Sanges, R., Kalmar, E., Claudiani, P., D'Amato, M., Muller, F., and Stupka, E. (2006) Shuffling of cis-regulatory elements is a pervasive feature of the vertebrate lineage. Genome biology. 7(7):R56.
BACKGROUND: All vertebrates share a remarkable degree of similarity in their development as well as in the basic functions of their cells. Despite this, attempts at unearthing genome-wide regulatory elements conserved throughout the vertebrate lineage using BLAST-like approaches have so far detected non-coding conservation in only a few hundred genes, mostly associated with regulation of transcription and development. Results: We used a unique combination of tools to obtain regional global-local alignments of orthologous loci. This approach takes into account shuffling of regulatory regions likely to occur over evolutionary distances greater than those separating mammalian genomes. This approach revealed one order of magnitude more vertebrate conserved elements than was previously reported in over 2,000 genes, including a high number of genes found in the membrane and extra-cellular regions. Our analysis reveals that 72% of the elements identified have undergone shuffling. We tested the ability of the elements identified to enhance transcription in zebrafish embryos and compared their activity to a set of control fragments. We show that more than 80% of the elements tested were able to significantly enhance transcription, prevalently in a tissue-restricted manner that corresponds to the expression domain of the neighboring gene. Conclusions: Our work elucidates the importance of shuffling in the detection of cis-regulatory elements. It also elucidates how similarities across the vertebrate lineage, which go well beyond development, can be explained not only within the realm of coding genes but also that of the sequences that ultimately govern their expression.