A novel non-coding DNA family in Caenorhabditis elegans

• Published in: Gene 2007-02, Vol.388 (1), p.61-73
• Main Authors: Takashima, Yasuo, Bando, Tetsuya, Kagawa, Hiroaki
• Format: Article
• Language: English
• Subjects: Animals; Base Sequence; Caenorhabditis elegans - genetics; DNA, Helminth - chemistry; DNA, Helminth - genetics; DNA, Helminth - metabolism; DNA, Intergenic; Enhancer; Gene Expression Regulation; Gene/element association; Genome organization; Green Fluorescent Proteins - genetics; Green Fluorescent Proteins - metabolism; Helminth Proteins - genetics; Introns; Lac Operon - genetics; Molecular Sequence Data; Nucleic Acid Conformation; Palindrome; Phylogeny; Plasmids; Protein Binding; Repetitive element; Repetitive Sequences, Nucleic Acid; Reverse Transcriptase Polymerase Chain Reaction; Sequence Alignment; Sequence Homology, Nucleic Acid; Transcription Factors - metabolism; Troponin C - genetics
• ISSN: 0378-1119; 1879-0038
• DOI: 10.1016/j.gene.2006.10.002

Many repetitive elements, for example, SINEs, LINEs, LTR-retrotransposons and other SSRs are dispersed throughout eukaryotic genomes. To understand the biological function of these repetitive elements is of great current research interest. In this study, we report on the identification of a novel non-coding DNA family, designated CE1 family, in the nematode C. elegans genome. Some CE1 elements constituted a large palindrome sequence. The CE1 elements were interspersed at 95 sites in the C. elegans genome. Most of the CE1 elements were associated with, or were within, protein-coding genes. The sequence of the CE1 elements indicated that some could form a hairpin structure. One of the CE1 family, CE1( bs258), is located in the first intron of a novel gene, C46H11.6 which encodes a PDZ/DHR/GLGF domain protein. In gfp and lacZ reporter gene assays the CE1( bs258) element appeared to behave as an enhancer element for the expression of C46H11.6 but no effect on the expression of the opposite direction gene, pat-10 which encodes the body-wall muscle troponin C. The CE1( bs258) RNA transcript was detected by RT-PCR even when CE1( bs258) was located in an intron. We conclude that CE1 elements are involved in the expression of adjacent genes and are therefore selectively retained in the C. elegans genome. We discussed a biological function of the CE1( bs258) having many transcription factor-binding sites.