| Summary: | <p>Abstract</p> <p>Background</p> <p>Ribosomal protein genes (RPGs) are essential, tightly regulated, and highly expressed during embryonic development and cell growth. Even though their protein sequences are strongly conserved, their mechanism of regulation is not conserved across yeast, <it>Drosophila</it>, and vertebrates. A recent investigation of genomic sequences conserved across both nematode species and associated with different gene groups indicated the existence of several elements in the upstream regions of <it>C. elegans</it> RPGs, providing a new insight regarding the regulation of these genes in <it>C. elegans</it>.</p> <p>Results</p> <p>In this study, we performed an in-depth examination of <it>C. elegans</it> RPG regulation and found nine highly conserved motifs in the upstream regions of <it>C. elegans</it> RPGs using the motif discovery algorithm DME. Four motifs were partially similar to transcription factor binding sites from <it>C. elegans</it>, <it>Drosophila</it>, yeast, and human. One pair of these motifs was found to co-occur in the upstream regions of 250 transcripts including 22 RPGs. The distance between the two motifs displayed a complex frequency pattern that was related to their relative orientation.</p> <p>We tested the impact of three of these motifs on the expression of <it>rpl-2</it> using a series of reporter gene constructs and showed that all three motifs are necessary to maintain the high natural expression level of this gene. One of the motifs was similar to the binding site of an orthologue of POP-1, and we showed that RNAi knockdown of <it>pop-1</it> impacts the expression of <it>rpl-2</it>. We further determined the transcription start site of <it>rpl-2</it> by 5’ RACE and found that the motifs lie 40–90 bases upstream of the start site. We also found evidence that a noncoding RNA, contained within the outron of <it>rpl-2</it>, is co-transcribed with <it>rpl-2</it> and cleaved during trans-splicing.</p> <p>Conclusions</p> <p>Our results indicate that <it>C. elegans</it> RPGs are regulated by a complex novel series of regulatory elements that is evolutionarily distinct from those of all other species examined up until now.</p>
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