A conserved sequence motif in 3' untranslated regions of ribosomal protein mRNAs in nematodes

Abstract

The 3' untranslated regions (3' UTR) of eukaryotic genes can contain motifs involved in regulation of gene expression or localization at the post-transcriptional level. This study concerns the identification of novel, conserved elements in 3' UTRs of many ribosomal protein mRNAs in Caenorhabditis elegans and Caenorhabditis briggsae. Analysis of the region around the polyadenylation signal in many ribosomal protein mRNAs indicates the conservation of a sequence motif UUGUU occurring both before and immediately after the polyadenylation signal. Building a statistical model of this motif and searching a database of C. elegans 3' UTRs reveals that this motif is also present in the 3' UTR of some genes involved in translation and ribosome maturation, among others. We suggest that this signal may be involved in translation or other message-level regulation of ribosomal genes in C. elegans.

FIGURE 1.

(A) A hand-edited alignment showing five of the 57 ribosomal protein 3′ UTR sequences from C. elegans and C. briggsae, containing UUGUU motifs on either side of the polyadenylation signal. (B) The bit score histogram resulting from finding the log(2) probability of various 3′ UTR sequence sets under the ribosomal model minus the log(2) probability under the standard model. (Dark blue) All C. elegans nonribosomal protein genes—this is the background distribution; (pink) C. elegans ribosomal protein genes; (green) C. elegans orthologs of yeast ribosomal assembly complex; (light blue) C. briggsae orthologs of C. elegans genes scoring >7.5 bits.