ArticleProceedings of the National Academy of Sciences of the United States of America2005
Identifying gene-independent noncoding functional elements in the yeast ribosomal DNA by phylogenetic footprinting.
Article in Proceedings of the National Academy of Sciences of the United States of America, 2005. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 19 papers.
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Who cites it
19 citing papers in PubMed, 49 citations in OpenAlex.
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- Structural basis of RNA polymerase I pre-initiation complex formation and promoter melting.Nature communications · 2020Article
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- A Novel Saccharomyces cerevisiae Killer Strain Secreting the X Factor Related to Killer Activity and Inhibition of S. cerevisiae K1, K2 and K28 Killer Toxins.Indian journal of microbiology · 2016Article
- The Nuts and Bolts of Transcriptionally Silent Chromatin in Saccharomyces cerevisiae.Genetics · 2016Review
- Transcription and recombination: when RNA meets DNA.Cold Spring Harbor perspectives in biology · 2014Review
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- RNAP-II molecules participate in the anchoring of the ORC to rDNA replication origins.PloS one · 2013Article
- How does genome instability affect lifespan?: roles of rDNA and telomeres.Genes to cells : devoted to molecular & cellular mechanisms · 2011Review
- Regulation of ribosomal RNA gene copy number and its role in modulating genome integrity and evolutionary adaptability in yeast.Cellular and molecular life sciences : CMLS · 2011Review
- Repetitive sequence variation and dynamics in the ribosomal DNA array of Saccharomyces cerevisiae as revealed by whole-genome resequencing.Genome research · 2009Article
- Actively transcribed rRNA genes in S. cerevisiae are organized in a specialized chromatin associated with the high-mobility group protein Hmo1 and are largely devoid of histone molecules.Genes & development · 2008Article
- Budding yeast RNA polymerases I and II employ parallel mechanisms of transcriptional termination.Genes & development · 2008Article
- Highly efficient concerted evolution in the ribosomal DNA repeats: total rDNA repeat variation revealed by whole-genome shotgun sequence data.Genome research · 2007Article
- Condensin function in mitotic nucleolar segregation is regulated by rDNA transcription.Cell cycle (Georgetown, Tex.) · 2006Article
- Sir2 represses endogenous polymerase II transcription units in the ribosomal DNA nontranscribed spacer.Molecular biology of the cell · 2006Article
- Functional single nucleotide polymorphism-based association studies.Human genomics · 2006Review
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Authors and funding
4 authors at 2 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
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 noncoding functional elements. Seventeen previously uncharacterized elements, showing high levels of conservation, were also discovered. The conservation of these elements suggests that they are functional, and we demonstrate the functionality of two classes of these elements, a putative bidirectional noncoding promoter and a series of conserved peaks with matches to the origin-of-replication core consensus. Our results paint a comprehensive picture of the functionality of the Saccharomyces ribosomal intergenic region and demonstrate that functional elements not involved in gene-coding function can be identified by using comparative genomics based on sequence conservation.
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