Computational discovery of DNA motifs associated with cell type-specific gene expression in Ciona

To link to full-text access for this article, visit this link: http://dx.doi.org/10.1016/j.ydbio.2004.09.037 Byline: Takehiro Kusakabe, Reiko Yoshida, Yoko Ikeda, Motoyuki Tsuda Keywords: Ascidian; Bioinformatics; Central nervous system; cis-regulatory element; Ciona; Muscle; Photoreceptor Abstract: Temporally and spatially co-expressed genes are expected to be regulated by common transcription factors and therefore to share cis-regulatory elements. In the ascidian Ciona intestinalis, the whole-genome sequences and genome-scale gene expression profiles allow the use of computational techniques to investigate cis-elements that control transcription. We collected 5' flanking sequences of 50 tissue-specific genes from genome databases of C. intestinalis and a closely related species Ciona savignyi. We searched for DNA motifs over-represented in upstream regions of a group of co-expressed genes. Several motifs were distributed predominantly in upstream regions of photoreceptor, pan-neuronal, or muscle-specific gene groups. One muscle-specific motif, M2, was distributed preferentially in regions from -200 to -100 bp relative to the translational start sites. Promoters of muscle-specific genes of C. intestinalis were isolated, connected with a green fluorescent protein gene (GFP), and introduced into C. intestinalis embryos. In muscle cells, these promoters specifically drove GFP expression, which mutations of the M2 sites greatly reduced. When M2 sites were located upstream of a basal promoter, the reporter GFP was specifically expressed in muscle cells. These results suggest the validity of our computational prediction of cis-regulatory elements. Thus, bioinformatics can help identify cis-regulatory elements involved in chordate development. Author Affiliation: Department of Life Science, Graduate School of Life Science, University of Hyogo, Kamigori, Ako-gun, Hyogo 678-1297, Japan Article History: Received 24 May 2004; Revised 30 August 2004; Accepted 28 September 2004