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Curr Biol 2002 Oct 15;1220:1756-61. doi: 10.1016/s0960-9822(02)01220-4.
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A ubiquitous and conserved signal for RNA localization in chordates.

Betley JN , Frith MC , Graber JH , Choo S , Deshler JO .

During oogenesis in Xenopus laevis, several RNAs that localize to the vegetal cortex via one of three temporally defined pathways have been identified. Although individual mRNAs utilize only one pathway, there is functional overlap and apparent continuity between them, suggesting that common cis-acting sequences may exist. Because previous work with the Vg1 mRNA revealed that short nontandem repeats are important for localization, we developed a new computer program, called REPFIND, to expedite the identification of repeated motifs in other localized RNAs. Here we show that clusters of short CAC-containing motifs characterize the localization elements (LEs) of virtually all mRNAs localized to the vegetal cortex of Xenopus oocytes. A search for this signal in GenBank [9] resulted in the identification of new localized mRNAs, demonstrating the applicability of REPFIND to predict localized RNAs. CAC-rich LEs are also found in ascidians and other vertebrates, indicating that these cis regulatory elements are conserved in chordates. Interestingly, biochemical evidence shows that distinct CAC-containing motifs have different functions in the localization process. Thus, clusters of CAC-containing motifs are a ubiquitous signal for RNA localization and can signal localization in a variety of pathways through slight variations in sequence composition.

PubMed ID: 12401170
Article link: Curr Biol

Species referenced: Xenopus laevis
Genes referenced: dazl ddx25 efnb1 gdf1 nanos1 otx2 pgat slc25a20 wnt11b zfp36l2

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