Regulatory elements of Caenorhabditis elegans ribosomal protein genes

作者：Monica C. Sleumer, Guifeng Wei, Yunfei Wang, Hao Chang, Tao Xu, Runsheng Chen, Michael Q. Zhang · 发表于：BMC Genomics · 年份：2012 · DOI：10.1186/1471-2164-13-433 · 被引用次数：14 · 研究领域：RNA and protein synthesis mechanisms、Genetics, Aging, and Longevity in Model Organisms、RNA modifications and cancer

BACKGROUND: 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, Drosophila, 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 C. elegans RPGs, providing a new insight regarding the regulation of these genes in C. elegans. RESULTS: In this study, we performed an in-depth examination of C. elegans RPG regulation and found nine highly conserved motifs in the upstream regions of C. elegans RPGs using the motif discovery algorithm DME. Four motifs were partially similar to transcription factor binding sites from C. elegans, Drosophila, 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.We tested the impact of three of these motifs on the expression of rpl-2 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 pop-1 impacts ...