ArticleGenome research2002
Genome-wide co-occurrence of promoter elements reveals a cis-regulatory cassette of rRNA transcription motifs in Saccharomyces cerevisiae.
Article in Genome research, 2002. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 49 papers.
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Who cites it
49 citing papers in PubMed, 92 citations in OpenAlex.
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- A self-attention model for inferring cooperativity between regulatory features.Nucleic acids research · 2021Article
- The combinatorial control of alternative splicing in C. elegans.PLoS genetics · 2017Article
- Statistically validated network of portfolio overlaps and systemic risk.Scientific reports · 2016Article
- Combinatorial Cis-regulation in Saccharomyces Species.G3 (Bethesda, Md.) · 2016Article
- Regulatory Cross-Talks and Cascades in Rice Hormone Biosynthesis Pathways Contribute to Stress Signaling.Frontiers in plant science · 2016Article
- Systematic dissection of the sequence determinants of gene 3' end mediated expression control.PLoS genetics · 2015Article
- Deciphering Cis-Regulatory Element Mediated Combinatorial Regulation in Rice under Blast Infected Condition.PloS one · 2015Article
- Article
- A novel unbiased measure for motif co-occurrence predicts combinatorial regulation of transcription.BMC genomics · 2012Article
- Curated collection of yeast transcription factor DNA binding specificity data reveals novel structural and gene regulatory insights.Genome biology · 2011Article
- Adjacent gene pairing plays a role in the coordinated expression of ribosome biogenesis genes MPP10 and YJR003C in Saccharomyces cerevisiae.Eukaryotic cell · 2011Article
- Transcription factor binding site positioning in yeast: proximal promoter motifs characterize TATA-less promoters.PloS one · 2011Article
- A network of conserved co-occurring motifs for the regulation of alternative splicing.Nucleic acids research · 2010Article
- Identifying regulatory elements in eukaryotic genomes.Briefings in functional genomics & proteomics · 2009Review
- Identification of yeast transcriptional regulation networks using multivariate random forests.PLoS computational biology · 2009Article
- Article
- Predicting functional transcription factor binding through alignment-free and affinity-based analysis of orthologous promoter sequences.Bioinformatics (Oxford, England) · 2008Article
- Functional characterization of variations on regulatory motifs.PLoS genetics · 2008Article
- Two different classes of co-occurring motif pairs found by a novel visualization method in human promoter regions.BMC genomics · 2008Article
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Authors and funding
3 authors at 1 institution in 1 country.
Funding
Abstract
Combinatorial regulation is an important feature of eukaryotic transcription. However, only a limited number of studies have characterized this aspect on a whole-genome level. We have conducted a genome-wide computational survey to identify cis-regulatory motif pairs that co-occur in a significantly high number of promoters in the S. cerevisiae genome. A pair of novel motifs, mRRPE and PAC, co-occur most highly in the genome, primarily in the promoters of genes involved in rRNA transcription and processing. The two motifs show significant positional and orientational bias with mRRPE being closer to the ATG than PAC in most promoters. Two additional rRNA-related motifs, mRRSE3 and mRRSE10, also co-occur with mRRPE and PAC. mRRPE and PAC are the primary determinants of expression profiles while mRRSE3 and mRRSE10 modulate these patterns. We describe a new computational approach for studying the functional significance of the physical locations of promoter elements that combine analyses of genome sequence and microarray data. Applying this methodology to the regulatory cassette containing the four rRNA motifs demonstrates that the relative promoter locations of these elements have a profound effect on the expression patterns of the downstream genes. These findings provide a function for these novel motifs and insight into the mechanism by which they regulate gene expression. The methodology introduced here should prove particularly useful for analyzing transcriptional regulation in more complex genomes.
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