Identifying gene-independent noncoding functional elements in the yeast ribosomal DNA by phylogenetic footprinting.

ABSTRACT: Sequences involved in the regulation of genetic and genomic processes are primarily located in noncoding regions. Identifying such cis-acting sequences from sequence data is difficult because their patterns are not readily apparent, and, to date, identification has concentrated on regions associated with gene-coding functions. Here, we used phylogenetic footprinting to look for gene-independent noncoding elements in the ribosomal RNA gene repeats from several Saccharomyces species. Similarity plots of ribosomal intergenic spacer alignments from six closely related Saccharomyces species allowed the identification of previously characterized functional elements, such as the origin-of-replication and replication-fork barrier sites, demonstrating that this method is a powerful predictor of non

SUBMITTER: Ganley AR 

PROVIDER: S-EPMC1182552 | biostudies-literature | 2005 Aug

REPOSITORIES: biostudies-literature