directing localization. To better understand the mechanism responsible for the use of the METRO and Late localization pathways, we sought to identify pathway-specific cis-acting localization elements contained in Xlsirts. The results showed that an intact 137 nucleotide element was necessary and sufficient to localize RNAs through the METRO and Late pathways. Further analysis of this element identified putative METRO and Late pathway localization sub-elements. Computer analysis relates the secondary structure of the 137 nt element to its ability to function as a localization element.