Background All vertebrates share a remarkable degree of similarity in their

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Background All vertebrates share a remarkable degree of similarity in their development as well as in the basic functions of their cells. 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 in that of the sequences that ultimately govern their expression. Background Enhancers are cis-acting sequences that increase the utilization and/or specificity of eukaryotic promoters, can function in either orientation, and often act in a distance and position independent manner [1]. The regulatory logic of enhancers is often conserved throughout vertebrates, and their activity relies on sequence modules containing binding sites that are crucial for transcriptional activation. However, recent studies on the cis-regulatory logic of Otx in ascidians pointed out that there can be great plasticity in the arrangement of binding sites within individual functional modules. This degeneracy, combined with the involvement of a few crucial binding sites, is sufficient to explain how the regulatory logic of an enhancer can be retained in the absence of detectable sequence conservation [2]. These observations together with the fact that we are still far from understanding fully the grammar of transcription factor binding sites and their conservation [3] make it difficult to assess the extent of conservation 58812-37-6 IC50 in vertebrate cis-regulatory elements. Very little is known about the evolutionary mobility of enhancer and promoter elements within the genome as well as within a specific locus. Sporadic studies of selected gene families have addressed questions related 58812-37-6 IC50 to the mobility of regulatory sequences involving promoter shuffling [4] and enhancer shuffling [5]; these describe the gain or loss of individual regulatory elements exchanged between specific genes in a cassette manner [6]. These studies suggested that a wide variety of different regulatory motifs and mutational mechanisms have operated upon noncoding regions over time. These studies, however, were conducted before the advent of large-scale genome sequencing, and thus they were performed on a scale that would not allow the authors to 58812-37-6 IC50 derive more general conclusions on the mobility and shuffling of regulatory elements. The basic tenet of comparative genomics is that constraint on functional genomic elements has kept their sequence conserved throughout evolution. The completion of the draft Rabbit polyclonal to BIK.The protein encoded by this gene is known to interact with cellular and viral survival-promoting proteins, such as BCL2 and the Epstein-Barr virus in order to enhance programed cell death. sequence of several mammalian genomes has been an important milestone in the search for conserved sequence elements in noncoding DNA. It has been estimated that the proportion of small segments in the mammalian genome that is under purifying selection within intergenic regions is about 5% and that this proportion is much greater than can be explained by protein-coding sequences alone, implying that the genome contains many additional features (such as untranslated regions, regulatory elements, non-protein-coding genes, and structural elements) that are under selection for biological functions [7-11]. In order to address this issue, sequence comparisons across longer evolutionary distances and, in particular, with the compact Fugu rubripes genome have been shown to be useful in dissecting 58812-37-6 IC50 the regulatory grammar of genes long before the advent of genome sequencing [12]. More recently, the completion of the draft sequence of several fish genomes has allowed larger scale approaches 58812-37-6 IC50 for the detection of several regulatory.